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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

The silencing hot spots of TaBCHV-1(A) and TaBCHV-2(B) genomes and the predicated secondary structure around the vsRNA at 6432 nt (C).The start and stop positions of the vsRNA6432 are marked by bold arrows.
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pone.0134147.g006: The silencing hot spots of TaBCHV-1(A) and TaBCHV-2(B) genomes and the predicated secondary structure around the vsRNA at 6432 nt (C).The start and stop positions of the vsRNA6432 are marked by bold arrows.

Mentions: There was no significant difference of the amount of the 21- and 22-nt vsRNAs mapped to the sense and antisense strands of the viral genome, and the vsRNAs from both senses were discontinuous and unevenly distributed along the viral genome (Fig 5). Meanwhile, one hotspot region located within ORF3 was identified. In the region, two vsRNAs started at 6432 nt and 6753 nt of TaBCHV-1 and TaBCHV-2 genome were highly repeated (Fig 6A and 6B). The secondary structure analysis of a 50-nt sequence around the hotspot by using the RNAfold program (http://rna.tbi.uninie.ac.at/cgi-bin/RNAfold.cgi) revealed that the sequence around the vsRNA6432 could form a highly structured stem-loop (Fig 6C), indicating that the secondary structure might contribute to the production of the vsRNA [40].


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)

The silencing hot spots of TaBCHV-1(A) and TaBCHV-2(B) genomes and the predicated secondary structure around the vsRNA at 6432 nt (C).The start and stop positions of the vsRNA6432 are marked by bold arrows.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134147.g006: The silencing hot spots of TaBCHV-1(A) and TaBCHV-2(B) genomes and the predicated secondary structure around the vsRNA at 6432 nt (C).The start and stop positions of the vsRNA6432 are marked by bold arrows.
Mentions: There was no significant difference of the amount of the 21- and 22-nt vsRNAs mapped to the sense and antisense strands of the viral genome, and the vsRNAs from both senses were discontinuous and unevenly distributed along the viral genome (Fig 5). Meanwhile, one hotspot region located within ORF3 was identified. In the region, two vsRNAs started at 6432 nt and 6753 nt of TaBCHV-1 and TaBCHV-2 genome were highly repeated (Fig 6A and 6B). The secondary structure analysis of a 50-nt sequence around the hotspot by using the RNAfold program (http://rna.tbi.uninie.ac.at/cgi-bin/RNAfold.cgi) revealed that the sequence around the vsRNA6432 could form a highly structured stem-loop (Fig 6C), indicating that the secondary structure might contribute to the production of the vsRNA [40].

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