Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis
Identifieur interne : 000614 ( Pmc/Curation ); précédent : 000613; suivant : 000615Identification 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
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Yue Zhang<affiliation><nlm:aff id="Aff1">Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</nlm:aff>
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<wicri:noCountry code="subfield">210095 Jiangsu Province P. R. China</wicri:noCountry>
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Le document en format XML
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<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>
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<author><name sortKey="Zhu, Xujun" sort="Zhu, Xujun" uniqKey="Zhu X" first="Xujun" last="Zhu">Xujun Zhu</name>
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<author><name sortKey="Chen, Xuan" sort="Chen, Xuan" uniqKey="Chen X" first="Xuan" last="Chen">Xuan Chen</name>
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<author><name sortKey="Fang, Wanping" sort="Fang, Wanping" uniqKey="Fang W" first="Wanping" last="Fang">Wanping Fang</name>
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<author><name sortKey="Li, Xinghui" sort="Li, Xinghui" uniqKey="Li X" first="Xinghui" last="Li">Xinghui Li</name>
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<series><title level="j">BMC Plant Biology</title>
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<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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Plant Biol</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Plant Biol</journal-id>
<journal-title-group><journal-title>BMC Plant Biology</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2229</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25330732</article-id>
<article-id pub-id-type="pmc">4209041</article-id>
<article-id pub-id-type="publisher-id">271</article-id>
<article-id pub-id-type="doi">10.1186/s12870-014-0271-x</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Identification and characterization of cold-responsive microRNAs in tea plant (<italic>Camellia sinensis</italic>
) and their targets using high-throughput sequencing and degradome analysis</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Zhang</surname>
<given-names>Yue</given-names>
</name>
<address><email>2011204025@njau.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zhu</surname>
<given-names>Xujun</given-names>
</name>
<address><email>zhuxujun@njau.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Xuan</given-names>
</name>
<address><email>chenxuan@naju.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Song</surname>
<given-names>Changnian</given-names>
</name>
<address><email>songchangnian@njau.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zou</surname>
<given-names>Zhongwei</given-names>
</name>
<address><email>zhongwei@tll.org.sg</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wang</surname>
<given-names>Yuhua</given-names>
</name>
<address><email>wangyuhua@njau.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wang</surname>
<given-names>Mingle</given-names>
</name>
<address><email>2012104092@njau.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Fang</surname>
<given-names>Wanping</given-names>
</name>
<address><email>fangwp@njau.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Li</surname>
<given-names>Xinghui</given-names>
</name>
<address><email>lxh@njau.edu.cn</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<aff id="Aff1"><label></label>
Tea Research Institute, Nanjing Agricultural University, Weigang No.1, Nanjing, 210095 Jiangsu Province P. R. China</aff>
<aff id="Aff2"><label></label>
College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 P. R. China</aff>
<aff id="Aff3"><label></label>
Molecular population genetics group, Temasek lifesciences laboratory, 1 Research link, National University of Singapore, Singapore, 117604 Singapore</aff>
</contrib-group>
<pub-date pub-type="epub"><day>21</day>
<month>10</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>21</day>
<month>10</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<volume>14</volume>
<elocation-id>271</elocation-id>
<history><date date-type="received"><day>20</day>
<month>6</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>3</day>
<month>10</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© Zhang et al.; licensee BioMed Central Ltd. 2014</copyright-statement>
<license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><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>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd><italic>Camellia sinensis</italic>
</kwd>
<kwd>MicroRNA</kwd>
<kwd>Cold-response</kwd>
<kwd>Microarray</kwd>
<kwd>Target identification</kwd>
</kwd-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2014</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
</record>
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