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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

Genome organization of Taro bacilliform CH virus (TaBCHV).The putative ORFs of TaBCHV are indicated by rectangles, domains identified within ORF 3 are shown (A), contigs obtained from samples T1 (C1– C5) and T2 (C'1–C'9) are presented by black lines (A1), and fragments F1–F8 amplified from the first cycle of PCR (A2) and F'1–F'7 amplified from the second cycle of PCR (A3) are represented by arrows. The genome organization of Taro bacilliform virus (TaBV) (B) is outlined to show its difference with that of TaBCHV.
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pone.0134147.g001: Genome organization of Taro bacilliform CH virus (TaBCHV).The putative ORFs of TaBCHV are indicated by rectangles, domains identified within ORF 3 are shown (A), contigs obtained from samples T1 (C1– C5) and T2 (C'1–C'9) are presented by black lines (A1), and fragments F1–F8 amplified from the first cycle of PCR (A2) and F'1–F'7 amplified from the second cycle of PCR (A3) are represented by arrows. The genome organization of Taro bacilliform virus (TaBV) (B) is outlined to show its difference with that of TaBCHV.

Mentions: A total of 15,748,273 and 11,425,217 raw reads were obtained from samples T1 and T2, respectively. After removing adapter sequences and selecting by size differences, 9,348,325 and 9,959,864 clean reads with sizes within the range of 18−26 nts were generated from the two samples. These sRNAs were assembled by using the Velvet software. The resulting contigs were searched using BLASTN and BLASTX [36] against NCBI GenBank. BLAST results showed that five (C1–C5) and nine (C'1–C'9) contigs from samples T1 and T2 matched to the genome sequences of badnaviruses of family Caulimoviridae, respectively (Fig 1A1), with the highest amino acid (aa) similarity of 70% to the corresponding regions of CYMV (NC_003382). In addition, seven contigs from T1 and fifteen contigs from T2 matched to the Dasheen mosaic virus (DsMV) in the family Potyviridae. Here, only a badnavirus was considered.


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)

Genome organization of Taro bacilliform CH virus (TaBCHV).The putative ORFs of TaBCHV are indicated by rectangles, domains identified within ORF 3 are shown (A), contigs obtained from samples T1 (C1– C5) and T2 (C'1–C'9) are presented by black lines (A1), and fragments F1–F8 amplified from the first cycle of PCR (A2) and F'1–F'7 amplified from the second cycle of PCR (A3) are represented by arrows. The genome organization of Taro bacilliform virus (TaBV) (B) is outlined to show its difference with that of TaBCHV.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4514669&req=5

pone.0134147.g001: Genome organization of Taro bacilliform CH virus (TaBCHV).The putative ORFs of TaBCHV are indicated by rectangles, domains identified within ORF 3 are shown (A), contigs obtained from samples T1 (C1– C5) and T2 (C'1–C'9) are presented by black lines (A1), and fragments F1–F8 amplified from the first cycle of PCR (A2) and F'1–F'7 amplified from the second cycle of PCR (A3) are represented by arrows. The genome organization of Taro bacilliform virus (TaBV) (B) is outlined to show its difference with that of TaBCHV.
Mentions: A total of 15,748,273 and 11,425,217 raw reads were obtained from samples T1 and T2, respectively. After removing adapter sequences and selecting by size differences, 9,348,325 and 9,959,864 clean reads with sizes within the range of 18−26 nts were generated from the two samples. These sRNAs were assembled by using the Velvet software. The resulting contigs were searched using BLASTN and BLASTX [36] against NCBI GenBank. BLAST results showed that five (C1–C5) and nine (C'1–C'9) contigs from samples T1 and T2 matched to the genome sequences of badnaviruses of family Caulimoviridae, respectively (Fig 1A1), with the highest amino acid (aa) similarity of 70% to the corresponding regions of CYMV (NC_003382). In addition, seven contigs from T1 and fifteen contigs from T2 matched to the Dasheen mosaic virus (DsMV) in the family Potyviridae. Here, only a badnavirus was considered.

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