Complete Genome Sequence of a Novel Pestivirus from Sheep

We report here the complete genome sequence of pestivirus strain Aydin/04-TR, which is the prototype of a group of similar viruses currently present in sheep and goats in Turkey. Sequence data from this virus showed that it clusters separately from the established and previously proposed tentative pestivirus species.     

Complete Genome Sequence of an Amur Virus Isolated from Apodemus peninsulae in Northeastern China

Amur virus was recently identified as the causative agent of hemorrhagic fever with renal syndrome. Here we report the complete genome sequence of an Amur virus isolated from Apodemus peninsulae in Northeastern China. The sequence information provided here is critical for the molecular epidemiology and evolution of Amur virus in China.     

Complete Genome Sequence of an Enterovirus 80 Strain Isolated in China

Enterovirus 80 (EV80) is a newly identified serotype of the species Human enterovirus B. An EV80 strain designated HZ01/SD/CHN/2004 was isolated from an acute flaccid paralysis case in Shandong, China, in 2004. Complete genome comparison revealed 79.5% similarity with the prototype strain and an insertion of 36 nucleotides in the 3′ end of the VP1 coding region. Intertypic recombination with other serotypes was observed. This is the first report of the complete genome of EV80 in China.     

Complete Genome Sequence of Mycobacterium massiliense

Mycobacterium massiliense is a rapidly growing bacterium associated with opportunistic infections. The genome of a representative isolate (strain GO 06) recovered from wound samples from patients who underwent arthroscopic or laparoscopic surgery was sequenced. To the best of our knowledge, this is the first announcement of the complete genome sequence of an M. massiliense strain.     

Complete Genome Sequence of Corynebacterium pseudotuberculosis Cp31, Isolated from an Egyptian Buffalo

Corynebacterium pseudotuberculosis is of major veterinary importance because it affects many animal species, causing economically significant livestock diseases and losses. Therefore, the genomic sequencing of various lines of this organism, isolated from different hosts, will aid in the development of diagnostic methods and new prevention and treatment strategies and improve our knowledge of the biology of this microorganism. In this study, we present the genome of C. pseudotuberculosis Cp31, isolated from a buffalo in Egypt.     

Complete Genome Sequence of a Porcine Orthoreovirus from Southern China

Porcine orthoreoviruses belong to the family Reoviridae and cause mainly mild enteritis in piglets. We present here the complete genome sequence of a novel porcine orthoreovirus strain (GD-1) isolated from a piglet in southern China. Our data will facilitate future investigations of the molecular characteristics and epidemiology of porcine orthoreoviruses.     

The High-Quality Complete Genome Sequence of the Opportunistic Fungal Pathogen Candida vulturna CBS 14366T

Mycopathologia - Candida vulturna is a new member of the Candida haemulonii species complex that recently received much attention as it includes the emerging multidrug-resistant pathogen Candida...     

Complete Genome Sequence of Finegoldia magna, an Anaerobic Opportunistic Pathogen

Finegoldia magna (formerly Peptostreptococcus magnus), a memberof the Gram-positive anaerobic cocci (GPAC), is a commensalbacterium colonizing human skin and mucous membranes. Moreover,it is also recognized as an opportunistic pathogen responsiblefor various infectious diseases. Here, we report the completegenome sequence of F. magna ATCC 29328. The genome consistsof a 1 797 577 bp circular chromosome and an 189 163bp plasmid (pPEP1). The metabolic maps constructed based onthe genome information confirmed that most F. magna strainscannot ferment most sugars, except fructose, and have variousaminopeptidase activities. Three homologs of albumin-bindingprotein, a known virulence factor useful for antiphagocytosis,are encoded on the chromosome, and one albumin-binding proteinhomolog is encoded on the plasmid. A unique feature of the genomeis that F. magna encodes many sortase genes, of which substratesmay be involved in bacterial pathogenesis, such as antiphagocytosisand adherence to the host cell. The plasmid pPEP1 encodes sevensortase and seven substrate genes, whereas the chromosome encodesfour sortase and 19 substrate genes. These plasmid-encoded sortasesmay play important roles in the pathogenesis of F. magna byenriching the variety of cell wall anchored surface proteins.     

科学家完成金小蜂基因组测序

<正>近日,美国罗切斯特大学生物学教授John H.Werren和贝勒医学院基因组测序中心的Stephen Richards领导完成了3种寄生性金小蜂(Nasonia vitripennis,N.giraulti和N.longicornis)的基因组测序。这一成果揭示     

The Mitochondrial Genome of Chlorogonium elongatum Inferred from the Complete Sequence

The 22,704-bp circular mitochondrial DNA (mtDNA) of the chlamydomonad alga Chlorogonium elongatum was completely cloned and sequenced. The genome encodes seven proteins of the respiratory electron transport chain, subunit 1 of the cytochrome oxidase complex (cox1), apocytochrome b (cob), five subunits of the NADH dehydrogenase complex (nad1, nad2, nad4, nad5, and nad6), a set of three tRNAs (Q, W, M), and the large (LSU)- and small (SSU)-subunit ribosomal RNAs. Six group-I introns were found, two each in the cox1, cob, and nad5 genes. In each intron an open reading frame (ORF) related to maturases or endonucleases was identified. Both the LSU and the SSU rRNA genes are split into fragments intermingled with each other and with other genes. Although the average A + T content is 62.2%, GC-rich clusters were detected in intergenic regions, in variable domains of the rRNA genes, and in introns and intron-encoded ORFs. A comparison of the genome maps reveals that C. elongatum and Chlamydomonas eugametos mtDNAs are more closely related to one another than either is to Chlamydomonas reinhardtii mtDNA. Received: 3 November 1997 / Accepted: 12 January 1998     

Complete Genome of a Novel Endornavirus Assembled from Next-Generation Sequence Data

Endornaviruses have large double-stranded RNA (dsRNA) genomes that carry a single open reading frame (ORF). Here we report the complete genome of a novel endornavirus, assembled from next-generation sequence data generated from Vitis vinifera-extracted dsRNA. Two different fungal hosts have been identified for this virus, suggesting that horizontal transmission of the virus is possible.     

Complete Genome Sequence of an Uncultured Bacterium of the Candidate Phylum Bipolaricaulota

Microbiology - Bacteria of the candidate phylum Bipolaricaulota, previously known as OP1 and Acetothermia, have been identified in various terrestrial and marine ecosystems as a result of molecular...     

Complete Genome Sequence of a Mink Calicivirus in China

We report the complete genome sequence of a novel calicivirus isolated from a diseased mink in China. The complete viral genome is approximately 8.4 kb in length and consists of three open reading frames. The availability of the complete genome sequence is helpful for further investigation into the molecular characteristics and epidemiology of calicivirus in mink.     

Complete Genome Sequence of Mycoplasma wenyonii Strain Massachusetts

Mycoplasma wenyonii is a hemotrophic mycoplasma that causes acute and chronic infections in cattle. Here, we announce the first complete genome sequence of this organism. The genome is a single circular chromosome with 650,228 bp and G+C% of 33.9. Analyses of M. wenyonii genome will provide insights into its biology.     

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).     

Complete Genome Sequence of Clostridium clariflavum DSM 19732

Clostridium clariflavum is a Cluster III Clostridium within the family Clostridiaceae isolated from thermophilic anaerobic sludge (Shiratori et al, 2009). This species is of interest because of its similarity to the model cellulolytic organism Clostridium thermocellum and for the ability of environmental isolates to break down cellulose and hemicellulose. Here we describe features of the 4,897,678 bp long genome and its annotation, consisting of 4,131 protein-coding and 98 RNA genes, for the type strain DSM 19732.     

Complete Genome Sequence of Haemophilus parasuis SH0165

Haemophilus parasuis is the causative agent of Glässer's disease, which produces big losses in swine populations worldwide. H. parasuis SH0165, belonging to the dominant serovar 5 in China, is a clinically isolated strain with high-level virulence. Here, we report the first completed genome sequence of this species.     

Complete Genome Sequence of Canine Papillomavirus Type 10

Papillomaviruses are epitheliotropic, nonenveloped, circular, double-stranded DNA viruses within the family Papillomaviridae that are associated with benign and malignant tumors in humans and animals. We report the complete genome sequence of canine papillomavirus type 10 identified from a pigmented plaque located on the head of a mixed-breed bloodhound.     

Complete Genome Sequence of Equine Herpesvirus Type 9

Equine herpesvirus type 9 (EHV-9), which we isolated from a case of epizootic encephalitis in a herd of Thomson''s gazelles (Gazella thomsoni) in 1993, has been known to cause fatal encephalitis in Thomson''s gazelle, giraffe, and polar bear in natural infections. Our previous report indicated that EHV-9 was similar to the equine pathogen equine herpesvirus type 1 (EHV-1), which mainly causes abortion, respiratory infection, and equine herpesvirus myeloencephalopathy. We determined the genome sequence of EHV-9. The genome has a length of 148,371 bp and all 80 of the open reading frames (ORFs) found in the genome of EHV-1. The nucleotide sequences of the ORFs in EHV-9 were 86 to 95% identical to those in EHV-1. The whole genome sequence should help to reveal the neuropathogenicity of EHV-9.