Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Identifieur interne : 000386 ( Pmc/Curation ); précédent : 000385; suivant : 000387Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Auteurs : Parameswari Paul ; Vignesh Dhandapani ; Jana Jeevan Rameneni ; Xiaonan Li ; Ganesan Sivanandhan ; Su Ryun Choi ; Wenxing Pang ; Subin Im ; Yong Pyo LimSource :
- PLoS ONE [ 1932-6203 ] ; 2016.
Abstract
Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in
Url:
DOI: 10.1371/journal.pone.0151522
PubMed: 27049520
PubMed Central: 4822780
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<author><name sortKey="Paul, Parameswari" sort="Paul, Parameswari" uniqKey="Paul P" first="Parameswari" last="Paul">Parameswari Paul</name>
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<author><name sortKey="Rameneni, Jana Jeevan" sort="Rameneni, Jana Jeevan" uniqKey="Rameneni J" first="Jana Jeevan" last="Rameneni">Jana Jeevan Rameneni</name>
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<author><name sortKey="Li, Xiaonan" sort="Li, Xiaonan" uniqKey="Li X" first="Xiaonan" last="Li">Xiaonan Li</name>
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<author><name sortKey="Sivanandhan, Ganesan" sort="Sivanandhan, Ganesan" uniqKey="Sivanandhan G" first="Ganesan" last="Sivanandhan">Ganesan Sivanandhan</name>
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<author><name sortKey="Choi, Su Ryun" sort="Choi, Su Ryun" uniqKey="Choi S" first="Su Ryun" last="Choi">Su Ryun Choi</name>
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<author><name sortKey="Pang, Wenxing" sort="Pang, Wenxing" uniqKey="Pang W" first="Wenxing" last="Pang">Wenxing Pang</name>
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<author><name sortKey="Im, Subin" sort="Im, Subin" uniqKey="Im S" first="Subin" last="Im">Subin Im</name>
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<author><name sortKey="Lim, Yong Pyo" sort="Lim, Yong Pyo" uniqKey="Lim Y" first="Yong Pyo" last="Lim">Yong Pyo Lim</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in <italic>Brassica rapa</italic>
</title>
<author><name sortKey="Paul, Parameswari" sort="Paul, Parameswari" uniqKey="Paul P" first="Parameswari" last="Paul">Parameswari Paul</name>
<affiliation><nlm:aff id="aff001"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Dhandapani, Vignesh" sort="Dhandapani, Vignesh" uniqKey="Dhandapani V" first="Vignesh" last="Dhandapani">Vignesh Dhandapani</name>
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</affiliation>
</author>
<author><name sortKey="Rameneni, Jana Jeevan" sort="Rameneni, Jana Jeevan" uniqKey="Rameneni J" first="Jana Jeevan" last="Rameneni">Jana Jeevan Rameneni</name>
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</affiliation>
</author>
<author><name sortKey="Li, Xiaonan" sort="Li, Xiaonan" uniqKey="Li X" first="Xiaonan" last="Li">Xiaonan Li</name>
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<author><name sortKey="Sivanandhan, Ganesan" sort="Sivanandhan, Ganesan" uniqKey="Sivanandhan G" first="Ganesan" last="Sivanandhan">Ganesan Sivanandhan</name>
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<author><name sortKey="Choi, Su Ryun" sort="Choi, Su Ryun" uniqKey="Choi S" first="Su Ryun" last="Choi">Su Ryun Choi</name>
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<author><name sortKey="Pang, Wenxing" sort="Pang, Wenxing" uniqKey="Pang W" first="Wenxing" last="Pang">Wenxing Pang</name>
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<author><name sortKey="Im, Subin" sort="Im, Subin" uniqKey="Im S" first="Subin" last="Im">Subin Im</name>
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<author><name sortKey="Lim, Yong Pyo" sort="Lim, Yong Pyo" uniqKey="Lim Y" first="Yong Pyo" last="Lim">Yong Pyo Lim</name>
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<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2016">2016</date>
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<front><div type="abstract" xml:lang="en"><p>Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in <italic>Brassica rapa</italic>
(<italic>B</italic>
. <italic>rapa</italic>
). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in <italic>B</italic>
. <italic>rapa</italic>
using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the <italic>B</italic>
. <italic>rapa</italic>
Aux/IAA (<italic>BrIAA</italic>
) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of <italic>BrIAA</italic>
with <italic>Arabidopsis thaliana</italic>
, <italic>Oryza sativa</italic>
and <italic>Zea mays</italic>
identified 51 sister pairs including 15 same species (<italic>BrIAA</italic>
—<italic>BrIAA</italic>
) and 36 cross species (<italic>BrIAA</italic>
—<italic>AtIAA</italic>
) <italic>IAA</italic>
genes. Among the 55 <italic>BrIAA</italic>
genes, expression of 43 and 45 genes were verified using Genebank <italic>B</italic>
. <italic>rapa</italic>
ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of <italic>BrIAA</italic>
genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the <italic>BrIAA</italic>
genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between <italic>IAA</italic>
genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in <italic>B</italic>
. <italic>rapa</italic>
. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of <italic>Brassica</italic>
crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in <italic>B</italic>
. <italic>rapa</italic>
.</p>
</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">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, CA USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">27049520</article-id>
<article-id pub-id-type="pmc">4822780</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0151522</article-id>
<article-id pub-id-type="publisher-id">PONE-D-15-44791</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Organisms</subject>
<subj-group><subject>Plants</subject>
<subj-group><subject>Brassica</subject>
<subj-group><subject>Arabidopsis Thaliana</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject>
<subj-group><subject>Model Organisms</subject>
<subj-group><subject>Plant and Algal Models</subject>
<subj-group><subject>Arabidopsis Thaliana</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Gene Expression</subject>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Molecular Biology</subject>
<subj-group><subject>Molecular Biology Techniques</subject>
<subj-group><subject>Sequencing Techniques</subject>
<subj-group><subject>Sequence Analysis</subject>
<subj-group><subject>Sequence Motif Analysis</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject>
<subj-group><subject>Molecular Biology Techniques</subject>
<subj-group><subject>Sequencing Techniques</subject>
<subj-group><subject>Sequence Analysis</subject>
<subj-group><subject>Sequence Motif Analysis</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Biochemistry</subject>
<subj-group><subject>Hormones</subject>
<subj-group><subject>Plant Hormones</subject>
<subj-group><subject>Auxins</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Biochemistry</subject>
<subj-group><subject>Plant Biochemistry</subject>
<subj-group><subject>Plant Hormones</subject>
<subj-group><subject>Auxins</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Plant Science</subject>
<subj-group><subject>Plant Biochemistry</subject>
<subj-group><subject>Plant Hormones</subject>
<subj-group><subject>Auxins</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject>
<subj-group><subject>Database and Informatics Methods</subject>
<subj-group><subject>Biological Databases</subject>
<subj-group><subject>Genomic Databases</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Computational Biology</subject>
<subj-group><subject>Genome Analysis</subject>
<subj-group><subject>Genomic Databases</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Genome Analysis</subject>
<subj-group><subject>Genomic Databases</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Genomics</subject>
<subj-group><subject>Plant Genomics</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Biotechnology</subject>
<subj-group><subject>Plant Biotechnology</subject>
<subj-group><subject>Plant Genomics</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Plant Science</subject>
<subj-group><subject>Plant Biotechnology</subject>
<subj-group><subject>Plant Genomics</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Genetics</subject>
<subj-group><subject>Plant Genetics</subject>
<subj-group><subject>Plant Genomics</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Plant Science</subject>
<subj-group><subject>Plant Genetics</subject>
<subj-group><subject>Plant Genomics</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Agriculture</subject>
<subj-group><subject>Crop Science</subject>
<subj-group><subject>Crops</subject>
<subj-group><subject>Cereal Crops</subject>
<subj-group><subject>Maize</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Organisms</subject>
<subj-group><subject>Plants</subject>
<subj-group><subject>Grasses</subject>
<subj-group><subject>Maize</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Research and Analysis Methods</subject>
<subj-group><subject>Model Organisms</subject>
<subj-group><subject>Plant and Algal Models</subject>
<subj-group><subject>Maize</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
<subj-group subj-group-type="Discipline-v3"><subject>Biology and Life Sciences</subject>
<subj-group><subject>Biochemistry</subject>
<subj-group><subject>Proteins</subject>
<subj-group><subject>Protein Domains</subject>
</subj-group>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in <italic>Brassica rapa</italic>
</article-title>
<alt-title alt-title-type="running-head">Aux/IAA Genes in <italic>B</italic>
. <italic>rapa</italic>
</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Paul</surname>
<given-names>Parameswari</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author" equal-contrib="yes"><name><surname>Dhandapani</surname>
<given-names>Vignesh</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rameneni</surname>
<given-names>Jana Jeevan</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Xiaonan</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sivanandhan</surname>
<given-names>Ganesan</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Choi</surname>
<given-names>Su Ryun</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pang</surname>
<given-names>Wenxing</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Im</surname>
<given-names>Subin</given-names>
</name>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lim</surname>
<given-names>Yong Pyo</given-names>
</name>
<xref ref-type="corresp" rid="cor001">*</xref>
<xref ref-type="aff" rid="aff001"></xref>
</contrib>
</contrib-group>
<aff id="aff001"><addr-line>Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305764, South Korea</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Li</surname>
<given-names>Maoteng</given-names>
</name>
<role>Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Huazhong university of Science and Technology, CHINA</addr-line>
</aff>
<author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: PP VD. Performed the experiments: JJR XL GS WP SI. Analyzed the data: PP VD SRC YPL. Contributed reagents/materials/analysis tools: SRC YPL. Wrote the paper: PP VD.</p>
</fn>
<corresp id="cor001">* E-mail: <email>yplim@cnu.ac.kr</email>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>6</day>
<month>4</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><year>2016</year>
</pub-date>
<volume>11</volume>
<issue>4</issue>
<elocation-id>e0151522</elocation-id>
<history><date date-type="received"><day>12</day>
<month>10</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>28</day>
<month>2</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© 2016 Paul et al</copyright-statement>
<copyright-year>2016</copyright-year>
<copyright-holder>Paul et al</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0151522.pdf"></self-uri>
<abstract><p>Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in <italic>Brassica rapa</italic>
(<italic>B</italic>
. <italic>rapa</italic>
). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in <italic>B</italic>
. <italic>rapa</italic>
using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the <italic>B</italic>
. <italic>rapa</italic>
Aux/IAA (<italic>BrIAA</italic>
) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of <italic>BrIAA</italic>
with <italic>Arabidopsis thaliana</italic>
, <italic>Oryza sativa</italic>
and <italic>Zea mays</italic>
identified 51 sister pairs including 15 same species (<italic>BrIAA</italic>
—<italic>BrIAA</italic>
) and 36 cross species (<italic>BrIAA</italic>
—<italic>AtIAA</italic>
) <italic>IAA</italic>
genes. Among the 55 <italic>BrIAA</italic>
genes, expression of 43 and 45 genes were verified using Genebank <italic>B</italic>
. <italic>rapa</italic>
ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of <italic>BrIAA</italic>
genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the <italic>BrIAA</italic>
genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between <italic>IAA</italic>
genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in <italic>B</italic>
. <italic>rapa</italic>
. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of <italic>Brassica</italic>
crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in <italic>B</italic>
. <italic>rapa</italic>
.</p>
</abstract>
<funding-group><funding-statement>This research was supported by the Golden Seed Project (No. 213002-04-4-SBI30), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Service (KFS).</funding-statement>
</funding-group>
<counts><fig-count count="5"></fig-count>
<table-count count="2"></table-count>
<page-count count="19"></page-count>
</counts>
<custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name>
<meta-value>All relevant data are within the paper and its Supporting Information files.</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes><title>Data Availability</title>
<p>All relevant data are within the paper and its Supporting Information files.</p>
</notes>
</front>
</pmc>
</record>
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