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Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach.

Su X, Fu S, Qian Y, Xu Y, Zhou X - Virol. J. (2015)

Bottom Line: A bias of HSVd-siRNAs toward sequences beginning with a 5'-Guanine was observed.Furthermore, hotspot analysis showed that a large amount of HSVd-siRNAs derived from the central and variant domains of the HSVd genome.Our results suggest that C. limon could set up a small RNA-mediated gene silencing response to Hop stunt viroid, Interestingly, based on bioinformatics analysis, our results also suggest that the large amounts of HSVd-siRNAs from central and variant domains might be involved in interference with host gene expression and affect symptom development.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029, People's Republic of China. suxiu@zafu.edu.cn.

ABSTRACT

Background: The advent of next generation sequencing technology has allowed for significant advances in plant virus discovery, particularly for identification of covert viruses and previously undescribed viruses. The Citrus limon Burm. f. (C. limon) is a small evergreen tree native to Asia, and . China is the world's top lemon-producing nation.

Findings: In this work, lemon samples were collected from southwestern of China, where an unknown disease outbreak had caused huge losses in the lemon production industry. Using high-throughput pyrosequencing and the assembly of small RNAs, we showed that the Hop stunt viroid (HSVd) was present in C. limon leaf sample. The majority of it is a main lemon producing agricultural cultivarHop stunt viroid derived siRNAs (HSVd-siRNAs) in C. limon were 21 nucleotides in length, and nearly equal amount of HSVd-siRNAs originated from the plus-genomic RNA strand as from the complementary strand. A bias of HSVd-siRNAs toward sequences beginning with a 5'-Guanine was observed. Furthermore, hotspot analysis showed that a large amount of HSVd-siRNAs derived from the central and variant domains of the HSVd genome.

Conclusions: Our results suggest that C. limon could set up a small RNA-mediated gene silencing response to Hop stunt viroid, Interestingly, based on bioinformatics analysis, our results also suggest that the large amounts of HSVd-siRNAs from central and variant domains might be involved in interference with host gene expression and affect symptom development.

No MeSH data available.


Related in: MedlinePlus

Profile of HSVd-siRNAs. 3a, Size distributions of vsiRNA sequences matching viroid genome. 3b, Statistical analysis of HSVd-siRNAs mapped to the genomic (+) or antigenomic (−) sequences. 3c, Relative frequency of 5′ terminal nucleotide, and the vsiRNAs were analyzed for both whole level (total) and different-sized species. 3d, Most HSVd-siRNAs derived from C (Central) and V (Variant) domains
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Fig3: Profile of HSVd-siRNAs. 3a, Size distributions of vsiRNA sequences matching viroid genome. 3b, Statistical analysis of HSVd-siRNAs mapped to the genomic (+) or antigenomic (−) sequences. 3c, Relative frequency of 5′ terminal nucleotide, and the vsiRNAs were analyzed for both whole level (total) and different-sized species. 3d, Most HSVd-siRNAs derived from C (Central) and V (Variant) domains

Mentions: To characterize and profile the HSVd-siRNAs along the viral genome, we aligned small RNA sequences with the HSVd genomic and antigenomic RNA sequences using bowtie tools and allowed zero mismatches [8]. The percentages of 20 to 24-nt HSVd-siRNAs identified in the viroid are shown in Fig. 3a; the 21-nt vsiRNAs predominate and account for almost 40 % of the total HSVd-siRNAs. 22-nt and 24-nt viroid-derived small RNAs account for 30.06 % and 17.22 % respectively. Our results are consistent with former reports that 21-nt vsiRNAs are predominant in viroid-infected plants [9, 10]. Furthermore, analysis of polarity distribution of the HSVd-siRNAs showed that HSVd-siRNAs were derived almost equally from the plus and minus strands of genome RNA (Fig. 3b), indicating that they might be produced from viroid replication intermediates during viroid replication by plant silencing machinery, and not by degradation of a plus-stranded viroid genomic RNA.Fig. 3


Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach.

Su X, Fu S, Qian Y, Xu Y, Zhou X - Virol. J. (2015)

Profile of HSVd-siRNAs. 3a, Size distributions of vsiRNA sequences matching viroid genome. 3b, Statistical analysis of HSVd-siRNAs mapped to the genomic (+) or antigenomic (−) sequences. 3c, Relative frequency of 5′ terminal nucleotide, and the vsiRNAs were analyzed for both whole level (total) and different-sized species. 3d, Most HSVd-siRNAs derived from C (Central) and V (Variant) domains
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4492010&req=5

Fig3: Profile of HSVd-siRNAs. 3a, Size distributions of vsiRNA sequences matching viroid genome. 3b, Statistical analysis of HSVd-siRNAs mapped to the genomic (+) or antigenomic (−) sequences. 3c, Relative frequency of 5′ terminal nucleotide, and the vsiRNAs were analyzed for both whole level (total) and different-sized species. 3d, Most HSVd-siRNAs derived from C (Central) and V (Variant) domains
Mentions: To characterize and profile the HSVd-siRNAs along the viral genome, we aligned small RNA sequences with the HSVd genomic and antigenomic RNA sequences using bowtie tools and allowed zero mismatches [8]. The percentages of 20 to 24-nt HSVd-siRNAs identified in the viroid are shown in Fig. 3a; the 21-nt vsiRNAs predominate and account for almost 40 % of the total HSVd-siRNAs. 22-nt and 24-nt viroid-derived small RNAs account for 30.06 % and 17.22 % respectively. Our results are consistent with former reports that 21-nt vsiRNAs are predominant in viroid-infected plants [9, 10]. Furthermore, analysis of polarity distribution of the HSVd-siRNAs showed that HSVd-siRNAs were derived almost equally from the plus and minus strands of genome RNA (Fig. 3b), indicating that they might be produced from viroid replication intermediates during viroid replication by plant silencing machinery, and not by degradation of a plus-stranded viroid genomic RNA.Fig. 3

Bottom Line: A bias of HSVd-siRNAs toward sequences beginning with a 5'-Guanine was observed.Furthermore, hotspot analysis showed that a large amount of HSVd-siRNAs derived from the central and variant domains of the HSVd genome.Our results suggest that C. limon could set up a small RNA-mediated gene silencing response to Hop stunt viroid, Interestingly, based on bioinformatics analysis, our results also suggest that the large amounts of HSVd-siRNAs from central and variant domains might be involved in interference with host gene expression and affect symptom development.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029, People's Republic of China. suxiu@zafu.edu.cn.

ABSTRACT

Background: The advent of next generation sequencing technology has allowed for significant advances in plant virus discovery, particularly for identification of covert viruses and previously undescribed viruses. The Citrus limon Burm. f. (C. limon) is a small evergreen tree native to Asia, and . China is the world's top lemon-producing nation.

Findings: In this work, lemon samples were collected from southwestern of China, where an unknown disease outbreak had caused huge losses in the lemon production industry. Using high-throughput pyrosequencing and the assembly of small RNAs, we showed that the Hop stunt viroid (HSVd) was present in C. limon leaf sample. The majority of it is a main lemon producing agricultural cultivarHop stunt viroid derived siRNAs (HSVd-siRNAs) in C. limon were 21 nucleotides in length, and nearly equal amount of HSVd-siRNAs originated from the plus-genomic RNA strand as from the complementary strand. A bias of HSVd-siRNAs toward sequences beginning with a 5'-Guanine was observed. Furthermore, hotspot analysis showed that a large amount of HSVd-siRNAs derived from the central and variant domains of the HSVd genome.

Conclusions: Our results suggest that C. limon could set up a small RNA-mediated gene silencing response to Hop stunt viroid, Interestingly, based on bioinformatics analysis, our results also suggest that the large amounts of HSVd-siRNAs from central and variant domains might be involved in interference with host gene expression and affect symptom development.

No MeSH data available.


Related in: MedlinePlus