High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with pistil development in Japanese apricot
Identifieur interne : 000B11 ( Pmc/Curation ); précédent : 000B10; suivant : 000B12High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with pistil development in Japanese apricot
Auteurs : Zhihong Gao [République populaire de Chine] ; Ting Shi [République populaire de Chine] ; Xiaoyan Luo [République populaire de Chine] ; Zhen Zhang [République populaire de Chine] ; Weibing Zhuang [République populaire de Chine] ; Liangju Wang [République populaire de Chine]Source :
- BMC Genomics [ 1471-2164 ] ; 2012.
Abstract
MicroRNAs (miRNAs) are a class of endogenous, small, non-coding RNAs that regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in high plants. However, the diversity of miRNAs and their roles in floral development in Japanese apricot (
Solexa sequencing was used to identify and quantitatively profile small RNAs from perfect and imperfect flower buds of Japanese apricot. A total of 22,561,972 and 24,952,690 reads were sequenced from two small RNA libraries constructed from perfect and imperfect flower buds, respectively. Sixty-one known miRNAs, belonging to 24 families, were identified. Comparative profiling revealed that seven known miRNAs exhibited significant differential expression between perfect and imperfect flower buds. A total of 61 potentially novel miRNAs/new members of known miRNA families were also identified by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that six potentially novel miRNAs were differentially expressed between perfect and imperfect flower buds. Target predictions of the 13 differentially expressed miRNAs resulted in 212 target genes. Gene ontology (GO) annotation revealed that high-ranking miRNA target genes are those implicated in the developmental process, the regulation of transcription and response to stress.
This study represents the first comparative identification of miRNAomes between perfect and imperfect Japanese apricot flowers. Seven known miRNAs and six potentially novel miRNAs associated with pistil development were identified, using high-throughput sequencing of small RNAs. The findings, both computationally and experimentally, provide valuable information for further functional characterisation of miRNAs associated with pistil development in plants.
Url:
DOI: 10.1186/1471-2164-13-371
PubMed: 22863067
PubMed Central: 3464595
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>MicroRNAs (miRNAs) are a class of endogenous, small, non-coding RNAs that regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in high plants. However, the diversity of miRNAs and their roles in floral development in Japanese apricot (<italic>Prunus mume</italic>
Sieb. et Zucc) remains largely unexplored. Imperfect flowers with pistil abortion seriously decrease production yields. To understand the role of miRNAs in pistil development, pistil development-related miRNAs were identified by Solexa sequencing in Japanese apricot.</p>
</sec>
<sec><title>Results</title>
<p>Solexa sequencing was used to identify and quantitatively profile small RNAs from perfect and imperfect flower buds of Japanese apricot. A total of 22,561,972 and 24,952,690 reads were sequenced from two small RNA libraries constructed from perfect and imperfect flower buds, respectively. Sixty-one known miRNAs, belonging to 24 families, were identified. Comparative profiling revealed that seven known miRNAs exhibited significant differential expression between perfect and imperfect flower buds. A total of 61 potentially novel miRNAs/new members of known miRNA families were also identified by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that six potentially novel miRNAs were differentially expressed between perfect and imperfect flower buds. Target predictions of the 13 differentially expressed miRNAs resulted in 212 target genes. Gene ontology (GO) annotation revealed that high-ranking miRNA target genes are those implicated in the developmental process, the regulation of transcription and response to stress.</p>
</sec>
<sec><title>Conclusions</title>
<p>This study represents the first comparative identification of miRNAomes between perfect and imperfect Japanese apricot flowers. Seven known miRNAs and six potentially novel miRNAs associated with pistil development were identified, using high-throughput sequencing of small RNAs. The findings, both computationally and experimentally, provide valuable information for further functional characterisation of miRNAs associated with pistil development in plants.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Genomics</journal-id>
<journal-title-group><journal-title>BMC Genomics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2164</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22863067</article-id>
<article-id pub-id-type="pmc">3464595</article-id>
<article-id pub-id-type="publisher-id">1471-2164-13-371</article-id>
<article-id pub-id-type="doi">10.1186/1471-2164-13-371</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with pistil development in Japanese apricot</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" equal-contrib="yes" id="A1"><name><surname>Gao</surname>
<given-names>Zhihong</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>gaozhihong@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" equal-contrib="yes" id="A2"><name><surname>Shi</surname>
<given-names>Ting</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2009104025@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Luo</surname>
<given-names>Xiaoyan</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2010104019@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Zhang</surname>
<given-names>Zhen</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>zhangzh@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Zhuang</surname>
<given-names>Weibing</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2009104027@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Wang</surname>
<given-names>Liangju</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>wlj@njau.edu.cn</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
College of Horticulture, Nanjing Agricultural University, No 1 Weigang, Nanjing, 210095, P. R. China</aff>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>3</day>
<month>8</month>
<year>2012</year>
</pub-date>
<volume>13</volume>
<fpage>371</fpage>
<lpage>371</lpage>
<history><date date-type="received"><day>21</day>
<month>11</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>25</day>
<month>7</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2012 Gao et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>Gao et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><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/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2164/13/371"></self-uri>
<abstract><sec><title>Background</title>
<p>MicroRNAs (miRNAs) are a class of endogenous, small, non-coding RNAs that regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in high plants. However, the diversity of miRNAs and their roles in floral development in Japanese apricot (<italic>Prunus mume</italic>
Sieb. et Zucc) remains largely unexplored. Imperfect flowers with pistil abortion seriously decrease production yields. To understand the role of miRNAs in pistil development, pistil development-related miRNAs were identified by Solexa sequencing in Japanese apricot.</p>
</sec>
<sec><title>Results</title>
<p>Solexa sequencing was used to identify and quantitatively profile small RNAs from perfect and imperfect flower buds of Japanese apricot. A total of 22,561,972 and 24,952,690 reads were sequenced from two small RNA libraries constructed from perfect and imperfect flower buds, respectively. Sixty-one known miRNAs, belonging to 24 families, were identified. Comparative profiling revealed that seven known miRNAs exhibited significant differential expression between perfect and imperfect flower buds. A total of 61 potentially novel miRNAs/new members of known miRNA families were also identified by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that six potentially novel miRNAs were differentially expressed between perfect and imperfect flower buds. Target predictions of the 13 differentially expressed miRNAs resulted in 212 target genes. Gene ontology (GO) annotation revealed that high-ranking miRNA target genes are those implicated in the developmental process, the regulation of transcription and response to stress.</p>
</sec>
<sec><title>Conclusions</title>
<p>This study represents the first comparative identification of miRNAomes between perfect and imperfect Japanese apricot flowers. Seven known miRNAs and six potentially novel miRNAs associated with pistil development were identified, using high-throughput sequencing of small RNAs. The findings, both computationally and experimentally, provide valuable information for further functional characterisation of miRNAs associated with pistil development in plants.</p>
</sec>
</abstract>
<kwd-group><kwd>Japanese apricot</kwd>
<kwd>microRNA</kwd>
<kwd>Pistil abortion</kwd>
<kwd>qRT-PCR</kwd>
<kwd>Solexa sequencing</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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