Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis
Identifieur interne : 000A51 ( Main/Exploration ); précédent : 000A50; suivant : 000A52Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis
Auteurs : Yue Zhang ; Xujun Zhu ; Xuan Chen ; Changnian Song [République populaire de Chine] ; Zhongwei Zou [Singapour] ; Yuhua Wang ; Mingle Wang ; Wanping Fang ; Xinghui LiSource :
- BMC Plant Biology [ 1471-2229 ] ; 2014.
Abstract
MicroRNAs (miRNAs) are approximately 19 ~ 21 nucleotide noncoding RNAs produced by Dicer-catalyzed excision from stem-loop precursors. Many plant miRNAs have critical functions in development, nutrient homeostasis, abiotic stress responses, and pathogen responses via interaction with specific target mRNAs.
Solexa sequencing technology was used for high-throughput sequencing of the small RNA library from the cold treatment of tea leaves. To align the sequencing data with known plant miRNAs, we characterized 106 conserved
We discovered 31 up-regulated miRNAs and 43 down-regulated miRNAs in ‘Yingshuang’, and 46 up-regulated miRNA and 45 down-regulated miRNAs in ‘Baiye 1’ in response to cold stress, respectively. A total of 763 related target genes were detected by degradome sequencing. The RLM-5′RACE procedure was successfully used to map the cleavage sites in six target genes of
The online version of this article (doi:10.1186/s12870-014-0271-x) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-014-0271-x
PubMed: 25330732
PubMed Central: 4209041
Affiliations:
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China</wicri:noCountry></affiliation></author><author><name sortKey="Chen, Xuan" sort="Chen, Xuan" uniqKey="Chen X" first="Xuan" last="Chen">Xuan Chen</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Song, Changnian" sort="Song, Changnian" uniqKey="Song C" first="Changnian" last="Song">Changnian Song</name><affiliation wicri:level="1"><nlm:aff id="Aff2">College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 P. R. China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Zou, Zhongwei" sort="Zou, Zhongwei" uniqKey="Zou Z" first="Zhongwei" last="Zou">Zhongwei Zou</name><affiliation wicri:level="4"><nlm:aff id="Aff3">Molecular population genetics group, Temasek lifesciences laboratory, 1 Research link, National University of Singapore, Singapore, 117604 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Molecular population genetics group, Temasek lifesciences laboratory, 1 Research link, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Wang, Yuhua" sort="Wang, Yuhua" uniqKey="Wang Y" first="Yuhua" last="Wang">Yuhua Wang</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Wang, Mingle" sort="Wang, Mingle" uniqKey="Wang M" first="Mingle" last="Wang">Mingle Wang</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Fang, Wanping" sort="Fang, Wanping" uniqKey="Fang W" first="Wanping" last="Fang">Wanping Fang</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Li, Xinghui" sort="Li, Xinghui" uniqKey="Li X" first="Xinghui" last="Li">Xinghui Li</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25330732</idno><idno type="pmc">4209041</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209041</idno><idno type="RBID">PMC:4209041</idno><idno type="doi">10.1186/s12870-014-0271-x</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000615</idno><idno type="wicri:Area/Pmc/Curation">000614</idno><idno type="wicri:Area/Pmc/Checkpoint">000796</idno><idno type="wicri:Area/Ncbi/Merge">001870</idno><idno type="wicri:Area/Ncbi/Curation">001870</idno><idno type="wicri:Area/Ncbi/Checkpoint">001870</idno><idno type="wicri:Area/Main/Merge">000A52</idno><idno type="wicri:Area/Main/Curation">000A51</idno><idno type="wicri:Area/Main/Exploration">000A51</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification and characterization of cold-responsive microRNAs in tea plant (<italic>Camellia sinensis</italic>) and their targets using high-throughput sequencing and degradome analysis</title><author><name sortKey="Zhang, Yue" sort="Zhang, Yue" uniqKey="Zhang Y" first="Yue" last="Zhang">Yue Zhang</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Zhu, Xujun" sort="Zhu, Xujun" uniqKey="Zhu X" first="Xujun" last="Zhu">Xujun Zhu</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Chen, Xuan" sort="Chen, Xuan" uniqKey="Chen X" first="Xuan" last="Chen">Xuan Chen</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Song, Changnian" sort="Song, Changnian" uniqKey="Song C" first="Changnian" last="Song">Changnian Song</name><affiliation wicri:level="1"><nlm:aff id="Aff2">College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 P. R. China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Horticulture, Nanjing Agricultural University, Nanjing</wicri:regionArea><wicri:noRegion>Nanjing</wicri:noRegion></affiliation></author><author><name sortKey="Zou, Zhongwei" sort="Zou, Zhongwei" uniqKey="Zou Z" first="Zhongwei" last="Zou">Zhongwei Zou</name><affiliation wicri:level="4"><nlm:aff id="Aff3">Molecular population genetics group, Temasek lifesciences laboratory, 1 Research link, National University of Singapore, Singapore, 117604 Singapore</nlm:aff><country xml:lang="fr">Singapour</country><wicri:regionArea>Molecular population genetics group, Temasek lifesciences laboratory, 1 Research link, National University of Singapore, Singapore</wicri:regionArea><orgName type="university">Université nationale de Singapour</orgName></affiliation></author><author><name sortKey="Wang, Yuhua" sort="Wang, Yuhua" uniqKey="Wang Y" first="Yuhua" last="Wang">Yuhua Wang</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Wang, Mingle" sort="Wang, Mingle" uniqKey="Wang M" first="Mingle" last="Wang">Mingle Wang</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Fang, Wanping" sort="Fang, Wanping" uniqKey="Fang W" first="Wanping" last="Fang">Wanping Fang</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author><author><name sortKey="Li, Xinghui" sort="Li, Xinghui" uniqKey="Li X" first="Xinghui" last="Li">Xinghui Li</name><affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff><wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>MicroRNAs (miRNAs) are approximately 19 ~ 21 nucleotide noncoding RNAs produced by Dicer-catalyzed excision from stem-loop precursors. Many plant miRNAs have critical functions in development, nutrient homeostasis, abiotic stress responses, and pathogen responses via interaction with specific target mRNAs. <italic>Camellia sinensis</italic> is one of the most important commercial beverage crops in the world. However, miRNAs associated with cold stress tolerance in <italic>C. sinensis</italic> remains unexplored. The use of high-throughput sequencing can provide a much deeper understanding of miRNAs. To obtain more insight into the function of miRNAs in cold stress tolerance, Illumina sequencing of <italic>C. sinensis</italic> sRNA was conducted.</p></sec><sec><title>Result</title><p>Solexa sequencing technology was used for high-throughput sequencing of the small RNA library from the cold treatment of tea leaves. To align the sequencing data with known plant miRNAs, we characterized 106 conserved <italic>C. sinensis</italic> miRNAs. In addition, 215 potential candidate miRNAs were found, among, which 98 candidates with star sequences were chosen as novel miRNAs. Both congruously and differentially regulated miRNAs were obtained, and cultivar-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The results were also confirmed by quantitative real-time polymerase chain reaction. To confirm the targets of miRNAs, two degradome libraries from two treatments were constructed. According to degradome sequencing, 455 and 591 genes were identified as cleavage targets of miRNAs from cold treatments and control libraries, respectively, and 283 targets were present in both libraries. Functional analysis of these miRNA targets indicated their involvement in important activities, such as development, regulation of transcription, and stress response.</p></sec><sec><title>Conclusions</title><p>We discovered 31 up-regulated miRNAs and 43 down-regulated miRNAs in ‘Yingshuang’, and 46 up-regulated miRNA and 45 down-regulated miRNAs in ‘Baiye 1’ in response to cold stress, respectively. A total of 763 related target genes were detected by degradome sequencing. The RLM-5′RACE procedure was successfully used to map the cleavage sites in six target genes of <italic>C. sinensis</italic>. These findings reveal important information about the regulatory mechanism of miRNAs in <italic>C. sinensis</italic>, and promote the understanding of miRNA functions during the cold response. The miRNA genotype-specific expression model might explain the distinct cold sensitivities between tea lines.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-014-0271-x) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name></author><author><name sortKey="Li, D" uniqKey="Li D">D Li</name></author><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name></author><author><name sortKey="Liu, F" uniqKey="Liu F">F Liu</name></author><author><name sortKey="Zhou, X" uniqKey="Zhou X">X Zhou</name></author><author><name sortKey="Wang, T" uniqKey="Wang T">T Wang</name></author><author><name sortKey="Ling, Y" uniqKey="Ling Y">Y Ling</name></author><author><name sortKey="Su, Z" 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sortKey="Li, Xinghui" sort="Li, Xinghui" uniqKey="Li X" first="Xinghui" last="Li">Xinghui Li</name><name sortKey="Wang, Mingle" sort="Wang, Mingle" uniqKey="Wang M" first="Mingle" last="Wang">Mingle Wang</name><name sortKey="Wang, Yuhua" sort="Wang, Yuhua" uniqKey="Wang Y" first="Yuhua" last="Wang">Yuhua Wang</name><name sortKey="Zhang, Yue" sort="Zhang, Yue" uniqKey="Zhang Y" first="Yue" last="Zhang">Yue Zhang</name><name sortKey="Zhu, Xujun" sort="Zhu, Xujun" uniqKey="Zhu X" first="Xujun" last="Zhu">Xujun Zhu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Song, Changnian" sort="Song, Changnian" uniqKey="Song C" first="Changnian" last="Song">Changnian Song</name></noRegion></country><country name="Singapour"><noRegion><name sortKey="Zou, Zhongwei" sort="Zou, Zhongwei" uniqKey="Zou Z" first="Zhongwei" last="Zou">Zhongwei Zou</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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