Extensive homologous recombination in classical swine fever virus: A re-evaluation of homologous recombination events in the strain AF407339

In this short report, the genome-wide homologous recombination events were re-evaluated for classical swine fever virus (CSFV) strain {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339. We challenged a previous study which suggested only one recombination event in {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339 based on 25 CSFV genomes. Through our re-analysis on the 25 genomes in the previous study and the 41 genomes used in the present study, we argued that there should be possibly at least two clear recombination events happening in {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339 through genome-wide scanning. The reasons for identifying only one recombination event in the previous study might be due to the limited number of available CSFV genome sequences at that time and the limited usage of detection methods. In contrast, as identified by most detection methods using all available CSFV genome sequences, two major recombination events were found at the starting and ending zones of the genome {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339, respectively. The first one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF333000","term_id":"13383931","term_text":"AF333000"}}AF333000 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"AY554397","term_id":"49860681","term_text":"AY554397"}}AY554397 (major) with beginning and ending breakpoints located at 19 and 607 nt of the genome respectively. The second one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF531433","term_id":"22347661","term_text":"AF531433"}}AF531433 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"GQ902941","term_id":"298113017","term_text":"GQ902941"}}GQ902941 (major) with beginning and ending breakpoints at 8397 and 11,078 nt of the genome respectively. Phylogenetic incongruence analysis using neighbor-joining algorithm with 1000 bootstrapping replicates further supported the existence of these two recombination events. In addition, we also identified additional 18 recombination events on the available CSFV strains. Some of them may be trivial and can be ignored. In conclusion, CSFV might have relatively high frequency of homologous recombination events. Genome-wide scanning of identifying recombination events should utilize multiple detection methods so as to reduce the risk of misidentification.     

Genomic Basis of a Polyagglutinating Isolate of Neisseria meningitidis

Containment strategies for outbreaks of invasive Neisseria meningitidis disease are informed by serogroup assays that characterize the polysaccharide capsule. We sought to uncover the genomic basis of conflicting serogroup assay results for an isolate ({"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917) from a patient with acute meningococcal disease. To this end, we characterized the complete genome sequence of the {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 isolate and performed a variety of comparative sequence analyses against N. meningitidis reference genome sequences of known serogroups. Multilocus sequence typing and whole-genome sequence comparison revealed that {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 is a member of the ST-11 sequence group, which is most often associated with serogroup C. However, sequence similarity comparisons and phylogenetic analysis showed that the serogroup diagnostic capsule polymerase gene (synD) of {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 belongs to serogroup B. These results suggest that a capsule-switching event occurred based on homologous recombination at or around the capsule locus of {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917. Detailed analysis of this locus uncovered the locations of recombination breakpoints in the {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917 genome sequence, which led to the introduction of an ∼2-kb serogroup B sequence cassette into the serogroup C genomic background. Since there is no currently available vaccine for serogroup B strains of N. meningitidis, this kind capsule-switching event could have public health relevance as a vaccine escape mutant.     

Identification and Genome Characterization of the First Sicinivirus Isolate from Chickens in Mainland China by Using Viral Metagenomics

Unlike traditional virus isolation and sequencing approaches, sequence-independent amplification based viral metagenomics technique allows one to discover unexpected or novel viruses efficiently while bypassing culturing step. Here we report the discovery of the first Sicinivirus isolate (designated as strain JSY) of picornaviruses from commercial layer chickens in mainland China by using a viral metagenomics technique. This Sicinivirus isolate, which contains a whole genome of 9,797 nucleotides (nt) excluding the poly(A) tail, possesses one of the largest picornavirus genome so far reported, but only shares 88.83% and 82.78% of amino acid sequence identity to that of ChPV1 100C ({"type":"entrez-nucleotide","attrs":{"text":"KF979332","term_id":"672942599","term_text":"KF979332"}}KF979332) and Sicinivirus 1 strain UCC001 ({"type":"entrez-nucleotide","attrs":{"text":"NC_023861","term_id":"602259859","term_text":"NC_023861"}}NC_023861), respectively. The complete 939 nt 5′UTR of the isolate strain contains at least twelve stem-loop domains (A–L), representing the highest set of loops reported within Sicinivirus genus. The conserved ''barbell-like'' structure was also present in the 272 nt 3′UTR of the isolate as that in the 3′ UTR of Sicinivirus 1 strain UCC001. The 8,586 nt large open reading frame encodes a 2,862 amino acids polyprotein precursor. Moreover, Sicinivirus infection might be widely present in commercial chicken farms in Yancheng region of the Jiangsu Province as evidenced by all the tested stool samples from three different farms being positive (17/17) for Sicinivirus detection. This is the first report on identification of Sicinivirus in commercial layer chickens with a severe clinical disease in mainland China, however, further studies are needed to evaluate the pathogenic potential of this picornavirus in chickens.     

Streptomyces antibioticalis, a Novel Species from a Sanitary Landfill Soil

A novel isolate belonging to the genus Streptomyces, strain SL-4^T, was isolated from soil sample collected from a sanitary landfill, New Delhi, India. The taxonomic status of this isolate was studied by polyphasic approach including morphological, physiological and chemo-taxonomic characterization. Spore chains of SL-4^T were open loops, hooks or extended spirals of wide diameter (retinaculiperti). The cell wall peptidoglycan of the isolate SL-4^T contained L,L-diaminopimelic acid, suggesting that the strain has a cell wall of chemotype-I. The polar lipid profile of the isolate was of Type II, with phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The 16SrRNA gene sequence similarity between SL-4^T and its phylogenetic relatives Streptomyces atrovirens NRRLB 16357^T ({"type":"entrez-nucleotide","attrs":{"text":"DQ026672","term_id":"68137786","term_text":"DQ026672"}}DQ026672), S. albogriseolus NRRLB 1305^T ({"type":"entrez-nucleotide","attrs":{"text":"AJ494865","term_id":"21742835","term_text":"AJ494865"}}AJ494865), S viridodiastaticus NBRC 13106^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184317","term_id":"90960133","term_text":"AB184317"}}AB184317), S. caelestis NRRL 2418^T ({"type":"entrez-nucleotide","attrs":{"text":"X80824","term_id":"587528","term_text":"X80824"}}X80824), S. flavoviridis NBRC 12772^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184842","term_id":"90960663","term_text":"AB184842"}}AB184842), S. pilosus NBRC 12807^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184161","term_id":"90959977","term_text":"AB184161"}}AB184161) and S. longispororuber NBRC 13488^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184440","term_id":"90960256","term_text":"AB184440"}}AB184440) was 99.65, 99.65, 99.64, 99.23, 99.15, 99.14 and 99.13 % respectively. Subsequent DNA–DNA hybridization experiments with the test strain and its clade members showed 55.27, 44.27, 36.86, and 15.65 % relatedness between SL-4^T and its relatives S. atrovirens,S. albogriseolus, S. viridodiastaticus and S. longispororuber respectively. The genotypic and phenotypic data was analyzed to verify possibility of the isolate SL-4^T representing novel member of the genus Streptomyces, for which the name S. antibioticalis is being proposed. The type strain is SL-4^T (=CCM 7434^T=MTCC 8588^T).     

Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes

DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome ({"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome ({"type":"entrez-nucleotide","attrs":{"text":"KJ830774","term_id":"662117268","term_text":"KJ830774"}}KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, {"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209 was more similar to the reference genome (O. sativa: {"type":"entrez-nucleotide","attrs":{"text":"AY522330","term_id":"42795537","term_text":"AY522330"}}AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the {"type":"entrez-nucleotide","attrs":{"text":"KJ830774","term_id":"662117268","term_text":"KJ830774"}}KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of {"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209 and {"type":"entrez-nucleotide","attrs":{"text":"KJ830774","term_id":"662117268","term_text":"KJ830774"}}KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of {"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.     

High Prevalence and Significant Association of ESBL and QNR Genes in Pathogenic Klebsiella pneumoniae Isolates of Patients from Kolkata, India

Pathogenic Klebsiella pneumoniae, resistant to beta-lactam and quinolone drugs, is widely recognized as important bacteria causing array of diseases. The resistance property is obtained by acquisition of plasmid encoded bla_TEM, bla_SHV, bla_CTX-M, QNRA, QNRB and QNRS genes. The aim of this study was to document the prevalence and association of these resistant genes in K. pneumoniae infecting patients in India. Approximately 97 and 76.7 % of the 73 K. pneumoniae isolates showed resistance towards beta-lactam and quinolone drugs respectively. Bla genes were detected in 74 % of K. pneumoniae isolates; with prevalence in the following order: bla_TEM > bla_SHV > bla_CTXM. QNR genes were detected in 67 % samples. Chi-square analysis revealed significant association between presence of bla and qnr genes in our study (P value = 0.000125). Sequence analysis of some bla_TEM, bla_SHV, bla_CTX-M and QNRB PCR products revealed presence of bla_TEM1 (GenBank accession: {"type":"entrez-nucleotide","attrs":{"text":"JN193522","term_id":"343796760","term_text":"JN193522"}}JN193522), bla_TEM116 ({"type":"entrez-nucleotide","attrs":{"text":"JN193523","term_id":"343796762","term_text":"JN193523"}}JN193523 and {"type":"entrez-nucleotide","attrs":{"text":"JN193524","term_id":"343796764","term_text":"JN193524"}}JN193524), bla_SHV11, bla_CTXM72 variants ({"type":"entrez-nucleotide","attrs":{"text":"JF523199","term_id":"329024835","term_text":"JF523199"}}JF523199) and QNRB1 ({"type":"entrez-nucleotide","attrs":{"text":"JN193526","term_id":"343796802","term_text":"JN193526"}}JN193526 and {"type":"entrez-nucleotide","attrs":{"text":"JN193527","term_id":"343796804","term_text":"JN193527"}}JN193527) in our samples.     

Molecular Identification of Cryptosporidium viatorum Infection in a Patient Suffering from Unusual Cryptosporidiosis in West Bengal,India

In this study, we have collected and screened a total of 268 stool samples from diarrheal patients admitted to an Infectious disease hospital in Kolkata for the presence of Cryptosporidium spp. The initial diagnosis was carried out by microscopy followed by genus specific polymerase chain reaction assays based on 70 kDa heat shock proteins (HSP70). DNA sequencing of the amplified locus has been employed for determination of genetic diversity of the local isolates. Out of 268 collected samples, 12 (4.48%) were positive for Cryptosporidium spp. Sequences analysis of 70 kDa heat shock proteins locus in 12 Cryptosporidium local isolates revealed that 2.24% and 1.86% of samples were showing 99% to 100% identity with C. parvum and C. hominis. Along with the other 2 major species one recently described globally distributed pathogenic species Cryptosporidium viatorum has been identified. The HSP70 locus sequence of the isolate showed 100% similarity with a previously described isolate of C. viatorum (Accession No. {"type":"entrez-nucleotide","attrs":{"text":"JX978274.1","term_id":"441431305","term_text":"JX978274.1"}}JX978274.1, {"type":"entrez-nucleotide","attrs":{"text":"JX978273.1","term_id":"441431303","term_text":"JX978273.1"}}JX978273.1, and {"type":"entrez-nucleotide","attrs":{"text":"JN846706.1","term_id":"385399407","term_text":"JN846706.1"}}JN846706.1) present in GenBank.     

Characterization of SNP and Structural Variations in the Mitochondrial Genomes of Tilletia indica and Its Closely Related Species Formed Basis for a Simple Diagnostic Assay

Tilletia indica causes the disease Karnal bunt in wheat. The disease is under international quarantine regulations. Comparative mitochondrial (mt) genome analysis of T. indica ({"type":"entrez-nucleotide","attrs":{"text":"KX394364","term_id":"1128620031","term_text":"KX394364"}}KX394364 and {"type":"entrez-nucleotide","attrs":{"text":"DQ993184","term_id":"115361453","term_text":"DQ993184"}}DQ993184) and T. walkeri ({"type":"entrez-nucleotide","attrs":{"text":"EF536375","term_id":"144925993","term_text":"EF536375"}}EF536375) has found 325 to 328 SNPs, 57 to 60 short InDels (from 1 to 13 nt), two InDels (30 and 61 nt) and five (>200 nt) presence/absence variations (PAVs) between the two species. The mt genomes of both species have identical gene order. The numbers of SNPs and InDels between the mt genomes of the two species are approximately nine times of the corresponding numbers between the two T. indica isolates. There are eight SNPs between T. indica and T. walkeri that resulted in amino acid substitutions in the mt genes of cob, nad2 and nad5. In contrast, there is no amino acid substitution in the mt genes of the T. indica isolates from the SNPs found. The five PAVs present in T. indica ({"type":"entrez-nucleotide","attrs":{"text":"DQ993184","term_id":"115361453","term_text":"DQ993184"}}DQ993184) are absent in T. walkeri. Four PAVs are more than 1 kb and are not present in every T. indica isolate. Analysis of their presence and absence separates a collection of T. indica isolates into 11 subgroups. Two PAVs have ORFs for the LAGLIDAG endonuclease and two have ORFs for the GIY-YIG endonuclease family, which are representatives of homing endonuclease genes (HEGs). These intron- encoded HEGs confer intron mobility and account for their fluid distribution in T. indica isolates. The small PAV of 221 bp, present in every T. indica isolate and unique to the species, was used as the genetic fingerprint for the successful development of a rapid, highly sensitive and specific loop mediated isothermal amplification (LAMP) assay. The simple procedure of the LAMP assay and the easy detection formats will enable the assay to be automated for high throughput diagnosis.     

Aberrantly Expressed lncRNAs in Primary Varicose Great Saphenous Veins

Long non-coding RNAs (lncRNAs) are key regulatory molecules involved in a variety of biological processes and human diseases. However, the pathological effects of lncRNAs on primary varicose great saphenous veins (GSVs) remain unclear. The purpose of the present study was to identify aberrantly expressed lncRNAs involved in the prevalence of GSV varicosities and predict their potential functions. Using microarray with 33,045 lncRNA and 30,215 mRNA probes, 557 lncRNAs and 980 mRNAs that differed significantly in expression between the varicose great saphenous veins and control veins were identified in six pairs of samples. These lncRNAs were sub-grouped and mRNAs expressed at different levels were clustered into several pathways with six focused on metabolic pathways. Quantitative real-time PCR replication of nine lncRNAs was performed in 32 subjects, validating six lncRNAs ({"type":"entrez-nucleotide","attrs":{"text":"AF119885","term_id":"7770206","term_text":"AF119885"}}AF119885, {"type":"entrez-nucleotide","attrs":{"text":"AK021444","term_id":"10432630","term_text":"AK021444"}}AK021444, {"type":"entrez-nucleotide","attrs":{"text":"NR_027830","term_id":"240255595","term_text":"NR_027830"}}NR_027830, {"type":"entrez-nucleotide","attrs":{"text":"G36810","term_id":"2734477","term_text":"G36810"}}G36810, {"type":"entrez-nucleotide","attrs":{"text":"NR_027927","term_id":"242246950","term_text":"NR_027927"}}NR_027927, uc.345-). A coding-non-coding gene co-expression network revealed that four of these six lncRNAs may be correlated with 11 mRNAs and pathway analysis revealed that they may be correlated with another 8 mRNAs associated with metabolic pathways. In conclusion, aberrantly expressed lncRNAs for GSV varicosities were here systematically screened and validated and their functions were predicted. These findings provide novel insight into the physiology of lncRNAs and the pathogenesis of varicose veins for further investigation. These aberrantly expressed lncRNAs may serve as new therapeutic targets for varicose veins. The Human Ethnics Committee of Shanghai East Hospital, Tongji University School of Medicine approved the study (NO.: 2011-DF-53).     

Characterization of the Invasive,Multidrug Resistant Non-typhoidal Salmonella Strain D23580 in a Murine Model of Infection

A distinct pathovar of Salmonella enterica serovar Typhimurium, ST313, has emerged in sub-Saharan Africa as a major cause of fatal bacteremia in young children and HIV-infected adults. {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580, a multidrug resistant clinical isolate of ST313, was previously shown to have undergone genome reduction in a manner that resembles that of the more human-restricted pathogen, Salmonella enterica serovar Typhi. It has since been shown through tissue distribution studies that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 is able to establish an invasive infection in chickens. However, it remains unclear whether ST313 can cause lethal disease in a non-human host following a natural course of infection. Herein we report that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 causes lethal and invasive disease in a murine model of infection following peroral challenge. The LD₅₀ of {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 in female BALB/c mice was 4.7 x 10⁵ CFU. Tissue distribution studies performed 3 and 5 days post-infection confirmed that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 was able to more rapidly colonize the spleen, mesenteric lymph nodes and gall bladder in mice when compared to the well-characterized S. Typhimurium strain SL1344. {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 exhibited enhanced resistance to acid stress relative to SL1344, which may lend towards increased capability to survive passage through the gastrointestinal tract as well as during its intracellular lifecycle. Interestingly, {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 also displayed higher swimming motility relative to SL1344, S. Typhi strain Ty2, and the ST313 strain A130. Biochemical tests revealed that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 shares many similar metabolic features with SL1344, with several notable differences in the Voges-Proskauer and catalase tests, as well alterations in melibiose, and inositol utilization. These results represent the first full duration infection study using an ST313 strain following the entire natural course of disease progression, and serve as a benchmark for ongoing and future studies into the pathogenesis of {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580.     

Draft Genome Sequence of Xylaria grammica EL000614, a Strain Producing Grammicin,a Potent Nematicidal Compound

An endolichenic fungus, Xylaria grammica strain {"type":"entrez-nucleotide","attrs":{"text":"EL000614","term_id":"124922317"}}EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica {"type":"entrez-nucleotide","attrs":{"text":"EL000614","term_id":"124922317"}}EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted.     

Design of tandem genes cluster and expression vector for biosynthesis of soybean isoflavones

A tandem gene cluster CHS-CHI-IFS (rIFS) for secondary metabolites of plant isoflavones was constructed by using the chalcone synthase (CHS), chalcone isomerase (CHI), and isoflavone synthase (IFS) (GenBank accession numbers {"type":"entrez-nucleotide","attrs":{"text":"EU526827","term_id":"170783761","term_text":"EU526827"}}EU526827, {"type":"entrez-nucleotide","attrs":{"text":"EU526829","term_id":"170783765","term_text":"EU526829"}}EU526829, {"type":"entrez-nucleotide","attrs":{"text":"EU526830","term_id":"170783767","term_text":"EU526830"}}EU526830) in a single recombination event with the pET22b vector. The resulting expression vector pET-rIFS was heterogeneously expressed. The highlights of the vector include ease of handling, high efficiency and universal application among diverse plant species. To the best of our knowledge, this is the first attempt at developing a novel method of constructing tandem gene cluster for future research involving secondary metabolism of isoflavones and isoflavones engineering.Key words: Isoflavones biosynthesis, Novel method, Secondary metabolism, Tandem gene cluster     

Prevalence,antimicrobial resistance profile,and characterization of multi-drug resistant bacteria from various infected wounds in North Egypt

Multi-drug resistant (MDR) bacteria associated with wounds are extremely escalating. This study aims to survey different wounds in Alexandria hospitals, North Egypt, to explore the prevalence and characteristics of MDR bacteria for future utilization in antibacterial wound dressing designs. Among various bacterial isolates, we determined 22 MDR bacteria could resist different classes of antibiotics. The collected samples exhibited the prevalence of mono-bacterial infections (60%), while 40% included poly-bacterial species due to previous antibiotic administration. Moreover, Gram-negative bacteria showed dominance with a ratio of 63.6%, while Gram-positive bacteria reported 36.4%. Subsequently, the five most virulent bacteria were identified following the molecular approach by 16S rRNA and physiological properties using the VITEK 2 automated system. They were deposited in GenBank as Staphylococcus haemolyticus MST1 ({"type":"entrez-nucleotide","attrs":{"text":"KY550377","term_id":"1304487819","term_text":"KY550377"}}KY550377), Pseudomonas aeruginosa MST2 ({"type":"entrez-nucleotide","attrs":{"text":"KY550378","term_id":"1304487820","term_text":"KY550378"}}KY550378), Klebsiella pneumoniae MST3 ({"type":"entrez-nucleotide","attrs":{"text":"KY550379","term_id":"1304487821","term_text":"KY550379"}}KY550379), Escherichia coli MST4 ({"type":"entrez-nucleotide","attrs":{"text":"KY550380","term_id":"1304487822","term_text":"KY550380"}}KY550380), and Escherichia coli MST5 ({"type":"entrez-nucleotide","attrs":{"text":"KY550381","term_id":"1304487823","term_text":"KY550381"}}KY550381). In terms of isolation source, S. haemolyticus MST1 was isolated from a traumatic wound, while P. aeruginosa MST2 and E. coli MST4 were procured from hernia surgical wounds, and K. pneumoniae MST3 and E. coli MST5 were obtained from diabetic foot ulcers. Antibiotic sensitivity tests exposed that K. pneumoniae MST3, E. coli MST4, and E. coli MST5 are extended-spectrum β-lactamases (ESBLs) bacteria. Moreover, S. haemolyticus MST1 belongs to the methicillin-resistant coagulase-negative staphylococcus (MRCoNS), whereas P. aeruginosa MST2 exhibited resistance to common empirical bactericidal antibiotics. Overall, the study provides new insights into the prevalent MDR bacteria in Egypt for further use as specific models in formulating antibacterial wound dressings.     

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Phylum Crenarchaeota

• Pyrobaculum strain 1860, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003098","term_id":"356640791","term_text":"CP003098"}}CP003098 [1]

Phylum Deinococcus-Thermus

• “Thermus sp.” Strain CCB_US3_UF1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003126","term_id":"359289533","term_text":"CP003126"}}CP003126 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003127","term_id":"359291781","term_text":"CP003127"}}CP003127 (plasmid) [2]

Phylum Proteobacteria

• “Achromobacter arsenitoxydans” SY8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGUF00000000","term_id":"359366799","term_text":"AGUF00000000"}}AGUF00000000 [3]
• Acidovorax sp. Strain NO1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGTS00000000","term_id":"363417938","term_text":"AGTS00000000"}}AGTS00000000 [4]
• Acinetobacter baumannii AB4857, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAG00000000","term_id":"371492156","term_text":"AHAG00000000"}}AHAG00000000 [5]
• Acinetobacter baumannii AB5075, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAH00000000","term_id":"371492114","term_text":"AHAH00000000"}}AHAH00000000 [5]
• Acinetobacter baumannii AB5256, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAI00000000","term_id":"371492153","term_text":"AHAI00000000"}}AHAI00000000 [5]
• Acinetobacter baumannii AB5711, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAJ00000000","term_id":"371492197","term_text":"AHAJ00000000"}}AHAJ00000000 [5]
• Aeromonas salmonicida, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVO00000000","term_id":"356689990","term_text":"AGVO00000000"}}AGVO00000000 [6]
• Aggregatibacter actinomycetemcomitans RHAA1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHGR00000000","term_id":"359757447","term_text":"AHGR00000000"}}AHGR00000000 [7]
• Agrobacterium tumefaciens 5A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVZ00000000","term_id":"358008163","term_text":"AGVZ00000000"}}AGVZ00000000 [8]
• Azoarcus sp. Strain KH32C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012304","term_id":"358635055","term_text":"AP012304"}}AP012304, {"type":"entrez-nucleotide","attrs":{"text":"AP012305","term_id":"358639587","term_text":"AP012305"}}AP012305 [9]
• Burkholderia sp. Strain YI23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003087","term_id":"357934279","term_text":"CP003087"}}CP003087 (Chromosome 1), {"type":"entrez-nucleotide","attrs":{"text":"CP003088","term_id":"357937049","term_text":"CP003088"}}CP003088 (Chromosome 2), {"type":"entrez-nucleotide","attrs":{"text":"CP003089","term_id":"357938589","term_text":"CP003089"}}CP003089 (Chromosome 3), {"type":"entrez-nucleotide","attrs":{"text":"CP003090","term_id":"357939954","term_text":"CP003090"}}CP003090 (plasmid BYI23_D), {"type":"entrez-nucleotide","attrs":{"text":"CP003091","term_id":"357941606","term_text":"CP003091"}}CP003091 (plasmid BYI23_E) {"type":"entrez-nucleotide","attrs":{"text":"CP003092","term_id":"357941997","term_text":"CP003092"}}CP003092 (plasmid BYI23_F) [10]
• Brucella suis VBI22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003128","term_id":"358257303","term_text":"CP003128"}}CP003128, {"type":"entrez-nucleotide","attrs":{"text":"CP003129","term_id":"358259429","term_text":"CP003129"}}CP003129 [11]
• Comamonas testosteroni ATCC 11996, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIL00000000","term_id":"371454882","term_text":"AHIL00000000"}}AHIL00000000 [12]
• “Commensalibacter intestini” A911^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFR00000000","term_id":"353673384","term_text":"AGFR00000000"}}AGFR00000000 [13]
• Edwardsiella ictaluri, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001600.1","term_id":"238867551","term_text":"CP001600.1"}}CP001600.1 [14]
• Enterobacter cloacae subsp. dissolvens SDM, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSY00000000","term_id":"357435944","term_text":"AGSY00000000"}}AGSY00000000 [15]
• “Gluconobacter morbifer” G707^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQV00000000","term_id":"356416073","term_text":"AGQV00000000"}}AGQV00000000 [16]
• Legionella dumoffii TEX-KL, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVT00000000","term_id":"358009168","term_text":"AGVT00000000"}}AGVT00000000 [17]
• Legionella dumoffii NY-23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVU00000000","term_id":"358009167","term_text":"AGVU00000000"}}AGVU00000000 [17]
• Legionella pneumophila serogroup 12 Strain 570-CO-H, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003192","term_id":"364506764","term_text":"CP003192"}}CP003192 [18]
• Marinobacterium stanieri S30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPL00000000","term_id":"339778849","term_text":"AFPL00000000"}}AFPL00000000 [19]
• “Marinobacter manganoxydans” MnI7-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP001978 to CP001980","start_term":"CP001978","end_term":"CP001980","start_term_id":"311692891","end_term_id":"311697125"}}CP001978 to CP001980 [20]
• Mesorhizobium alhagi CCNWXJ12-2T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAM00000000","term_id":"359256606","term_text":"AHAM00000000"}}AHAM00000000 [21]
• Mesorhizobium amorphae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSN00000000","term_id":"355545111","term_text":"AGSN00000000"}}AGSN00000000 [22]
• Methylomicrobium alcaliphilum 20Z, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FO082060","term_id":"351716053","term_text":"FO082060"}}FO082060 and {"type":"entrez-nucleotide","attrs":{"text":"FO082061","term_id":"351720036","term_text":"FO082061"}}FO082061 [23]
• Mitsuaria sp. Strain H24L5A, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFG01000001 to CAFG01000607","start_term":"CAFG01000001","end_term":"CAFG01000607","start_term_id":"354809229","end_term_id":"354808623"}}CAFG01000001 to CAFG01000607 [24]
• Novosphingobium pentaromativorans US6-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFM00000000","term_id":"357601355","term_text":"AGFM00000000"}}AGFM00000000 [25]
• Pantoea ananatis B1-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAEI01000001 to CAEI01000169","start_term":"CAEI01000001","end_term":"CAEI01000169","start_term_id":"344197887","end_term_id":"344197719"}}CAEI01000001 to CAEI01000169 [26]
• Pantoea ananatis LMG 5342, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE617160","term_id":"365184443","term_text":"HE617160"}}HE617160 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"HE617161","term_id":"365188784","term_text":"HE617161"}}HE617161 (pPANA10) [27]
• Pantoea ananatis Strain PA13, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003085","term_id":"354986417","term_text":"CP003085"}}CP003085 and {"type":"entrez-nucleotide","attrs":{"text":"CP003086","term_id":"354685304","term_text":"CP003086"}}CP003086 [28]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXI00000000","term_id":"343788111","term_text":"AFXI00000000"}}AFXI00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXJ00000000","term_id":"343788109","term_text":"AFXJ00000000"}}AFXJ00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXK00000000","term_id":"343788110","term_text":"AFXK00000000"}}AFXK00000000 [29]
• Pseudomonas chlororaphis GP72, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAY01000000","term_id":"359757954","term_text":"gb||AHAY01000000"}}AHAY01000000 [30]
• Pseudomonas fluorescens F113, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003150","term_id":"359757955","term_text":"CP003150"}}CP003150 [31]
• Pseudomonas fluorescens Wayne 1R, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CADX01000001 to CADX01000090","start_term":"CADX01000001","end_term":"CADX01000090","start_term_id":"354924103","end_term_id":"354924014"}}CADX01000001 to CADX01000090 [32]
• Pseudomonas fluorescens Wood1R, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAFF01000001","term_id":"354698772","term_text":"CAFF01000001"}}CAFF01000001 to {"type":"entrez-nucleotide","attrs":{"text":"CAFF01001437","term_id":"354697336","term_text":"CAFF01001437"}}CAFF01001437 [32]
• Pseudomonas psychrotolerans L19, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBD00000000","term_id":"359372666","term_text":"AHBD00000000"}}AHBD00000000 [33]
• Pseudoalteromonas rubra ATCC 29570^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHCD00000000","term_id":"540289291","term_text":"AHCD00000000"}}AHCD00000000 [34]
• Pseudomonas stutzeri SDM-LAC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSX00000000","term_id":"357435965","term_text":"AGSX00000000"}}AGSX00000000 [35]
• Pseudoxanthomonas spadix BD-a59, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003093","term_id":"357433120","term_text":"CP003093"}}CP003093 [36]
• Rickettsia slovaca, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002428","term_id":"360041315","term_text":"CP002428"}}CP002428 [37]
• Salmonella enterica serovar Pullorum RKS5078, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003047","term_id":"357204415","term_text":"CP003047"}}CP003047 [38]
• Sinorhizobium meliloti CCNWSX0020, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVV00000000","term_id":"359507569","term_text":"AGVV00000000"}}AGVV00000000 [39]
• Sphingobium sp. Strain SYK-6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012222","term_id":"345135066","term_text":"AP012222"}}AP012222 and {"type":"entrez-nucleotide","attrs":{"text":"AP012223","term_id":"345138980","term_text":"AP012223"}}AP012223 [40]
• Sphingomonas sp. Strain PAMC 26605, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIS00000000","term_id":"366040305","term_text":"AHIS00000000"}}AHIS00000000 [41]
• Stenotrophomonas maltophilia RR-10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGRB00000000","term_id":"359757773","term_text":"AGRB00000000"}}AGRB00000000 [42]
• Strain HIMB30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIG00000000","term_id":"349602640","term_text":"AGIG00000000"}}AGIG00000000 [43]
• Taylorella equigenitalis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003059","term_id":"347973256","term_text":"CP003059"}}CP003059 [44]
• Vibrio campbellii DS40M4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIE00000000","term_id":"358251732","term_text":"AGIE00000000"}}AGIE00000000 [45]
• Vibrio fischeri SR5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIH00000000","term_id":"371496097","term_text":"AHIH00000000"}}AHIH00000000 [46]
• Yersinia enterocolitica, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQO00000000","term_id":"351780838","term_text":"AGQO00000000"}}AGQO00000000 [47]

Phylum Tenericutes

• Candidatus Mycoplasma haemominutum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613254","term_id":"357978897","term_text":"HE613254"}}HE613254 [48]
• Mycoplasma haemocanis strain Illinois, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003199","term_id":"363988676","term_text":"CP003199"}}CP003199 [49]
• Mycoplasma iowae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFP00000000","term_id":"349504222","term_text":"AGFP00000000"}}AGFP00000000 [50]
• Mycoplasma pneumoniae Type 2a Strain 309, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012303","term_id":"358640274","term_text":"AP012303"}}AP012303 [51]

Phylum Firmicutes

• Bacillus cereus F837/76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003187","term_id":"364509831","term_text":"CP003187"}}CP003187 (chromosome) {"type":"entrez-nucleotide","attrs":{"text":"CP003188","term_id":"364515227","term_text":"CP003188"}}CP003188 (pF837_55kb), {"type":"entrez-nucleotide","attrs":{"text":"CP003189","term_id":"364515372","term_text":"CP003189"}}CP003189 (pF837_10kb) [52]
• Brevibacillus laterosporus Strain GI-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGD01000001 to CAGD01000061","start_term":"CAGD01000001","end_term":"CAGD01000061","start_term_id":"359745324","end_term_id":"359745264"}}CAGD01000001 to CAGD01000061 [53]
• Clostridium sporogenes PA 3679, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGAH00000000","term_id":"364889226","term_text":"AGAH00000000"}}AGAH00000000 [54]
• Enterococcus mundtii CRL1656, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFWZ00000000.1","term_id":"354620965","term_text":"AFWZ00000000.1"}}AFWZ00000000.1 [55]
• Geobacillus thermoleovorans CCB_US3_UF5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003125","term_id":"359285645","term_text":"CP003125"}}CP003125 [56]
• Lactobacillus curvatus Strain CRL705, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBU01000000","term_id":"354514905","term_text":"gb||AGBU01000000"}}AGBU01000000 [57]
• Lactobacillus rhamnosus ATCC 8530, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003094","term_id":"355393429","term_text":"CP003094"}}CP003094 [58]
• Lactobacillus rhamnosus R0011, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKC00000000","term_id":"357540515","term_text":"AGKC00000000"}}AGKC00000000 [59]
• Lactococcus garvieae TB25, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQX01000000","term_id":"359031556","term_text":"gb||AGQX01000000"}}AGQX01000000 [60]
• Lactococcus garvieae LG9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQY01000000","term_id":"359031592","term_text":"gb||AGQY01000000"}}AGQY01000000 [60]
• Lactococcus lactis subsp. cremoris A76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003132","term_id":"358748197","term_text":"CP003132"}}CP003132 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003136","term_id":"358750967","term_text":"CP003136"}}CP003136 (pQA505), {"type":"entrez-nucleotide","attrs":{"text":"CP003135","term_id":"358750954","term_text":"CP003135"}}CP003135 (PQA518), {"type":"entrez-nucleotide","attrs":{"text":"CP003134","term_id":"358750911","term_text":"CP003134"}}CP003134 (pQA549), {"type":"entrez-nucleotide","attrs":{"text":"CP003133","term_id":"358750841","term_text":"CP003133"}}CP003133 (pQA554) [61]
• Leuconostoc citreum LBAE C10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGE00000000","term_id":"365487970","term_text":"CAGE00000000"}}CAGE00000000 [62]
• Leuconostoc citreum LBAE C11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGF00000000","term_id":"365512054","term_text":"CAGF00000000"}}CAGF00000000 [62]
• Leuconostoc citreum LBAE E16, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGG00000000","term_id":"365528100","term_text":"CAGG00000000"}}CAGG00000000 [62]
• Leuconostoc mesenteroides subsp. mesenteroides Strain J18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003101","term_id":"948298071","term_text":"CP003101"}}CP003101 [63]
• Paenibacillus peoriae Strain KCTC 3763^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFX00000000","term_id":"359367787","term_text":"AGFX00000000"}}AGFX00000000 [64]
• Pediococcus acidilactici MA18/5M, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKB00000000","term_id":"357540603","term_text":"AGKB00000000"}}AGKB00000000 [65]
• Pediococcus claussenii ATCC BAA-344^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003137","term_id":"361055534","term_text":"CP003137"}}CP003137 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003138","term_id":"361057275","term_text":"CP003138"}}CP003138 (pPECL-1), {"type":"entrez-nucleotide","attrs":{"text":"CP003139","term_id":"361057278","term_text":"CP003139"}}CP003139 (pPECL-2), {"type":"entrez-nucleotide","attrs":{"text":"CP003140","term_id":"361057281","term_text":"CP003140"}}CP003140 (pPECL-3), {"type":"entrez-nucleotide","attrs":{"text":"CP003141","term_id":"361057302","term_text":"CP003141"}}CP003141 (pPECL-4), {"type":"entrez-nucleotide","attrs":{"text":"CP003142","term_id":"361057319","term_text":"CP003142"}}CP003142 (pPECL-5), {"type":"entrez-nucleotide","attrs":{"text":"CP003143","term_id":"361057355","term_text":"CP003143"}}CP003143 (pPECL-6), {"type":"entrez-nucleotide","attrs":{"text":"CP003144","term_id":"361057377","term_text":"CP003144"}}CP003144 (pPECL-7), {"type":"entrez-nucleotide","attrs":{"text":"CP003145","term_id":"380450589","term_text":"CP003145"}}CP003145 (pPECL-8) [66]
• Staphylococcus aureus M013, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003166","term_id":"359829121","term_text":"CP003166"}}CP003166 [67]
• Staphylococcus aureus subsp. aureus TW20, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FN433596","term_id":"269939526","term_text":"FN433596"}}FN433596 [68]
• Weissella confusa LBAE C39-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGH00000000","term_id":"365549261","term_text":"CAGH00000000"}}CAGH00000000 [69]

Phylum Actinobacteria

• Corynebacterium casei, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFW01000001 to CAFW01000106","start_term":"CAFW01000001","end_term":"CAFW01000106","start_term_id":"356609265","end_term_id":"356606462"}}CAFW01000001 to CAFW01000106 [70]
• Corynebacterium glutamicum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQQ00000000","term_id":"658109743","term_text":"AGQQ00000000"}}AGQQ00000000 [71]
• Leucobacter chromiiresistens, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGCW00000000","term_id":"353529976","term_text":"AGCW00000000"}}AGCW00000000 [72]
• Mycobacterium abscessus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQU00000000","term_id":"353453148","term_text":"AGQU00000000"}}AGQU00000000 [73]
• Propionibacterium acnes ST9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003195","term_id":"365742920","term_text":"CP003195"}}CP003195 [74]
• Propionibacterium acnes ST22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003196","term_id":"365740656","term_text":"CP003196"}}CP003196 [74]
• Propionibacterium acnes ST27, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003197","term_id":"365738411","term_text":"CP003197"}}CP003197 [74]
• Saccharomonospora azurea SZMC 14600, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBX00000000","term_id":"359740650","term_text":"AHBX00000000"}}AHBX00000000 [75]
• Streptomyces sp. Strain TOR3209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNH00000000","term_id":"359357427","term_text":"AGNH00000000"}}AGNH00000000 [76]
• Streptomyces sp. Strain W007, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSW00000000","term_id":"364010697","term_text":"AGSW00000000"}}AGSW00000000 [77]

Phylum Spirochaetes

• Borrelia valaisiana VS116, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABCY02000001","term_id":"224510974","term_text":"ABCY02000001"}}ABCY02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001439","term_id":"224497263","term_text":"CP001439"}}CP001439 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001437","term_id":"224497187","term_text":"CP001437"}}CP001437 (Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP001440","term_id":"224497290","term_text":"CP001440"}}CP001440 (plasmid Ip 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001442","term_id":"224497476","term_text":"CP001442"}}CP001442 (plasmid Ip28-8), {"type":"entrez-nucleotide","attrs":{"text":"CP001436","term_id":"224497148","term_text":"CP001436"}}CP001436 (Ip 36), {"type":"entrez-nucleotide","attrs":{"text":"CP001433","term_id":"224496993","term_text":"CP001433"}}CP001433 (plasmid Ip 54), {"type":"entrez-nucleotide","attrs":{"text":"CP001438","term_id":"224497250","term_text":"CP001438"}}CP001438 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001432","term_id":"224496964","term_text":"CP001432"}}CP001432 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP001441","term_id":"224497433","term_text":"CP001441"}}CP001441 (plasmid cp32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP001434","term_id":"224497064","term_text":"CP001434"}}CP001434 (plasmid cp32-7), {"type":"entrez-nucleotide","attrs":{"text":"CP001435","term_id":"224497109","term_text":"CP001435"}}CP001435 (plasmid cp32-10) [78]
• “Borrelia bissettii” DN127, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002746","term_id":"342222012","term_text":"CP002746"}}CP002746 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002756","term_id":"342223236","term_text":"CP002756"}}CP002756 (plasmid Ip12), {"type":"entrez-nucleotide","attrs":{"text":"CP002757","term_id":"342223270","term_text":"CP002757"}}CP002757 (plasmid Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP002758","term_id":"342223295","term_text":"CP002758"}}CP002758 (plasmid 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002759","term_id":"342223320","term_text":"CP002759"}}CP002759 (plasmid Ip 28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002760","term_id":"342223351","term_text":"CP002760"}}CP002760 (Ip28-7), {"type":"entrez-nucleotide","attrs":{"text":"CP002761","term_id":"342223388","term_text":"CP002761"}}CP002761 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"CP002762","term_id":"342223459","term_text":"CP002762"}}CP002762 (plasmid Ip56), {"type":"entrez-nucleotide","attrs":{"text":"CP002755","term_id":"342223223","term_text":"CP002755"}}CP002755 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP002747","term_id":"342222829","term_text":"CP002747"}}CP002747 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP002749","term_id":"342222904","term_text":"CP002749"}}CP002749 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002750","term_id":"342222947","term_text":"CP002750"}}CP002750 (plasmid cp32-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002751","term_id":"342222990","term_text":"CP002751"}}CP002751 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP002752","term_id":"342223034","term_text":"CP002752"}}CP002752 (plasmid cp32-6), {"type":"entrez-nucleotide","attrs":{"text":"CP002753","term_id":"342223077","term_text":"CP002753"}}CP002753 (plasmid cp32-7), CP0027554 (plasmid cp32-9), {"type":"entrez-nucleotide","attrs":{"text":"CP002748","term_id":"342222857","term_text":"CP002748"}}CP002748 (plasmid cp32-11) [78]
• Borrelia spielmanii A14S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000001","term_id":"224514548","term_text":"ABKB02000001"}}ABKB02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001468","term_id":"224497637","term_text":"CP001468"}}CP001468 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001471","term_id":"224497796","term_text":"CP001471"}}CP001471 (Ip28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001470","term_id":"224497745","term_text":"CP001470"}}CP001470 (plasmid Ip28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP001465","term_id":"224497532","term_text":"CP001465"}}CP001465 (plasmid Ip28-2), {"type":"entrez-nucleotide","attrs":{"text":"CP001466","term_id":"224497566","term_text":"CP001466"}}CP001466 (plasmid Ip36), {"type":"entrez-nucleotide","attrs":{"text":"CP001464","term_id":"224497496","term_text":"CP001464"}}CP001464 (plasmid Ip38), {"type":"entrez-nucleotide","attrs":{"text":"CP001469","term_id":"224497671","term_text":"CP001469"}}CP001469 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000016","term_id":"224513758","term_text":"ABKB02000016"}}ABKB02000016, {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000020","term_id":"224513743","term_text":"ABKB02000020"}}ABKB02000020 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001467","term_id":"224497607","term_text":"CP001467"}}CP001467 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000026","term_id":"224513697","term_text":"ABKB02000026"}}ABKB02000026 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000031","term_id":"224513641","term_text":"ABKB02000031"}}ABKB02000031 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000021","term_id":"224513736","term_text":"ABKB02000021"}}ABKB02000021 (plasmid cp32-12), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000014","term_id":"224513768","term_text":"ABKB02000014"}}ABKB02000014 (unidentified) [78]

Non-Bacterial genomes

• Aspergillus flavus, sequence accession {"type":"entrez-geo","attrs":{"text":"GSE32177","term_id":"32177"}}GSE32177 [79]
• Bacteriophage SPN3UB, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ288021","term_id":"378408798","term_text":"JQ288021"}}JQ288021 [80]
• Bamboo mitochondria, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"JQ235166 to JQ235179","start_term":"JQ235166","end_term":"JQ235179","start_term_id":"372861916","end_term_id":"372861969"}}JQ235166 to JQ235179 [81]
• Boea hygrometrica chloroplast, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107811","term_id":"340549387","term_text":"JN107811"}}JN107811 [82]
• Boea hygrometrica mitochondrial, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107812","term_id":"340549473","term_text":"JN107812"}}JN107812 [82]
• Canine Picornavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831356","term_id":"377826518","term_text":"JN831356"}}JN831356 [83]
• Chandipura virus (CHPV) CIN0327, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212856.1","term_id":"309261828","term_text":"GU212856.1"}}GU212856.1 [84]
• Chandipura virus (CHPV) CIN0451, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212857.1","term_id":"309261834","term_text":"GU212857.1"}}GU212857.1 [84]
• Chandipura virus (CHPV) CIN0751, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212858.1","term_id":"309261840","term_text":"GU212858.1"}}GU212858.1 [84]
• Chandipura virus (CHPV) CIN0755, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU190711.1","term_id":"309099431","term_text":"GU190711.1"}}GU190711.1 [84]
• Chinese Porcine Parvovirus Strain PPV2010, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN872448","term_id":"374676766","term_text":"JN872448"}}JN872448 [85]
• Common midwife toad megavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ231222","term_id":"375281729","term_text":"JQ231222"}}JQ231222 [86]
• Dengue Virus Serotype 4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN983813","term_id":"372290533","term_text":"JN983813"}}JN983813 [87]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF270480","term_id":"367465451","term_text":"JF270480"}}JF270480 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314464","term_id":"377824036","term_text":"JQ314464"}}JQ314464 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314465","term_id":"377824038","term_text":"JQ314465"}}JQ314465 [88]
• Emiliania huxleyi Virus 202, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ634145","term_id":"356927554","term_text":"HQ634145"}}HQ634145 [89]
• Emiliania huxleyi Virus EhV-88, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974310","term_id":"347600450","term_text":"JF974310"}}JF974310 [89]
• Emiliania huxleyi EhV-201, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974311","term_id":"357972615","term_text":"JF974311"}}JF974311 [89]
• Emiliania huxleyi EhV-207, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974317","term_id":"347600924","term_text":"JF974317"}}JF974317 [89]
• Emiliania huxleyi EhV-208, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974318","term_id":"347601393","term_text":"JF974318"}}JF974318 [89]
• Glarea lozoyensis, sequence accession GUE00000000 [90]
• Nannochloropis gaditana, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNI00000000","term_id":"366047505","term_text":"AGNI00000000"}}AGNI00000000 [91]
• Oryza sativa cv., sequence accession DRA000499 [92]
• Partetravirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN990269","term_id":"374718987","term_text":"JN990269"}}JN990269 [93]
• Porcine Bocavirus PBoV5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831651","term_id":"371449604","term_text":"JN831651"}}JN831651 [94]
• Porcine epidemic diarrhea virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ282909","term_id":"377824029","term_text":"JQ282909"}}JQ282909 [95]
• Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HM624080","term_id":"315418954","term_text":"HM624080"}}HM624080 [96]
• Pseudomonas fluorescens phage OBP, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"JN627160","term_id":"359842892","term_text":"JN627160"}}JN627160 [97]
• RNA Virus from Avocado, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN880414","term_id":"371444768","term_text":"JN880414"}}JN880414 [98]
• Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN391180","term_id":"370344404","term_text":"JN391180"}}JN391180 [99]
• Schistosoma haematobium, sequence accession PRJNA78265 [100]
• Schistosoma mansoni, sequence accession {"type":"entrez-protein","attrs":{"text":"ERP00038","term_id":"550209647","term_text":"ERP00038"}}ERP00038 [101]
• Stenopirates sp., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN100019","term_id":"340008214","term_text":"JN100019"}}JN100019 [102]
• T7-Like Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN651747","term_id":"374713556","term_text":"JN651747"}}JN651747 [103]
• Vibrio harveyi siphophage VHS1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF713456","term_id":"334898816","term_text":"JF713456"}}JF713456 [104]
• Tyrolean ice man, sequence accession ERP001144 [105]

     

Genome sequences published outside of Standards in Genomic Sciences, March-April 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Phylum Euryarchaeota

• Halococcus hamelinensis, sequence accession PRJNA80845 [1]
• “Methanocella conradii” HZ254, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003243","term_id":"379319823","term_text":"CP003243"}}CP003243 [2]
• Thermococcus litoralis NS-C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHVB00000000","term_id":"374743520","term_text":"AHVB00000000"}}AHVB00000000 [3]

Phylum Crenarchaeota

• Candidatus Nitrosopumilus salaria” BD31, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEXL00000000","term_id":"386807666","term_text":"AEXL00000000"}}AEXL00000000 [4]
• Candidatus Nitrosoarchaeum limnia, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHJG00000000","term_id":"367466343","term_text":"AHJG00000000"}}AHJG00000000 [5]

Phylum Deinococcus-Thermus

• Deinococcus gobiensis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002536","term_id":"324314064","term_text":"CP002536"}}CP002536 [6]

Phylum Proteobacteria

• Aggregatibacter actinomycetemcomitans strain ANH9381, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003099","term_id":"365745154","term_text":"CP003099"}}CP003099 [7]
• Alishewanella jeotgali, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHTH00000000","term_id":"374571619","term_text":"AHTH00000000"}}AHTH00000000 [8]
• Enterobacter aerogenes KCTC 2190, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002824","term_id":"334732565","term_text":"CP002824"}}CP002824 [9]
• Escherichia coli O104:H4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOB02000092","term_id":"340739517","term_text":"AFOB02000092"}}AFOB02000092 [10]
• Helicobacter pylori strains 17874, sequence accession PRJNA76569 [11]
• Helicobacter pylori strains P79, sequence accession PRJNA76567 [11]
• Janthinobacterium sp. Strain PAMC 25724, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHB00000000","term_id":"372292151","term_text":"AHHB00000000"}}AHHB00000000 [12]
• Klebsiella oxytoca KCTC 1686, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003218","term_id":"365906294","term_text":"CP003218"}}CP003218 [13]
• Klebsiella pneumoniae subsp. pneumoniae HS11286, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003200","term_id":"364515570","term_text":"CP003200"}}CP003200 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003223","term_id":"365803686","term_text":"CP003223"}}CP003223 (plasmid pKPHS1), {"type":"entrez-nucleotide","attrs":{"text":"CP003224","term_id":"365803828","term_text":"CP003224"}}CP003224 (plasmid pKPHS2), {"type":"entrez-nucleotide","attrs":{"text":"CP003225","term_id":"365803989","term_text":"CP003225"}}CP003225 (plasmid pKPHS3), {"type":"entrez-nucleotide","attrs":{"text":"CP003226","term_id":"365804142","term_text":"CP003226"}}CP003226 (plasmid pKPHS4), {"type":"entrez-nucleotide","attrs":{"text":"CP003227","term_id":"365804147","term_text":"CP003227"}}CP003227 (plasmid pKPHS5), {"type":"entrez-nucleotide","attrs":{"text":"CP003228","term_id":"365804153","term_text":"CP003228"}}CP003228 (plasmid pKPHS6) [14]
• Oceanimonas sp. GK1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003171","term_id":"372983507","term_text":"CP003171"}}CP003171 [15]
• “Pseudogulbenkiania ferrooxidans” Strain 2002, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NZ_ACIS01000000","term_id":"224827334","term_text":"ref||NZ_ACIS01000000"}}NZ_ACIS01000000 [16]
• Pseudomonas extremaustralis 14-3b, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIP00000000","term_id":"371721769","term_text":"AHIP00000000"}}AHIP00000000 [17]
• Pseudomonas sp. Strain PAMC 25886, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHC00000000","term_id":"372002201","term_text":"AHHC00000000"}}AHHC00000000 [18]
• Psychrobacter, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHVZ00000000","term_id":"375126956","term_text":"AHVZ00000000"}}AHVZ00000000 [19]
• Rahnella sp. Strain Y9602, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002505","term_id":"321165934","term_text":"CP002505"}}CP002505 [20]
• Rhizobium sp. Strain PDO1-076, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHZC00000000","term_id":"375058045","term_text":"AHZC00000000"}}AHZC00000000 [21]
• Rhodospirillum photometricum DSM122, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE663493","term_id":"378401447","term_text":"HE663493"}}HE663493 [22]
• “Rickettsia sibirica sibirica”, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIZ00000000","term_id":"374669031","term_text":"AHIZ00000000"}}AHIZ00000000 [23]
• Rickettsia sibirica subsp. mongolitimonae strain HA-91, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHZB00000000","term_id":"375318263","term_text":"AHZB00000000"}}AHZB00000000 [24]
• Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5, sequence accession [25]
• Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGQ00000000","term_id":"379987603","term_text":"CAGQ00000000"}}CAGQ00000000 [26]
• Salmonella enterica subsp. enterica Serovar Typhi P-stx-12, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003278","term_id":"374352002","term_text":"CP003278"}}CP003278 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP003279","term_id":"374356693","term_text":"CP003279"}}CP003279 (plasmid) [27]
• Sphingomonas echinoides ATCC 14820, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIR00000000","term_id":"366040205","term_text":"AHIR00000000"}}AHIR00000000 [28]
• Strain HIMB55, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIF00000000","term_id":"374304583","term_text":"AGIF00000000"}}AGIF00000000 [29]
• Vibrio harveyi CAIM 1792, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHQ00000000","term_id":"374671508","term_text":"AHHQ00000000"}}AHHQ00000000 [30]
• Wolbachia Strain wAlbB, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGB01000001 to CAGB01000165","start_term":"CAGB01000001","end_term":"CAGB01000165","start_term_id":"371933004","end_term_id":"371931774"}}CAGB01000001 to CAGB01000165 [31]
• Xanthomonas axonopodis pv. punicae Strain LMG 859, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGJ01000001 to CAGJ01000217","start_term":"CAGJ01000001","end_term":"CAGJ01000217","start_term_id":"372556075","end_term_id":"372551622"}}CAGJ01000001 to CAGJ01000217 [32]

Phylum Tenericutes

• Mycoplasma hyorhinis Strain GDL-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003231","term_id":"367460291","term_text":"CP003231"}}CP003231 [33]

Phylum Firmicutes

• Bacillus subtilis, sequence accession BGSCID 3A27 through BGSCID 28A4 [34]
• Clostridium difficile Strain CD37, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHJJ00000000","term_id":"371930118","term_text":"AHJJ00000000"}}AHJJ00000000 [35]
• Clostridium perfringens, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFES00000000","term_id":"380306484","term_text":"AFES00000000"}}AFES00000000 [36]
• Lactobacillus fructivorans KCTC 3543, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEQY00000000","term_id":"316986063","term_text":"AEQY00000000"}}AEQY00000000 [37]
• Lactococcus lactis IO-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012281","term_id":"374672113","term_text":"AP012281"}}AP012281 [38]
• Lactobacillus plantarum strain NC8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGRI00000000","term_id":"376011245","term_text":"AGRI00000000"}}AGRI00000000 [39]
• Paenibacillus dendritiformis C454, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHKH00000000","term_id":"374393106","term_text":"AHKH00000000"}}AHKH00000000 [40]
• Paenibacillus sp. Strain Aloe-11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFI00000000","term_id":"374477730","term_text":"AGFI00000000"}}AGFI00000000 [41]
• “Peptoniphilus rhinitidis” 1-13^T, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BAEW01000001 to BAEW01000056","start_term":"BAEW01000001","end_term":"BAEW01000056","start_term_id":"374722129","end_term_id":"374722074"}}BAEW01000001 to BAEW01000056 [42]
• Streptococcus macedonicus ACA-DC 198, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613569","term_id":"372283141","term_text":"HE613569"}}HE613569 and {"type":"entrez-nucleotide","attrs":{"text":"HE613570","term_id":"372285142","term_text":"HE613570"}}HE613570 [43]
• Staphylococcus aureus VC40, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003033","term_id":"374362062","term_text":"CP003033"}}CP003033 [44]
• Streptococcus infantarius subsp. infantarius Strain CJ18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003295","term_id":"374681091","term_text":"CP003295"}}CP003295 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003296","term_id":"374682963","term_text":"CP003296"}}CP003296 (plasmid) [45]
• Streptococcus macedonicus ACA-DC 198, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613569","term_id":"372283141","term_text":"HE613569"}}HE613569 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"HE613570","term_id":"372285142","term_text":"HE613570"}}HE613570 (plasmid pSMA198) [46]

Phylum Actinobacteria

• Actinoplanes sp. SE50/110, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003170","term_id":"359832573","term_text":"CP003170"}}CP003170 [47]
• Amycolatopsis sp. Strain ATCC 39116, sequence accession [48]
• Nocardia cyriacigeorgica GUH-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FO082843","term_id":"374843763","term_text":"FO082843"}}FO082843 [49]
• Salinibacterium sp., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHWA00000000","term_id":"375323651","term_text":"AHWA00000000"}}AHWA00000000 [50]
• Streptomyces acidiscabies 84-104, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBF00000000","term_id":"372137622","term_text":"AHBF00000000"}}AHBF00000000 [51]

Non-Bacterial genomes

• Bluetongue Virus Serotype 2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AJ783905","term_id":"70907482","term_text":"AJ783905"}}AJ783905 (Seg-6) and {"type":"entrez-nucleotide","attrs":{"text":"JQ681257","term_id":"383932043","term_text":"JQ681257"}}JQ681257 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ681257","term_id":"383932043","term_text":"JQ681257"}}JQ681257 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ681258","term_id":"383932045","term_text":"JQ681258"}}JQ681258 (Seg-2), {"type":"entrez-nucleotide","attrs":{"text":"JQ681259","term_id":"383932047","term_text":"JQ681259"}}JQ681259 (Seg-3), {"type":"entrez-nucleotide","attrs":{"text":"JQ681260","term_id":"383932049","term_text":"JQ681260"}}JQ681260 (Seg-4), {"type":"entrez-nucleotide","attrs":{"text":"JQ681261","term_id":"383932051","term_text":"JQ681261"}}JQ681261 (Seg-5), {"type":"entrez-nucleotide","attrs":{"text":"JQ681262","term_id":"383932053","term_text":"JQ681262"}}JQ681262 (Seg-7), JQ6812563 (Seg-8), JQ6812564 (Seg-9), to {"type":"entrez-nucleotide","attrs":{"text":"JQ681265","term_id":"383932059","term_text":"JQ681265"}}JQ681265 (Seg-10) [52]
• Virus Serotype 1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AJ585111","term_id":"118420282","term_text":"AJ585111"}}AJ585111 (Seg-2), {"type":"entrez-nucleotide","attrs":{"text":"AJ586659","term_id":"47826214","term_text":"AJ586659"}}AJ586659 (Seg-6), {"type":"entrez-nucleotide","attrs":{"text":"JQ282770","term_id":"383215071","term_text":"JQ282770"}}JQ282770 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ282771","term_id":"383215073","term_text":"JQ282771"}}JQ282771 (Seg-3), {"type":"entrez-nucleotide","attrs":{"text":"JQ282772","term_id":"383215075","term_text":"JQ282772"}}JQ282772 (Seg-4), {"type":"entrez-nucleotide","attrs":{"text":"JQ282773","term_id":"383215077","term_text":"JQ282773"}}JQ282773 (Seg-5), {"type":"entrez-nucleotide","attrs":{"text":"JQ282774","term_id":"383215079","term_text":"JQ282774"}}JQ282774 (Seg-7), {"type":"entrez-nucleotide","attrs":{"text":"JQ282775","term_id":"383215081","term_text":"JQ282775"}}JQ282775 (Seg-8), {"type":"entrez-nucleotide","attrs":{"text":"JQ282776","term_id":"383215083","term_text":"JQ282776"}}JQ282776 (Seg-9), and {"type":"entrez-nucleotide","attrs":{"text":"JQ282777","term_id":"383215085","term_text":"JQ282777"}}JQ282777 (Seg-10) [52]
• Chloroplast genome of Erycina pusilla, sequence accession JF_746994 [53]
• Danio rerio, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ434101","term_id":"384872525","term_text":"JQ434101"}}JQ434101 [54]
• Enterococcal Bacteriophage SAP6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF731128","term_id":"343411857","term_text":"JF731128"}}JF731128 [55]
• Eubenangee virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070376","term_id":"383513837","term_text":"JQ070376"}}JQ070376 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070385","term_id":"383513855","term_text":"JQ070385"}}JQ070385 [56]
• Fujian/411-like viruses, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CY087969 to CY088568","start_term":"CY087969","end_term":"CY088568","start_term_id":"380506411","end_term_id":"380507803"}}CY087969 to CY088568 [57]
• Hantavirus Variant of Rio Mamoré Virus, Maripa Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ611712","term_id":"384382977","term_text":"JQ611712"}}JQ611712 (segment S), {"type":"entrez-nucleotide","attrs":{"text":"JQ611713","term_id":"384382979","term_text":"JQ611713"}}JQ611713 (segment M), and {"type":"entrez-nucleotide","attrs":{"text":"JQ611714","term_id":"384382981","term_text":"JQ611714"}}JQ611714 (segment L) [58]
• Pata virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070386","term_id":"383513857","term_text":"JQ070386"}}JQ070386 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070395","term_id":"383513875","term_text":"JQ070395"}}JQ070395 [59]
• Porcine Circovirus 2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ413808","term_id":"383215164","term_text":"JQ413808"}}JQ413808 [60]
• Porcine Reproductive and Respiratory Syndrome Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ326271","term_id":"382929416","term_text":"JQ326271"}}JQ326271 [61]
• Streptococcus mutans Phage M102AD, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"DQ386162","term_id":"88698119","term_text":"DQ386162"}}DQ386162 [62]
• Tilligery virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070366","term_id":"383513817","term_text":"JQ070366"}}JQ070366 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070375","term_id":"383513835","term_text":"JQ070375"}}JQ070375 [63]

     

BAC-End Microsatellites from Intra and Inter-Genic Regions of the Common Bean Genome and Their Correlation with Cytogenetic Features

Highly polymorphic markers such as simple sequence repeats (SSRs) or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES) from non-contigged, non-overlapping bacterial artificial clones (BACs) in common bean (Phaseolus vulgaris L.). These so called “singleton” BACs were from the {"type":"entrez-nucleotide","attrs":{"text":"G19833","term_id":"1340404","term_text":"G19833"}}G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×{"type":"entrez-nucleotide","attrs":{"text":"G19833","term_id":"1340404","term_text":"G19833"}}G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally) and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×{"type":"entrez-nucleotide","attrs":{"text":"G19833","term_id":"1340404","term_text":"G19833"}}G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.     

Phenotypic Assessment of Probiotic and Bacteriocinogenic Efficacy of Indigenous LAB Strains from Human Breast Milk

Breast milk is the combination of bioactive compounds and microflora that promote newborn’s proper growth, gut flora, and immunity. Thus, it is always considered the perfect food for newborns. Amongst their bioactives, probiotic communities—especially lactic acid bacteria (LAB)—are characterized from breast milk over the first month of parturition. In this study, seven LAB were characterized phenotypically and genotypically as Levilactobacillus brevis BDUMBT08 ({"type":"entrez-nucleotide","attrs":{"text":"MT673657","term_id":"1863149999"}}MT673657), L. gastricus BDUMBT09 ({"type":"entrez-nucleotide","attrs":{"text":"MT774596","term_id":"1873222494"}}MT774596), L. paracasei BDUMBT10 ({"type":"entrez-nucleotide","attrs":{"text":"MT775430","term_id":"1874262304"}}MT775430), L. brevis BDUMBT11 ({"type":"entrez-nucleotide","attrs":{"text":"MW785062","term_id":"2009762994"}}MW785062), L. casei BDUMBT12 ({"type":"entrez-nucleotide","attrs":{"text":"MW785063","term_id":"2009820773"}}MW785063), L. casei BDUMBT13 ({"type":"entrez-nucleotide","attrs":{"text":"MW785178","term_id":"2010296340"}}MW785178), and Brevibacillus brevis M2403 ({"type":"entrez-nucleotide","attrs":{"text":"MK371781","term_id":"1548854744"}}MK371781) from human breast milk. Their tolerance to lysozyme, acid, bile, gastric juice, pancreatic juice, and NaCl and potential for mucoadhesion, auto-aggregation, and co-aggregation with pathogens are of great prominence in forecasting their gut colonizing ability. They proved their safety aspects as they were negative for virulence determinants such as hemolysis and biofilm production. Antibiogram of LAB showed their sensitivity to more than 90% of the antibiotics tested. Amongst seven LAB, three isolates (L. brevis BDUMBT08 and BDUMBT11, and L. gatricus BDUMBT09) proved their bacteriocin producing propensity. Although the seven LAB isolates differed in their behavior, their substantial probiotic properties with safety could be taken as promising probiotics for further studies to prove their in vivo effects, such as health benefits, in humans.