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Characterization of a Novel Hepadnavirus in the White Sucker (Catostomus commersonii) from the Great Lakes Region of the United States.

Hahn CM, Iwanowicz LR, Cornman RS, Conway CM, Winton JR, Blazer VS - J. Virol. (2015)

Bottom Line: Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses.These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker.This may also offer another model system for mechanistic research.

View Article: PubMed Central - PubMed

Affiliation: West Virginia University, School of Natural Resources, Morgantown, West Virginia, USA U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, USA.

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Genome coverage per base of the WSHBV in the pooled liver sample utilized for high-throughput sequencing of RNA transcripts (RNA-seq) analysis (131,080 reads). Locations of the open reading frames that encode the core, polymerase, and surface proteins are indicated at the top of the figure.
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Figure 4: Genome coverage per base of the WSHBV in the pooled liver sample utilized for high-throughput sequencing of RNA transcripts (RNA-seq) analysis (131,080 reads). Locations of the open reading frames that encode the core, polymerase, and surface proteins are indicated at the top of the figure.

Mentions: De novo assembly of ribosome-depleted RNA isolated from white sucker included a linear contig of 3,519 bp with blastx similarity to hepadnaviruses. Our finished genome, 2014 WSHBV RR173 (GenBank accession number KR229754), was 3,542 bp. Dideoxy sequencing confirmed a circular architecture of the genome (Fig. 3). Remapping Illumina reads to the complete genome included 131,080 reads. Genome coverage was high (average coverage, 3,184×; maximum coverage, 7,215×) with a mismatch frequency of 0.2% (Fig. 4). The genome size of WSHBV was larger than the sizes of other previously described hepadnaviruses genomes (3,542 versus 3,377 bp from HBHBV) and included an atypical, presumably noncoding, region comprised of 679 bp (nucleotides [nt] 2538 to 3214). We confirmed the presence of this region as authentic viral sequence using primer sets anchored in the polymerase and core ORFs or in one of these ORFs and the noncoding region (see Fig. S2 and Table S2 in the supplemental material). This presumably noncoding region terminated with a noncanonical polyadenylation signal (TATAAA; nt 3211 to 3216). Three additional polyadenylation signals were identified at nt 596 to 601, 1954 to 1959, and 3148 to 4158. Traditional polyadenylation signals were located at nt 2544 to 2549, 3201 to 3206, and 3425 to 3430. Local remapping of the short reads identified the noncanonical hexanucleotide polyadenylation signal (TATAAA; nt 3211 to 3216) that terminated the presumptively noncoding region as the single polyadenylation site. The GC content of the complete genome was 42% while the noncoding region had a considerably lower GC content of 34%.


Characterization of a Novel Hepadnavirus in the White Sucker (Catostomus commersonii) from the Great Lakes Region of the United States.

Hahn CM, Iwanowicz LR, Cornman RS, Conway CM, Winton JR, Blazer VS - J. Virol. (2015)

Genome coverage per base of the WSHBV in the pooled liver sample utilized for high-throughput sequencing of RNA transcripts (RNA-seq) analysis (131,080 reads). Locations of the open reading frames that encode the core, polymerase, and surface proteins are indicated at the top of the figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4645335&req=5

Figure 4: Genome coverage per base of the WSHBV in the pooled liver sample utilized for high-throughput sequencing of RNA transcripts (RNA-seq) analysis (131,080 reads). Locations of the open reading frames that encode the core, polymerase, and surface proteins are indicated at the top of the figure.
Mentions: De novo assembly of ribosome-depleted RNA isolated from white sucker included a linear contig of 3,519 bp with blastx similarity to hepadnaviruses. Our finished genome, 2014 WSHBV RR173 (GenBank accession number KR229754), was 3,542 bp. Dideoxy sequencing confirmed a circular architecture of the genome (Fig. 3). Remapping Illumina reads to the complete genome included 131,080 reads. Genome coverage was high (average coverage, 3,184×; maximum coverage, 7,215×) with a mismatch frequency of 0.2% (Fig. 4). The genome size of WSHBV was larger than the sizes of other previously described hepadnaviruses genomes (3,542 versus 3,377 bp from HBHBV) and included an atypical, presumably noncoding, region comprised of 679 bp (nucleotides [nt] 2538 to 3214). We confirmed the presence of this region as authentic viral sequence using primer sets anchored in the polymerase and core ORFs or in one of these ORFs and the noncoding region (see Fig. S2 and Table S2 in the supplemental material). This presumably noncoding region terminated with a noncanonical polyadenylation signal (TATAAA; nt 3211 to 3216). Three additional polyadenylation signals were identified at nt 596 to 601, 1954 to 1959, and 3148 to 4158. Traditional polyadenylation signals were located at nt 2544 to 2549, 3201 to 3206, and 3425 to 3430. Local remapping of the short reads identified the noncanonical hexanucleotide polyadenylation signal (TATAAA; nt 3211 to 3216) that terminated the presumptively noncoding region as the single polyadenylation site. The GC content of the complete genome was 42% while the noncoding region had a considerably lower GC content of 34%.

Bottom Line: Phylogenetic analyses confirmed WSHBV as distinct from previously documented hepadnaviruses.These results are not sufficient to draw inferences regarding the association of WSHBV and carcinogenesis in white sucker.This may also offer another model system for mechanistic research.

View Article: PubMed Central - PubMed

Affiliation: West Virginia University, School of Natural Resources, Morgantown, West Virginia, USA U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, USA.

Show MeSH
Related in: MedlinePlus