Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e Pbi

Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335-bp genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in public databases, including some that are the first of their kind to be detected in a virus. For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion transporter protein and an alkyl sulfatase in FR483, and a dTDP–glucose pyrophosphorylase in both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three viruses. Supplementary data to accompany this article is archived in this repository as 4 separate documents

Supplementary Data for “Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e Pbi”: Appendix B: Gene Names M001L through M807R

Appendix B: Gene Names M001L through M807R Document, in spreadsheet format, shows Gene Name, Genome Position, A.A. length, Peptid e Mw, pI, CDD Hit Number, COGs, COG Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, Hit from-to, BLASTp Hit Number, Hit Accession, BLASTp Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, and Hit from-to

Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e Pbi

Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335-bp genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in public databases, including some that are the first of their kind to be detected in a virus. For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion transporter protein and an alkyl sulfatase in FR483, and a dTDP–glucose pyrophosphorylase in both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three viruses. Supplementary data to accompany this article is archived in this repository as 4 separate documents

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts

BACKGROUND: More than 12,000 simple sequence repeats (SSRs) have been identified in the genome of Burkholderia mallei ATCC 23344. As a demonstrated mechanism of phase variation in other pathogenic bacteria, these may function as mutable loci leading to altered protein expression or structure variation. To determine if such alterations are occurring in vivo, the genomes of various single-colony passaged B. mallei ATCC 23344 isolates, one from each source, were sequenced from culture, a mouse, a horse, and two isolates from a single human patient, and the sequence compared to the published B. mallei ATCC 23344 genome sequence. RESULTS: Forty-nine insertions and deletions (indels) were detected at SSRs in the five passaged strains, a majority of which (67.3%) were located within noncoding areas, suggesting that such regions are more tolerant of sequence alterations. Expression profiling of the two human passaged isolates compared to the strain before passage revealed alterations in the mRNA levels of multiple genes when grown in culture. CONCLUSION: These data support the notion that genome variability upon passage is a feature of B. mallei ATCC23344, and that within a host B. mallei generates a diverse population of clones that accumulate genome sequence variation at SSR and other loci

Draft Genome of the Filarial Nematode Parasite \u3ci\u3eBrugia malayi\u3c/i\u3e

Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the ∼90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict ∼11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during ∼350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi to niches in its human and vector hosts and insights into the molecular basis of a mutualistic relationship with its Wolbachia endosymbiont. These findings offer a foundation for rational drug design

Supplementary Data for “Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e NC64A”: Appendix D: Gene Names C006R – C815L

Appendix D: Gene Names C006R – C815L Document shows Gene Name, Genome Position, A.A. length, Peptide Mw, pI, CDD Hit Number, COGs, COG Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, Hit from-to, BLASTp Hit Number, Hit Accession, BLASTp Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, and Hit from-to

Supplementary Data for “Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e Pbi”: Appendix D: Gene Names N003L through N847R

Appendix D: Gene Names N003L through N847R Document, in spreadsheet format, shows Gene Name, Genome Position, A.A. length, Peptid e Mw, pI, CDD Hit Number, COGs, COG Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, Hit from-to, BLASTp Hit Number, Hit Accession, BLASTp Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, and Hit from-to

Supplementary Data for “Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e NC64A”: Appendix B: Gene Names B001L – B886R

Appendix B: Gene Names B001L – B886R Document shows Gene Name, Genome Position, A.A. length, Peptide Mw, pI, CDD Hit Number, COGs, COG Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, Hit from-to, BLASTp Hit Number, Hit Accession, BLASTp Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, and Hit from-to

Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect \u3ci\u3eChlorella\u3c/i\u3e NC64A

Viruses NY-2A and AR158, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella NC64A. The 368,683-bp genome of NY-2A and the 344,690-bp genome of AR158 are the two largest chlorella virus genomes sequenced to date; NY-2A contains 404 putative protein-encoding and 7 tRNA-encoding genes and AR158 contains 360 putative protein-encoding and 6 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Two of the NY-2A genes encode inteins, the large subunit of ribonucleotide reductase and a superfamily II helicase. These are the first inteins to be detected in the chlorella viruses. Approximately 40% of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. These include GDP-d-mannose dehydratase, fucose synthase, aspartate transcarbamylase, Ca++ transporting ATPase and ubiquitin. Comparison of NY-2A and AR158 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that 85% of the genes are present in all three viruses. Supplementary data for this article is posted in this repository in 4 separate files

Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A

AbstractViruses NY-2A and AR158, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella NC64A. The 368,683-bp genome of NY-2A and the 344,690-bp genome of AR158 are the two largest chlorella virus genomes sequenced to date; NY-2A contains 404 putative protein-encoding and 7 tRNA-encoding genes and AR158 contains 360 putative protein-encoding and 6 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Two of the NY-2A genes encode inteins, the large subunit of ribonucleotide reductase and a superfamily II helicase. These are the first inteins to be detected in the chlorella viruses. Approximately 40% of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. These include GDP-d-mannose dehydratase, fucose synthase, aspartate transcarbamylase, Ca++ transporting ATPase and ubiquitin. Comparison of NY-2A and AR158 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that 85% of the genes are present in all three viruses