Complete Genome Sequence of Croceibacter Bacteriophage P2559S

Croceibacter atlanticus HTCC2559(T), a marine bacterium isolated from the Sargasso Sea, is a phylogenetically unique member of the family Flavobacteriaceae. Strain HTCC2559(T) possesses genes related to interaction with primary producers, which makes studies on bacteriophages infecting the strain interesting. Here we report the genome sequence of bacteriophage P2559S, which was isolated off the coast of the Republic of Korea and lytically infects HTCC2559(T). Many genes predicted in the P2559S genome had their homologs in Bacteroides phages.     

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 Plastid Genome Sequence of the Brown Alga Undaria pinnatifida

In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.     

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium''s thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain was isolated, show that close relatives of T. roseum DSM 5159 are present but have some key differences from the strain sequenced.     

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.     

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.     

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     

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601^T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601^T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601^T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601^T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601^T. Genes involved in cyclohexanol degradation were only found in strain K601^T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.     

Complete Genome Sequence and Genome Analysis of Eggplant mottled dwarf virus‐Iranian Isolate

The full‐length nucleotide sequence of the Iranian isolate of Eggplant mottled dwarf virus (EMDV), a phytorhabdovirus, was determined using the random polymerase chain reaction method (rPCR) followed by PCR with specific primers to fill in the gaps. The negative‐sense RNA genome of the Iranian isolate of EMDV contains 13154 nucleotides and seven open‐reading frames (ORFs) in the order 3′‐leader‐N‐X‐P‐Y‐M‐G‐L‐trailer‐5′. These ORFs encode the nucleocapsid, X protein (of unknown function), phosphoprotein, Y protein (putative movement protein), matrix protein, glycoprotein and RNA‐dependent RNA polymerase, respectively. EMDV has a 199 nt 3′ leader RNA and a 151 nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. Phylogenetic analyses indicate that EMDV is most closely related to Potato yellow dwarf virus, which has a distinctly different geographical distribution.     

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 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.     

Complete Genome Sequence of a Novel Human Parechovirus

Human parechoviruses (HPeVs) belonging to the family Picornaviridae are widely spread pathogens among young children. We report the complete genome sequence of a novel HPeV isolated from the stool sample of a hospitalized child with diarrhea in China. The genome consists of 7,305 nucleotides, excluding the 3′ poly(A) tail, and has an open reading frame that maps between nucleotide positions 675 and 7217 and encodes a 2,180-amino-acid polyprotein. The genome sequence of the virus was sufficiently distinct from the 8 known HPeV types. Phylogenetic analysis based on the complete genome indicated that the HPeV strain represents a new genotype.     

Complete Genome Sequence of Rhodobacter sphaeroides KD131

Rhodobacter sphaeroides is a purple nonsulfur photosynthetic bacterium that is considered a possible source of H₂ production. R. sphaeroides KD131, which was isolated from sea mud in South Korea, was found to produce high levels of H₂. Here we report the complete and annotated genome sequence of R. sphaeroides KD131.Rhodobacter sphaeroides KD131 (KCTC12085) is a halophilic, purple nonsulfur photosynthetic bacterium that produces high levels of biohydrogen (H₂). The strain, KD131, was originally isolated from sea mud off the coast of DaeBu Island, South Korea (8). Recently, the strain was genetically developed for H₂ production under any conditions, regardless of the presence of light (6).We have determined the complete genome sequence of strain KD131, which consists of two chromosomes and two plasmids, using the traditional shotgun whole-genome sequencing method. To accomplish this, two genome libraries (∼2 kb and ∼35 kb) were generated using randomly sheared genomic DNA of strain KD131. The sequences with as much as five times more genomic information were obtained from the 38,063 chromatograms produced by the libraries using ABI 3730xl autosequencers. The DNA-sequencing chromatograms were then analyzed automatically by base calling, fragment assembly, and contig editing using the Phred/Phrap/Consed software package (http://www.phrap.org) (4). For gap closing and to improve the quality of regions with a low Phred quality score or depth, noncloned PCR products amplified using the primers designed by Consed and genomic DNA as a template were sequenced. In addition, we performed manual curation based on the preannotated information in the draft genome sequence to ensure the quality of the genome database. The final assembly of the total genome was then performed manually based on the location and mate information to avoid improper assembly due to the presence of repeat sequences using Consed. The final predicted error rates were 0.07, 0.05, 0.15, and 0.04/10 kb in chromosome 1, chromosome 2, plasmid A, and plasmid B, respectively.The complete sequences were analyzed using Glimmer3 (3) for the protein-coding gene, tRNAscan-SE (9) for the tRNA, and RNAmmer (7) for the rRNA. The functions of predicted protein-coding genes were then annotated through comparisons with the databases of UniRef90 (11), NCBI-NR (1), COG (12), and KEGG (5). The genome of R. sphaeroides KD131 consists of chromosome 1, which contains 3,152,792 bp (3,101 open reading frames [ORFs], 39 tRNAs, and one 16S-23S-5S rRNA), chromosome 2, which contains 1,297,647 bp (1,224 ORFs, 15 tRNAs, and three 16S-23S-5S rRNAs), plasmid A, which contains 157,345 bp (142 ORFs), and plasmid B (102 ORFs), which contains 103,355 bp. In addition, the genome has a G+C content of ∼68.7% to ∼70.1%.The aspect of distribution and content of the genes in strain KD131 were highly similar to those of a closely related cognate strain, 2.4.1, which has been analyzed by the Department of Energy Joint Genome Institute (2). However, the genome of R. sphaeroides KD131 may have a more-developed H₂-evolving system that consists mainly of an uptake hydrogenase and two nitrogenases. An uptake hydrogenase gene cluster and a molybdenum nitrogenase gene cluster are found in strain 2.4.1, but another iron nitrogenase gene cluster that is not found in strain 2.4.1 is highly similar to the homologue of Rhodopseudomonas palustris CGA009 (10). The information regarding the complete genome of strain KD131 that we report here will facilitate proteomic and metabolic studies designed to develop this strain for H₂ production.     

Complete Genome Sequence of Bifidobacterium longum JDM301

Bifidobacteria, known as probiotic bacteria, are high-G+C Gram-positive bacteria which naturally inhabit the human gastrointestinal tract and vagina. Recently, we completely sequenced Bifidobacterium longum JDM301, which is a widely used Chinese commercial strain with several probiotic properties.Bifidobacterium spp., which are considered model probiotic bacteria like Lactobacillus spp., play an important role in the stability of the intestinal microflora, the modulation of the immune response, and so on (6, 8). We determined the complete genome sequence of B. longum JDM301, which is commercially used in China as a probiotic strain, using the GS 20 system (454 Life Science Corporation) (7). A total of 192,888 reads with an average length of 210 bp were assembled into 112 contigs by the 454 assembly tool. Among these, 92 large contigs were larger than 500 bp. We determined the order of the largest contigs through BLAST analysis with the reference strain B. longum ATCC 15697 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"CP001095","term_id":"213522389","term_text":"CP001095"}}CP001095) (10) and arranged the others by multiplex PCR. Gaps were closed by sequencing gap-spanning PCR products or clones using ABI 3730 xl DNA sequencers. Primer design and sequence assembly were performed with the Phred/Phrap/Consed software package (2, 3).The complete genome of B. longum JDM301 is composed of a 59.8% G+C circular chromosome of 2,477,838 bp without any plasmid. The genome of JDM301 (2.48 Mb) is smaller than that of B. longum ATCC 15697 (2.83 Mb) and slightly larger than the complete genomes of B. longum NCC2705 (2.26 Mb; GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"AE014295","term_id":"58012118","term_text":"AE014295"}}AE014295) and DJO10A (2.38 Mb; GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"CP000605","term_id":"189427298","term_text":"CP000605"}}CP000605). The JDM301 genome contains 1,959 protein-coding genes, three rRNA operons, and 55 tRNA genes. There are four rRNA operons with two cascaded in the three reference B. longum strains, while there are three in JDM301. We resequenced the three regions containing rRNA operons in the genome of JDM301 and found no cascaded rRNA operon. However, the locations of the three rRNA operons in JDM301 are the same as in the other three B. longum strains. No complete prophages were found in the genome sequence, but 12 phage-related fragments were identified. The genome also contains 15 pseudogenes, which is evidence of the recent and ongoing genome reduction of lactic acid bacilli (9). In addition, 15 complete or disrupted insertion sequence (IS) elements were found in the entire genome, which were identified as 5 derivatives of ISBlo5, 3 complete copies of ISBlo3, and 7 other ISs or derivatives belonging to the IS256, IS3, IS21, and IS30 family elements, respectively. One of them, named ISBad1, was 98.08% identical to that of B. adolescentis, and the others have been reported in the B. longum NCC2705 genome (8).Genome analysis revealed 14 response regulators and 14 sensor histidine kinases throughout the JDM301 chromosome, which may suggest a less complex regulatory network in JDM301 than that in ATCC 15697 (10). JDM301 has been grown as a commercial strain in stable and rich nutritional medium for such a long time that the regulatory networks in the genome may degenerate slowly, which is required for responses to dynamic environmental cues in the gastrointestinal tract.A gene (for BLJ_1359) encoding a serpin (serine protease inhibitor) with 92.69% identity to that of NCC2705 (4) was found in the genome sequence. The serpin is a potential probiotic effector molecule, and it may contribute to the immunomodulation of this B. longum strain. As we know, modulation of the immune system is one of probiotic functions of lactic acid bacteria (5).As model probiotic bacteria, Bifidobacterium spp. attract more and more interest since the molecular mechanisms of their probiotic activities remain unclear to a large degree (11). On the other hand, the biosafety of probiotics has attracted more attention with their enlarged and wide applications in food and drug products (1). We believe that this work will bring us deeper insight into the probiotic activities and safety of the strain widely used in China.