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Identification and characterization of a maize-associated mastrevirus in China by deep sequencing small RNA populations.

Chen S, Huang Q, Wu L, Qian Y - Virol. J. (2015)

Bottom Line: There was a slightly higher representation of MSRV-YN siRNAs derived from the virion-sense strand genome than the complementary-sense strand genome.Moreover, MSRV-YN vsiRNAs were not uniformly distributed along the genome, and hotspots were detected in the movement protein and coat protein-coding region.This vsiRNAs profile derived from MSRV-YN was characterized, which might contribute to get an insight into the host RNA silencing defense induced by MSRV-YN, and provide guidelines on designing antiviral strategies using RNAi against MSRV-YN.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China. 415748559@qq.com.

ABSTRACT

Background: Maize streak Reunion virus (MSRV) is a member of the Mastrevirus genus in the family Geminiviridae. Of the diverse and increasing number of mastrevirus species found so far, only Wheat dwarf virus and Sweetpotato symptomless virus 1 have been discovered in China. Recently, a novel, unbiased approach based on deep sequencing of small interfering RNAs followed by de novo assembly of siRNA, has greatly offered opportunities for plant virus identification.

Methods: Samples collected from maize leaves was deep sequencing for virus identification. Subsequently, the assay of PCR, rolling circle amplification and Southern blot were used to confirm the presence of a mastrevirus.

Results: Maize streak Reunion virus Yunnan isolate (MSRV-[China:Yunnan 06:2014], abbreviated to MSRV-YN) was identified from maize collected from Yunnan Province, China, by small RNA deep sequencing. The complete genome of this virus was ascertained as 2,880 nucleotides long by conventional sequencing. A phylogenetic analysis showed it shared 96.3 % nucleotide sequence identity with the isolate of Maize streak Reunion virus from La Reunion Island. To our knowledge, this is the first identification of MSRV in China. Analyses of the viral derived small interfering RNAs (vsiRNAs) profile showed that the most abundant MSRV-YN vsiRNAs were 21, 22 and 24 nt long and biased for A and G at their 5' terminal residue. There was a slightly higher representation of MSRV-YN siRNAs derived from the virion-sense strand genome than the complementary-sense strand genome. Moreover, MSRV-YN vsiRNAs were not uniformly distributed along the genome, and hotspots were detected in the movement protein and coat protein-coding region.

Conclusions: A mastrevirus MSRV-YN collected in Yunnan Province, China, was identified by small RNA deep sequencing. This vsiRNAs profile derived from MSRV-YN was characterized, which might contribute to get an insight into the host RNA silencing defense induced by MSRV-YN, and provide guidelines on designing antiviral strategies using RNAi against MSRV-YN.

No MeSH data available.


Related in: MedlinePlus

Structural analysis of MSRV-YN vsiRNA hotspots. a The secondary structures were predicted using the thermodynamic prediction of minimal free energy (MFE). A mountain plot representation of the MFE structure is shown. b Profile of the MSRV-YN-derived siRNAs. An asterisk indicates that vsiRNA production was consistent with the predicted highly structured regions. Positions and orientations of the four predicted ORFs are shown by colored arrows
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Fig5: Structural analysis of MSRV-YN vsiRNA hotspots. a The secondary structures were predicted using the thermodynamic prediction of minimal free energy (MFE). A mountain plot representation of the MFE structure is shown. b Profile of the MSRV-YN-derived siRNAs. An asterisk indicates that vsiRNA production was consistent with the predicted highly structured regions. Positions and orientations of the four predicted ORFs are shown by colored arrows

Mentions: A genome-wide view of vsiRNAs revealed that the vsiRNAs of MSRV-YN were not uniformly distributed along each genome segment, with the most abundant siRNAs matched both positive and negative strands of the MP and CP-coding region (Fig. 5), indicating the accessibility of target sites with MP and CP. The peaks of hotspots were particularly observed in the position of 75 to 385 nt and 882 to 954 nt along MSRV-YN genome. Hotspots for vsiRNAs generation have been extensively described and discussed for many viruses, yet the reasons for this phenomenon are not entirely clear [22–25]. Previous reports indicated that imperfect duplexes in the most-folded regions might be targeted for specific DCLs cleavage and thus affect vsiRNAs production [24]. On the other hand, evidence showed that a hairpin structure of Cucumber mosaic virus satellite RNA could be targeted more efficiently by DCL4 [26]. Since MSRV-YN is a DNA virus, we inferred that the vsiRNAs might be predominantly produced by DCL cleavage of highly structured transcripts. To get a clearer insight into the relationship between secondary structure and hotspots generation, we analyzed the putative secondary structures formed by MSRV-YN transcripts using RNAfold [27]. A great degree of coincidence between secondary structures and hotspot generation was demonstrated as expected (Fig. 5), indicating that the secondary structures of the MSRV-YN transcripts contributed greatly to the production of viral siRNAs. Yet, we cannot rule out that other reasons contribute to the greater suitability of certain regions for the formation of siRNAs. More work is still needed to understand this asymmetry of siRNAs generated from different region of viral genome.Fig. 5


Identification and characterization of a maize-associated mastrevirus in China by deep sequencing small RNA populations.

Chen S, Huang Q, Wu L, Qian Y - Virol. J. (2015)

Structural analysis of MSRV-YN vsiRNA hotspots. a The secondary structures were predicted using the thermodynamic prediction of minimal free energy (MFE). A mountain plot representation of the MFE structure is shown. b Profile of the MSRV-YN-derived siRNAs. An asterisk indicates that vsiRNA production was consistent with the predicted highly structured regions. Positions and orientations of the four predicted ORFs are shown by colored arrows
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4594918&req=5

Fig5: Structural analysis of MSRV-YN vsiRNA hotspots. a The secondary structures were predicted using the thermodynamic prediction of minimal free energy (MFE). A mountain plot representation of the MFE structure is shown. b Profile of the MSRV-YN-derived siRNAs. An asterisk indicates that vsiRNA production was consistent with the predicted highly structured regions. Positions and orientations of the four predicted ORFs are shown by colored arrows
Mentions: A genome-wide view of vsiRNAs revealed that the vsiRNAs of MSRV-YN were not uniformly distributed along each genome segment, with the most abundant siRNAs matched both positive and negative strands of the MP and CP-coding region (Fig. 5), indicating the accessibility of target sites with MP and CP. The peaks of hotspots were particularly observed in the position of 75 to 385 nt and 882 to 954 nt along MSRV-YN genome. Hotspots for vsiRNAs generation have been extensively described and discussed for many viruses, yet the reasons for this phenomenon are not entirely clear [22–25]. Previous reports indicated that imperfect duplexes in the most-folded regions might be targeted for specific DCLs cleavage and thus affect vsiRNAs production [24]. On the other hand, evidence showed that a hairpin structure of Cucumber mosaic virus satellite RNA could be targeted more efficiently by DCL4 [26]. Since MSRV-YN is a DNA virus, we inferred that the vsiRNAs might be predominantly produced by DCL cleavage of highly structured transcripts. To get a clearer insight into the relationship between secondary structure and hotspots generation, we analyzed the putative secondary structures formed by MSRV-YN transcripts using RNAfold [27]. A great degree of coincidence between secondary structures and hotspot generation was demonstrated as expected (Fig. 5), indicating that the secondary structures of the MSRV-YN transcripts contributed greatly to the production of viral siRNAs. Yet, we cannot rule out that other reasons contribute to the greater suitability of certain regions for the formation of siRNAs. More work is still needed to understand this asymmetry of siRNAs generated from different region of viral genome.Fig. 5

Bottom Line: There was a slightly higher representation of MSRV-YN siRNAs derived from the virion-sense strand genome than the complementary-sense strand genome.Moreover, MSRV-YN vsiRNAs were not uniformly distributed along the genome, and hotspots were detected in the movement protein and coat protein-coding region.This vsiRNAs profile derived from MSRV-YN was characterized, which might contribute to get an insight into the host RNA silencing defense induced by MSRV-YN, and provide guidelines on designing antiviral strategies using RNAi against MSRV-YN.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China. 415748559@qq.com.

ABSTRACT

Background: Maize streak Reunion virus (MSRV) is a member of the Mastrevirus genus in the family Geminiviridae. Of the diverse and increasing number of mastrevirus species found so far, only Wheat dwarf virus and Sweetpotato symptomless virus 1 have been discovered in China. Recently, a novel, unbiased approach based on deep sequencing of small interfering RNAs followed by de novo assembly of siRNA, has greatly offered opportunities for plant virus identification.

Methods: Samples collected from maize leaves was deep sequencing for virus identification. Subsequently, the assay of PCR, rolling circle amplification and Southern blot were used to confirm the presence of a mastrevirus.

Results: Maize streak Reunion virus Yunnan isolate (MSRV-[China:Yunnan 06:2014], abbreviated to MSRV-YN) was identified from maize collected from Yunnan Province, China, by small RNA deep sequencing. The complete genome of this virus was ascertained as 2,880 nucleotides long by conventional sequencing. A phylogenetic analysis showed it shared 96.3 % nucleotide sequence identity with the isolate of Maize streak Reunion virus from La Reunion Island. To our knowledge, this is the first identification of MSRV in China. Analyses of the viral derived small interfering RNAs (vsiRNAs) profile showed that the most abundant MSRV-YN vsiRNAs were 21, 22 and 24 nt long and biased for A and G at their 5' terminal residue. There was a slightly higher representation of MSRV-YN siRNAs derived from the virion-sense strand genome than the complementary-sense strand genome. Moreover, MSRV-YN vsiRNAs were not uniformly distributed along the genome, and hotspots were detected in the movement protein and coat protein-coding region.

Conclusions: A mastrevirus MSRV-YN collected in Yunnan Province, China, was identified by small RNA deep sequencing. This vsiRNAs profile derived from MSRV-YN was characterized, which might contribute to get an insight into the host RNA silencing defense induced by MSRV-YN, and provide guidelines on designing antiviral strategies using RNAi against MSRV-YN.

No MeSH data available.


Related in: MedlinePlus