Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach
Identifieur interne : 000597 ( Main/Exploration ); précédent : 000596; suivant : 000598Identification of Hop stunt viroid infecting Citrus limon in China using small RNAs deep sequencing approach
Auteurs : Xiu Su [République populaire de Chine] ; Shuai Fu [République populaire de Chine] ; Yajuan Qian [République populaire de Chine] ; Yi Xu [République populaire de Chine] ; Xueping Zhou [République populaire de Chine]Source :
- Virology Journal [ 1743-422X ] ; 2015.
Abstract
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
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
Our results suggest that
Url:
DOI: 10.1186/s12985-015-0332-2
PubMed: 26148502
PubMed Central: 4492010
Affiliations:
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Fu</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Qian, Yajuan" sort="Qian, Yajuan" uniqKey="Qian Y" first="Yajuan" last="Qian">Yajuan Qian</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Xu, Yi" sort="Xu, Yi" uniqKey="Xu Y" first="Yi" last="Xu">Yi Xu</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Zhou, Xueping" sort="Zhou, Xueping" uniqKey="Zhou X" first="Xueping" last="Zhou">Xueping Zhou</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">Institute of Plant Protection, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26148502</idno><idno type="pmc">4492010</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492010</idno><idno type="RBID">PMC:4492010</idno><idno type="doi">10.1186/s12985-015-0332-2</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000707</idno><idno type="wicri:Area/Pmc/Curation">000706</idno><idno type="wicri:Area/Pmc/Checkpoint">000468</idno><idno type="wicri:Area/Ncbi/Merge">001C09</idno><idno type="wicri:Area/Ncbi/Curation">001C09</idno><idno type="wicri:Area/Ncbi/Checkpoint">001C09</idno><idno type="wicri:Area/Main/Merge">000597</idno><idno type="wicri:Area/Main/Curation">000597</idno><idno type="wicri:Area/Main/Exploration">000597</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of <italic>Hop stunt viroid</italic> infecting <italic>Citrus limon</italic> in China using small RNAs deep sequencing approach</title><author><name sortKey="Su, Xiu" sort="Su, Xiu" uniqKey="Su X" first="Xiu" last="Su">Xiu Su</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Fu, Shuai" sort="Fu, Shuai" uniqKey="Fu S" first="Shuai" last="Fu">Shuai Fu</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Qian, Yajuan" sort="Qian, Yajuan" uniqKey="Qian Y" first="Yajuan" last="Qian">Yajuan Qian</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Xu, Yi" sort="Xu, Yi" uniqKey="Xu Y" first="Yi" last="Xu">Yi Xu</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation></author><author><name sortKey="Zhou, Xueping" sort="Zhou, Xueping" uniqKey="Zhou X" first="Xueping" last="Zhou">Xueping Zhou</name><affiliation wicri:level="4"><nlm:aff id="Aff1">Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310029 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Biotechnology, State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou</wicri:regionArea><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName><orgName type="university">Université de Zhejiang</orgName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">Institute of Plant Protection, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Plant Protection, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>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 <italic>Citrus limon Burm. f.</italic> (<italic>C. limon</italic>) is a small evergreen tree native to Asia, and . China is the world’s top lemon-producing nation.</p></sec><sec><title>Findings</title><p>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 <italic>Hop stunt viroid</italic> (HSVd) was present in <italic>C. limon</italic> leaf sample. The majority of it is a main lemon producing agricultural cultivar<italic>Hop stunt viroid</italic> derived siRNAs (HSVd-siRNAs) in <italic>C. limon</italic> 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.</p></sec><sec><title>Conclusions</title><p>Our results suggest that <italic>C. limon</italic> could set up a small RNA-mediated gene silencing response to <italic>Hop stunt viroid</italic>, 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<italic>.</italic></p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Flores, R" uniqKey="Flores R">R Flores</name></author><author><name sortKey="Gago Zachert, S" uniqKey="Gago Zachert S">S Gago-Zachert</name></author><author><name sortKey="Serra, P" uniqKey="Serra P">P Serra</name></author><author><name sortKey="Sanjuan, R" uniqKey="Sanjuan R">R 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Shuai" uniqKey="Fu S" first="Shuai" last="Fu">Shuai Fu</name><name sortKey="Qian, Yajuan" sort="Qian, Yajuan" uniqKey="Qian Y" first="Yajuan" last="Qian">Yajuan Qian</name><name sortKey="Xu, Yi" sort="Xu, Yi" uniqKey="Xu Y" first="Yi" last="Xu">Yi Xu</name><name sortKey="Zhou, Xueping" sort="Zhou, Xueping" uniqKey="Zhou X" first="Xueping" last="Zhou">Xueping Zhou</name><name sortKey="Zhou, Xueping" sort="Zhou, Xueping" uniqKey="Zhou X" first="Xueping" last="Zhou">Xueping Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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