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Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

Identifieur interne : 000A17 ( Pmc/Checkpoint ); précédent : 000A16; suivant : 000A18

Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

Auteurs : Cai-Yun He [République populaire de Chine] ; Kai Cui [République populaire de Chine] ; Jian-Guo Zhang [République populaire de Chine] ; Ai-Guo Duan [République populaire de Chine] ; Yan-Fei Zeng [République populaire de Chine]

Source :

RBID : PMC:3765735

Abstract

Background

As one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (Phyllostachys heterocycla cv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level.

Results

Our anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms.

Conclusions

This is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms.


Url:
DOI: 10.1186/1471-2229-13-119
PubMed: 23964682
PubMed Central: 3765735


Affiliations:


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PMC:3765735

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<title>Background</title>
<p>As one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (
<italic>Phyllostachys heterocycla</italic>
cv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level.</p>
</sec>
<sec>
<title>Results</title>
<p>Our anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms.</p>
</sec>
<sec>
<title>Conclusions</title>
<p>This is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms.</p>
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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 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>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">23964682</article-id>
<article-id pub-id-type="pmc">3765735</article-id>
<article-id pub-id-type="publisher-id">1471-2229-13-119</article-id>
<article-id pub-id-type="doi">10.1186/1471-2229-13-119</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" id="A1">
<name>
<surname>He</surname>
<given-names>Cai-yun</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>hecy@caf.ac.cn</email>
</contrib>
<contrib contrib-type="author" id="A2">
<name>
<surname>Cui</surname>
<given-names>Kai</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I3">3</xref>
<email>cafcuikai@163.com</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A3">
<name>
<surname>Zhang</surname>
<given-names>Jian-guo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>zhangjg@caf.ac.cn</email>
</contrib>
<contrib contrib-type="author" id="A4">
<name>
<surname>Duan</surname>
<given-names>Ai-guo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>duanag@caf.ac.cn</email>
</contrib>
<contrib contrib-type="author" id="A5">
<name>
<surname>Zeng</surname>
<given-names>Yan-fei</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>zengyf@caf.ac.cn</email>
</contrib>
</contrib-group>
<aff id="I1">
<label>1</label>
State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China</aff>
<aff id="I2">
<label>2</label>
Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China</aff>
<aff id="I3">
<label>3</label>
Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming 650224, China</aff>
<pub-date pub-type="collection">
<year>2013</year>
</pub-date>
<pub-date pub-type="epub">
<day>21</day>
<month>8</month>
<year>2013</year>
</pub-date>
<volume>13</volume>
<fpage>119</fpage>
<lpage>119</lpage>
<history>
<date date-type="received">
<day>24</day>
<month>6</month>
<year>2013</year>
</date>
<date date-type="accepted">
<day>15</day>
<month>8</month>
<year>2013</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright © 2013 He et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>He 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/1471-2229/13/119"></self-uri>
<abstract>
<sec>
<title>Background</title>
<p>As one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (
<italic>Phyllostachys heterocycla</italic>
cv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level.</p>
</sec>
<sec>
<title>Results</title>
<p>Our anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms.</p>
</sec>
<sec>
<title>Conclusions</title>
<p>This is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>République populaire de Chine</li>
</country>
<settlement>
<li>Pékin</li>
</settlement>
</list>
<tree>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="He, Cai Yun" sort="He, Cai Yun" uniqKey="He C" first="Cai-Yun" last="He">Cai-Yun He</name>
</noRegion>
<name sortKey="Cui, Kai" sort="Cui, Kai" uniqKey="Cui K" first="Kai" last="Cui">Kai Cui</name>
<name sortKey="Cui, Kai" sort="Cui, Kai" uniqKey="Cui K" first="Kai" last="Cui">Kai Cui</name>
<name sortKey="Cui, Kai" sort="Cui, Kai" uniqKey="Cui K" first="Kai" last="Cui">Kai Cui</name>
<name sortKey="Duan, Ai Guo" sort="Duan, Ai Guo" uniqKey="Duan A" first="Ai-Guo" last="Duan">Ai-Guo Duan</name>
<name sortKey="Duan, Ai Guo" sort="Duan, Ai Guo" uniqKey="Duan A" first="Ai-Guo" last="Duan">Ai-Guo Duan</name>
<name sortKey="He, Cai Yun" sort="He, Cai Yun" uniqKey="He C" first="Cai-Yun" last="He">Cai-Yun He</name>
<name sortKey="Zeng, Yan Fei" sort="Zeng, Yan Fei" uniqKey="Zeng Y" first="Yan-Fei" last="Zeng">Yan-Fei Zeng</name>
<name sortKey="Zeng, Yan Fei" sort="Zeng, Yan Fei" uniqKey="Zeng Y" first="Yan-Fei" last="Zeng">Yan-Fei Zeng</name>
<name sortKey="Zhang, Jian Guo" sort="Zhang, Jian Guo" uniqKey="Zhang J" first="Jian-Guo" last="Zhang">Jian-Guo Zhang</name>
<name sortKey="Zhang, Jian Guo" sort="Zhang, Jian Guo" uniqKey="Zhang J" first="Jian-Guo" last="Zhang">Jian-Guo Zhang</name>
</country>
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</record>

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