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Characterization by Small RNA Sequencing of Taro Bacilliform CH Virus (TaBCHV), a Novel Badnavirus.

Kazmi SA, Yang Z, Hong N, Wang G, Wang Y - PLoS ONE (2015)

Bottom Line: Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses.In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal.Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.

ABSTRACT
RNA silencing is an antiviral immunity that regulates gene expression through the production of small RNAs (sRNAs). In this study, deep sequencing of small RNAs was used to identify viruses infecting two taro plants. Blast searching identified five and nine contigs assembled from small RNAs of samples T1 and T2 matched onto the genome sequences of badnaviruses in the family Caulimoviridae. Complete genome sequences of two isolates of the badnavirus determined by sequence specific amplification comprised of 7,641 nucleotides and shared overall nucleotide similarities of 44.1%‒55.8% with other badnaviruses. Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses. Phylogenetic analysis also supports that the virus is a new member in the genus Badnavirus. The virus is tentatively named as Taro bacilliform CH virus (TaBCHV), and it is the second badnavirus infecting taro plants, following Taro bacilliform virus (TaBV). In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal. Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region.

No MeSH data available.


Related in: MedlinePlus

Neighbor-joining phylogenetic trees of badnaviruses generated from the full genomic sequences (A) and putative amino acid sequences of ORF3 (B).The phylogenetic trees were rooted by using the genome sequence of Rice tungro bacilliform virus (RTBV) (A) and the polypeptide of RTBV (B). Branch lengths are proportional to genetic distances. Numbers at the nodes of the branches represent bootstrap values (1000 replicates).
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pone.0134147.g003: Neighbor-joining phylogenetic trees of badnaviruses generated from the full genomic sequences (A) and putative amino acid sequences of ORF3 (B).The phylogenetic trees were rooted by using the genome sequence of Rice tungro bacilliform virus (RTBV) (A) and the polypeptide of RTBV (B). Branch lengths are proportional to genetic distances. Numbers at the nodes of the branches represent bootstrap values (1000 replicates).

Mentions: Phylogenetic relationships between the two TaBCHV isolates and other badnaviruses were estimated basing on their full genome sequences (Fig 3A) and aa sequences of ORF3 (Fig 3B). The two phylogenetic trees had similar topology structures, and all tested viruses were clustered into three major groups, namely groups 1‒3. In both phylogenetic trees, TaBCHV isolates consistently had the same phylogenetic positions with CSSV, CYMV, DsBV, FBV, HBV, and PYMoV in the group 1, but was distant from TaBV.


Characterization by Small RNA Sequencing of Taro Bacilliform CH Virus (TaBCHV), a Novel Badnavirus.

Kazmi SA, Yang Z, Hong N, Wang G, Wang Y - PLoS ONE (2015)

Neighbor-joining phylogenetic trees of badnaviruses generated from the full genomic sequences (A) and putative amino acid sequences of ORF3 (B).The phylogenetic trees were rooted by using the genome sequence of Rice tungro bacilliform virus (RTBV) (A) and the polypeptide of RTBV (B). Branch lengths are proportional to genetic distances. Numbers at the nodes of the branches represent bootstrap values (1000 replicates).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4514669&req=5

pone.0134147.g003: Neighbor-joining phylogenetic trees of badnaviruses generated from the full genomic sequences (A) and putative amino acid sequences of ORF3 (B).The phylogenetic trees were rooted by using the genome sequence of Rice tungro bacilliform virus (RTBV) (A) and the polypeptide of RTBV (B). Branch lengths are proportional to genetic distances. Numbers at the nodes of the branches represent bootstrap values (1000 replicates).
Mentions: Phylogenetic relationships between the two TaBCHV isolates and other badnaviruses were estimated basing on their full genome sequences (Fig 3A) and aa sequences of ORF3 (Fig 3B). The two phylogenetic trees had similar topology structures, and all tested viruses were clustered into three major groups, namely groups 1‒3. In both phylogenetic trees, TaBCHV isolates consistently had the same phylogenetic positions with CSSV, CYMV, DsBV, FBV, HBV, and PYMoV in the group 1, but was distant from TaBV.

Bottom Line: Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses.In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal.Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.

ABSTRACT
RNA silencing is an antiviral immunity that regulates gene expression through the production of small RNAs (sRNAs). In this study, deep sequencing of small RNAs was used to identify viruses infecting two taro plants. Blast searching identified five and nine contigs assembled from small RNAs of samples T1 and T2 matched onto the genome sequences of badnaviruses in the family Caulimoviridae. Complete genome sequences of two isolates of the badnavirus determined by sequence specific amplification comprised of 7,641 nucleotides and shared overall nucleotide similarities of 44.1%‒55.8% with other badnaviruses. Six open reading frames (ORFs) were identified on the plus strand, showed amino acid similarities ranging from 59.8% (ORF3) to 10.2% (ORF6) to the corresponding proteins encoded by other badnaviruses. Phylogenetic analysis also supports that the virus is a new member in the genus Badnavirus. The virus is tentatively named as Taro bacilliform CH virus (TaBCHV), and it is the second badnavirus infecting taro plants, following Taro bacilliform virus (TaBV). In addition, analyzes of viral derived small RNAs (vsRNAs) from TaBCHV showed that almost equivalent number of vsRNAs were generated from both strands and the most abundant vsRNAs were 21 nt, with uracil bias at 5' terminal. Furthermore, TaBCHV vsRNAs were asymmetrically distributed on its entire circular genome at both orientations with the hotspots mainly generated in the ORF5 region.

No MeSH data available.


Related in: MedlinePlus