Insights from the Complete Chloroplast Genome into the Evolution of Sesamum indicum L

Sesame (Sesamum indicum L.) is one of the oldest oilseed crops. In order to investigate the evolutionary characters according to the Sesame Genome Project, apart from sequencing its nuclear genome, we sequenced the complete chloroplast genome of S. indicum cv. Yuzhi 11 (white seeded) using Illumina and 454 sequencing. Comparisons of chloroplast genomes between S. indicum and the 18 other higher plants were then analyzed. The chloroplast genome of cv. Yuzhi 11 contains 153,338 bp and a total of 114 unique genes ({"type":"entrez-nucleotide","attrs":{"text":"KC569603","term_id":"496538580","term_text":"KC569603"}}KC569603). The number of chloroplast genes in sesame is the same as that in Nicotiana tabacum, Vitis vinifera and Platanus occidentalis. The variation in the length of the large single-copy (LSC) regions and inverted repeats (IR) in sesame compared to 18 other higher plant species was the main contributor to size variation in the cp genome in these species. The 77 functional chloroplast genes, except for ycf1 and ycf2, were highly conserved. The deletion of the cp ycf1 gene sequence in cp genomes may be due either to its transfer to the nuclear genome, as has occurred in sesame, or direct deletion, as has occurred in Panax ginseng and Cucumis sativus. The sesame ycf2 gene is only 5,721 bp in length and has lost about 1,179 bp. Nucleotides 1–585 of ycf2 when queried in BLAST had hits in the sesame draft genome. Five repeats (R10, R12, R13, R14 and R17) were unique to the sesame chloroplast genome. We also found that IR contraction/expansion in the cp genome alters its rate of evolution. Chloroplast genes and repeats display the signature of convergent evolution in sesame and other species. These findings provide a foundation for further investigation of cp genome evolution in Sesamum and other higher plants.     

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species

Background and Aims

Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne ‘Cashel’. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species.

Methods

Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species.

Key Results

All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A₈ mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively.

Conclusions

The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species.     

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.     

Draft Genome Sequences of Two Neisseria meningitidis Serogroup C Clinical Isolates

Neisseria meningitidis is a human-specific pathogen known for its capability to cause sepsis and meningitis. Here we report the availability of 2 draft genome sequences obtained from patients infected during the same epidemic outbreak. Both bacterial isolates belong to serogroup C, but their genome sequences show local and remarkable differences compared with each other or with the reference genome of strain FAM18.Neisseria meningitidis is found as a commensal organism of the human nasopharynx in 8 to 25% of the adult population (9), but sporadically, it is able to cross the mucosa and reach the bloodstream, causing severe septicemia and meningitis. Even though the reasons triggering these pathogenic outbreaks are not well understood, several factors related either to the host or the bacterium have been proposed 3, 8).So far, complete genome sequences for N. meningitidis serogroups A (strain Z2491 [GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AL157959","term_id":"30407145","term_text":"AL157959"}}AL157959]) (4), B (strain MC58 [GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AE002098","term_id":"66731897","term_text":"AE002098"}}AE002098]) (10), and C (strains FAM18, 8013, and 053442 [GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AM421808","term_id":"120865607","term_text":"AM421808"}}AM421808, {"type":"entrez-nucleotide","attrs":{"text":"FM999788","term_id":"261391559","term_text":"FM999788"}}FM999788, and {"type":"entrez-nucleotide","attrs":{"text":"CP000381","term_id":"161594571","term_text":"CP000381"}}CP000381, respectively]) (1, 5, 6) have been reported, together with the unencapsulated strain α14 (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AM889136","term_id":"254667570","term_text":"AM889136"}}AM889136) (7). Here we announce the availability of 2 draft genome sequences for N. meningitidis serogroup C, strains K1207 and S0108, isolated from the same epidemic cluster which occurred in the Veneto region in northern Italy during the 2007-2008 winter (2).The genomes were sequenced using 454 pyrosequencing (Roche), combining shotgun and 30-kb paired-end strategies, according to the manufacturer''s recommendations. The coverage was nearly 27×, and assemblies were performed with Newbler. We obtained 223 and 226 contigs for the 2 genomes, which were finally mapped in 17 and 16 scaffolds, respectively. From both samples, we also isolated a 7-kb plasmid, whose sequence was nearly identical to that of pJS-B, already available in GenBank (accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_004758","term_id":"30250494","term_text":"NC_004758"}}NC_004758).The first analysis was performed by comparing sequences of the two isolates with the most similar complete genome available, strain FAM18. This analysis showed that the genome lengths were almost identical (about 2.2 Mb) and GC contents were comparable (51.91% in both isolates versus 51.62% of strain FAM18). Then, to identify potential differences in coding sequence content, the contigs obtained for both isolates were aligned with those for strain FAM18 using MEGABLAST (11) and LASTZ tools, which showed that in the genomes of the two N. meningitidis isolates, several genes were missing or nonfunctional because of the presence of insertions or deletions. For example, a couple of FAM18 outer membrane proteins (NMC0214 and NMC0215) were completely missing in both genomes, due to a 3-kb deletion, and no homologues were present in other genomic regions.Sequences that did not map on the genome of strain FAM18 were investigated by performing a BLAST analysis on a nonredundant database. Interestingly, besides genes or partial genes belonging to the other completely sequenced N. meningitidis serogroup C strain 053442, the genomes of our isolates contained coding sequences from N. meningitidis serogroups A and B, from other Neisseria species, such as N. gonorrhoeae, N. cinerea, and N. mucosa, and even from other bacterial species, such as cobyrinic acid ac-diamide synthase from Shewanella baltica, attesting once more to the great capability of horizontal gene transfer, which is peculiar to this microorganism.A detailed report of our two isolates will be included in a future publication, with the results of a full comparative analysis between the genomes.     

Genome Sequence of the Oligotrophic Marine Gammaproteobacterium HTCC2143, Isolated from the Oregon Coast

Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction culturing. Here we present the genome of strain HTCC2143 from the BD1-7 clade of the oligotrophic marine Gammaproteobacteria group. The genome of HTCC2143 contains genes for carotenoid biosynthesis and proteorhodopsin and for proteins that have potential biotechnological significance: epoxide hydrolases, Baeyer-Villiger monooxygenases, and polyketide synthases.Strain HTCC2143 was sampled and isolated from surface waters (depth, 10 m) off the Coastal Pacific Ocean, Newport, OR (44°36′0"N, 124°6′0"W). In the course of dilution-to-extinction culture studies on coastal microbial communities, strain HTCC2143 was isolated in a pristine seawater-based medium (2). Phylogenetic analysis of 16S rRNA gene sequences placed strain HTCC2143 in the BD1-7 clade of the oligotrophic marine Gammaproteobacteria (OMG) group (2) and indicated that it is related to Dasania marina, isolated from Arctic marine sediment (3, 8). The HTCC2143 16S rRNA gene sequence is 95.3% similar to that of D. marina ({"type":"entrez-nucleotide","attrs":{"text":"AY771747","term_id":"157384056","term_text":"AY771747"}}AY771747) and is 96.6% similar to that of environmental gene clone 20m-45 ({"type":"entrez-nucleotide","attrs":{"text":"GU061297","term_id":"262072220","term_text":"GU061297"}}GU061297), taken from intertidal beach seawater of the Yellow Sea, South Korea. Other closer relatives of HTCC2143 included uncultured gammaproteobacterial clones from seafloor lava (clone P0X3b5B06 from Hawaii South Point X3, {"type":"entrez-nucleotide","attrs":{"text":"EU491383","term_id":"169640639","term_text":"EU491383"}}EU491383; 96.3%) (9), deep-sea sediment (Ucp1554 from the South Atlantic Ocean, Cape Basin, {"type":"entrez-nucleotide","attrs":{"text":"AM997645","term_id":"283475537","term_text":"AM997645"}}AM997645; 95.9%) (10), Yellow Sea sediment (95.8%; D8S-33, {"type":"entrez-nucleotide","attrs":{"text":"EU652559","term_id":"186462116","term_text":"EU652559"}}EU652559), and Arctic sediment (from Kings Bay, Svalbard, Norway; clone SS1_B_07_55, {"type":"entrez-nucleotide","attrs":{"text":"EU050825","term_id":"156453922","term_text":"EU050825"}}EU050825; 95.7%).Genomic DNA was prepared at Oregon State University and sequenced by the J. Craig Venter Institute. The finished contigs were automatically annotated with a system based on the program GenDB (5) and manually annotated as described in previous reports (7, 12). The annotation is available at http://bioinfo.cgrb.oregonstate.edu/microbes/. The draft genome of strain HTCC2143 comprises 3,925,629 bases and 3,662 predicted coding sequences with a G+C content of 47.0%. The genome of HTCC2143 was predicted to contain 40 tRNAs, 1 16S rRNA, 2 5S rRNAs, and 2 23S rRNA genes. Four genes for selenocysteine metabolism were found, including a selenophosphate-dependent tRNA 2-selenouridine synthase and an l-seryl-tRNA(Sec) selenium transferase (EC 2.9.1.1).Strain HTCC2143 had genes for a complete tricarboxylic acid cycle, glycolysis, a pentose phosphate pathway, and an Entner-Doudoroff pathway. Genes were present for a high-affinity phosphate transporter and a pho regulon for sensing of environmental inorganic phosphate availability, as well as genes from the NUDIX (nucleoside diphosphate linked to some other moiety X) hydrolase domain family (1) that reflects the metabolic complexity of prokaryotes (4). Genes for ammonium transporters, nitrate reductase, and sulfate reductase were also present in the HTCC2143 genome.Carotenoid and proteorhodopsin genes were also found in the genome, as well as genes for polyketide synthase modules and related proteins. Carotenoid and proteorhodopsin genes were reported previously from another member of the OMG group, strain HTCC2207, a SAR92 clade isolate (11). HTCC2143 also encoded two epoxide hydrolases, two cyclohexanone monooxygenases (CHMOs) and a cyclododecanone monooxygenase (CDMO). CDMOs and CHMOs are members of the Baeyer-Villiger monooxygenase (BVMO) family. BVMOs are “green” alternatives to the chemically mediated Baeyer-Villiger reactions that allow the conversion of ketones into esters or of cyclic ketones into lactones (6).This genome provides further evidence that dilution-to-extinction culturing methods that make use of low-nutrient media that are similar to the conditions of the natural environment can result in the isolation of novel, environmentally significant organisms with potential biotechnological value (13).     

Detection of Naegleria species in environmental samples from Peninsular Malaysia

Background

In Malaysia, researchers and medical practitioners are unfamiliar with Naegleria infections. Thus little is known about the existence of pathogenic Naegleria fowleri, and the resultant primary amoebic meningoencephalitis (PAM) is seldom included in the differential diagnosis of central nervous system infections. This study was conducted to detect the presence of Naegleria species in various environmental samples.

Methods/Findings

A total of 41 Naegleria-like isolates were isolated from water and dust samples. All these isolates were subjected to PCR using two primer sets designed from the ITS1-ITS2 regions. The N. fowleri species-specific primer set failed to produce the expected amplicon. The Naegleria genus-specific primers produced amplicons of 408 bp (35), 450 bp (2), 457 bp (2) or 381 bp (2) from all 41 isolates isolated from aquatic (33) and dust (8) samples. Analysis of the sequences from 10 representative isolates revealed that amplicons with fragments 408, 450 and 457 bp showed homology with non-pathogenic Naegleria species, and 381 bp showed homology with Vahlkampfia species. These results concurred with the morphological observation that all 39 isolates which exhibited flagella were Naegleria, while 2 isolates (AC7, {"type":"entrez-nucleotide","attrs":{"text":"JN034055","term_id":"347448982","term_text":"JN034055"}}JN034055 and AC8, {"type":"entrez-nucleotide","attrs":{"text":"JN034056","term_id":"347448983","term_text":"JN034056"}}JN034056) that did not exhibit flagella were Vahlkampfia species.

Conclusion

To date, pathogenic species of N. fowleri have not been isolated from Malaysia. All 39 isolates that produced amplicons (408, 450 and 457 bp) from the genus-specific primers were identified as being similar to nonpathogenic Naegleria. Amplicon 408 bp from 5 representative isolates showed 100% and 99.7% identity to Naegleria philippinensis isolate RJTM ({"type":"entrez-nucleotide","attrs":{"text":"AM167890","term_id":"83423362","term_text":"AM167890"}}AM167890) and is thus believed to be the most common species in our environment. Amplicons 450 bp and 457 bp were respectively believed to be from 2 new species of Naegleria, since representative isolates showed lower homology and had a longer base pair length when compared to the reference species in the Genbank, Naegleria schusteri ({"type":"entrez-nucleotide","attrs":{"text":"AJ566626","term_id":"37605481","term_text":"AJ566626"}}AJ566626) and Naegleria laresi ({"type":"entrez-nucleotide","attrs":{"text":"AJ566630","term_id":"37605485","term_text":"AJ566630"}}AJ566630), respectively.     

Complete Genome Sequence of Lactobacillus plantarum JDM1

Lactobacillus plantarum is a lactic acid bacterium (LAB) species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a Chinese commercial LAB with several probiotic functions, using a GS 20 system. We recommend that each commercial probiotic strain should undergo complete genome sequencing to ensure safety and stability.Lactic acid bacteria (LAB) play a prominent role in the world food supply, performing the main bioconversions in fermented food, and are also used as probiotic supplements in dairy products and other foods. Lactobacillus plantarum is a LAB species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a widely used Chinese commercial LAB with several probiotic functions, using a GS 20 system (454 Life Science Corporation) (11). Two hundred thirty-six thousand, five hundred sixty-three high-quality reads were assembled with the 454 assembly tool, which had an average depth of 18.6-fold coverage of the genome and yielded 367 contigs. Among these, 225 large contigs represented 99.17% of the draft sequence. In the finishing process, the order of the selected large contigs was determined by BLAST analysis with the originally published genome sequence of strain WCFS1 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"AL935263","term_id":"342240345","term_text":"AL935263"}}AL935263) (8). Physical gaps were filled through sequencing of PCR products that spanned these regions using ABI 3730 xl DNA sequencers. Sequence assembly was accomplished by using the Phred/Phrap/Consed software package (4, 7). To ensure final accuracy, the errors in homopolymer sites that arose from the pyrosequencing method were solved via comparison with the corresponding sites on WCFS1 and then resequencing of the ambiguous bases using the ABI 3730 xl DNA sequencer.The complete genome of Lactobacillus plantarum JDM1 contains a single, circular chromosome of 3,197,759 bp and two plasmids (pLP2000 [2,062 bp] and pLP9000 [9,254 bp]). The two plasmids have been sequenced and published, with GenBank accession numbers {"type":"entrez-nucleotide","attrs":{"text":"AY096004","term_id":"20853777","term_text":"AY096004"}}AY096004 and {"type":"entrez-nucleotide","attrs":{"text":"AY096005","term_id":"20853804","term_text":"AY096005"}}AY096005 (3). The overall GC content of the chromosome is 44.66%, whereas the plasmids have a GC content slightly lower than that of the chromosome. The entire genome of JDM1 contains 2,948 protein-coding genes, 62 tRNA-encoding genes, and 16 rRNA-encoding genes. Several repeated sequences, designated ISP2, were found in the chromosome which were almost the same as those in WCSF1, identified as a class of transposase-encoding regions representing mobile genetic elements. The other repeated sequence, ISP1 of WCSF1, was absent in JDM1.The entire genomic sequence of L. plantarum JDM1 was a little shorter than that of L. plantarum WCSF1 (3.3 Mb). The two genomes were highly similar (>90% by BLASTN analysis) with respect to genome structure and gene order. Intraspecies diversity may be required for successful adaptation in a complex ecological habitat (2). L. plantarum JDM1 has been grown as a probiotic in rich nutritional medium for so long that the genome may have gradually contracted. As supporting evidence, many sugar transport and metabolism genes in WCFS1 were absent in JDM1.The prophage sequences and locations of JDM1 and WCFS1 are highly variable. L. plantarum JDM1 contains three prophage elements in its genome. R-Pg1, representing a short prophage remnant, is about 14 kb in size, which is similar to R-Lp3 in WCFS1. Pg2 and Pg3 are two ∼39-kb-long prophages that are closely related to Listeria phage B025 (accession no. {"type":"entrez-nucleotide","attrs":{"text":"DQ003639","term_id":"66733223","term_text":"DQ003639"}}DQ003639) and the phage Pediococcus pentosaceus ATCC 25745 (accession no. {"type":"entrez-nucleotide","attrs":{"text":"CP000422","term_id":"116101968","term_text":"CP000422"}}CP000422), respectively.The genomes of LAB evolve actively to adapt to nutritionally rich environments. Even for two strains of the same species, differences obviously exist. The degradation of the genome appears to be an ongoing process not only in all species of Lactobacillus (10) but also in different strains of the same species(2).With the development of better living conditions, the biosafety of food and medicine has received more attention. Lactobacillus bacteria have been supposed to have a “generally accepted as safe” status, but they still have been associated with negative reports (1, 6, 9). More about the functional mechanisms of JDM1 and potential side effects would be explored by complete genome sequencing and data mining. Furthermore, comparative genomics analysis could be carried out with Chinese and European strains. We believe the complete genome of each probiotic strain should be sequenced to ensure safety and stability. At the end of the day, we will get what we pay for in terms of microbial genome sequencing projects (5).     

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]

     

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.     

Efficient and accurate whole genome assembly and methylome profiling of E. coli

Background

With the price of next generation sequencing steadily decreasing, bacterial genome assembly is now accessible to a wide range of researchers. It is therefore necessary to understand the best methods for generating a genome assembly, specifically, which combination of sequencing and bioinformatics strategies result in the most accurate assemblies. Here, we sequence three E. coli strains on the Illumina MiSeq, Life Technologies Ion Torrent PGM, and Pacific Biosciences RS. We then perform genome assemblies on all three datasets alone or in combination to determine the best methods for the assembly of bacterial genomes.

Results

Three E. coli strains – BL21(DE3), Bal225, and DH5α – were sequenced to a depth of 100× on the MiSeq and Ion Torrent machines and to at least 125× on the PacBio RS. Four assembly methods were examined and compared. The previously published BL21(DE3) genome [GenBank:{"type":"entrez-nucleotide","attrs":{"text":"AM946981.2","term_id":"313848522","term_text":"AM946981.2"}}AM946981.2], allowed us to evaluate the accuracy of each of the BL21(DE3) assemblies. BL21(DE3) PacBio-only assemblies resulted in a 90% reduction in contigs versus short read only assemblies, while N50 numbers increased by over 7-fold. Strikingly, the number of SNPs in PacBio-only assemblies were less than half that seen with short read assemblies (~20 SNPs vs. ~50 SNPs) and indels also saw dramatic reductions (~2 indel >5 bp in PacBio-only assemblies vs. ~12 for short-read only assemblies). Assemblies that used a mixture of PacBio and short read data generally fell in between these two extremes. Use of PacBio sequencing reads also allowed us to call covalent base modifications for the three strains. Each of the strains used here had a known covalent base modification genotype, which was confirmed by PacBio sequencing.

Conclusion

Using data generated solely from the Pacific Biosciences RS, we were able to generate the most complete and accurate de novo assemblies of E. coli strains. We found that the addition of other sequencing technology data offered no improvements over use of PacBio data alone. In addition, the sequencing data from the PacBio RS allowed for sensitive and specific calling of covalent base modifications.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-675) contains supplementary material, which is available to authorized users.     

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.     

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.     

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.     

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.     

Complete chloroplast genome of the medicinal plant Evolvulus alsinoides: comparative analysis,identification of mutational hotspots and evolutionary dynamics with species of Solanales

Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa ‘Evolvulus’ could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01051-w.     

An optimized chloroplast DNA extraction protocol for grasses (Poaceae) proves suitable for whole plastid genome sequencing and SNP detection

Background

Obtaining chloroplast genome sequences is important to increase the knowledge about the fundamental biology of plastids, to understand evolutionary and ecological processes in the evolution of plants, to develop biotechnological applications (e.g. plastid engineering) and to improve the efficiency of breeding schemes. Extraction of pure chloroplast DNA is required for efficient sequencing of chloroplast genomes. Unfortunately, most protocols for extracting chloroplast DNA were developed for eudicots and do not produce sufficiently pure yields for a shotgun sequencing approach of whole plastid genomes from the monocot grasses.

Methodology/Principal Findings

We have developed a simple and inexpensive method to obtain chloroplast DNA from grass species by modifying and extending protocols optimized for the use in eudicots. Many protocols for extracting chloroplast DNA require an ultracentrifugation step to efficiently separate chloroplast DNA from nuclear DNA. The developed method uses two more centrifugation steps than previously reported protocols and does not require an ultracentrifuge.

Conclusions/Significance

The described method delivered chloroplast DNA of very high quality from two grass species belonging to highly different taxonomic subfamilies within the grass family (Lolium perenne, Pooideae; Miscanthus×giganteus, Panicoideae). The DNA from Lolium perenne was used for whole chloroplast genome sequencing and detection of SNPs. The sequence is publicly available on EMBL/GenBank.