Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear
Identifieur interne : 000142 ( Pmc/Checkpoint ); précédent : 000141; suivant : 000143Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear
Auteurs : Maosong Pei ; Jianxin Niu ; Chenjing Li ; Fujun Cao ; Shaowen QuanSource :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (
Comparison of the transcriptome sequences for SC_hua and TL_hua indicated 26 differentially expressed genes (DEGs) with known relationship to abscission and 10 DEGs with unknown function. We identified 98 MYB and 21 SPL genes from the assembled unigenes. From SC_zf vs TL_zf, we identified 21 DEGs with known relationship to abscission and 18 DEGs with unknown function. From SC_ep vs TL_ep, 12 DEGs with known relationship to abscission were identified along with 11 DEGs with unknown function. Ten DEGs were identified by both transcriptome sequencing and DGE sequencing.
More than 50 DEGs were observed that were related to calyx persistence in Korla fragrant pear. Some of the genes were related to cell wall degradation, plant hormone signal transduction, and stress response. Other DEGs were identified as zinc finger protein genes and lipid transfer protein genes. Further analysis showed that calyx persistence in Korla fragment pear was a metabolic process regulated by many genes related to cell wall degradation and plant hormones.
The online version of this article (doi:10.1186/s12864-016-2470-3) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-2470-3
PubMed: 26911295
PubMed Central: 4765163
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear</title><author><name sortKey="Pei, Maosong" sort="Pei, Maosong" uniqKey="Pei M" first="Maosong" last="Pei">Maosong Pei</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Niu, Jianxin" sort="Niu, Jianxin" uniqKey="Niu J" first="Jianxin" last="Niu">Jianxin Niu</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Li, Chenjing" sort="Li, Chenjing" uniqKey="Li C" first="Chenjing" last="Li">Chenjing Li</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Cao, Fujun" sort="Cao, Fujun" uniqKey="Cao F" first="Fujun" last="Cao">Fujun Cao</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Quan, Shaowen" sort="Quan, Shaowen" uniqKey="Quan S" first="Shaowen" last="Quan">Shaowen Quan</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26911295</idno><idno type="pmc">4765163</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765163</idno><idno type="RBID">PMC:4765163</idno><idno type="doi">10.1186/s12864-016-2470-3</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000603</idno><idno type="wicri:Area/Pmc/Curation">000602</idno><idno type="wicri:Area/Pmc/Checkpoint">000142</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear</title><author><name sortKey="Pei, Maosong" sort="Pei, Maosong" uniqKey="Pei M" first="Maosong" last="Pei">Maosong Pei</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Niu, Jianxin" sort="Niu, Jianxin" uniqKey="Niu J" first="Jianxin" last="Niu">Jianxin Niu</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Li, Chenjing" sort="Li, Chenjing" uniqKey="Li C" first="Chenjing" last="Li">Chenjing Li</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Cao, Fujun" sort="Cao, Fujun" uniqKey="Cao F" first="Fujun" last="Cao">Fujun Cao</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author><author><name sortKey="Quan, Shaowen" sort="Quan, Shaowen" uniqKey="Quan S" first="Shaowen" last="Quan">Shaowen Quan</name><affiliation><nlm:aff id="Aff1">Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2">Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</nlm:aff><wicri:noCountry code="subfield">832003 Xinjiang China</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (<italic>Pyrus brestschneideri</italic> Rehd). Flowers were collected at early bloom, full bloom, and late bloom. The RNA was extracted from the flowers and then combined according to calyx type. Transcriptome and digital gene expression (DGE) profiles of flowers, ovaries, and sepals with persistent calyx (SC_hua, SC_ep, and SC_zf, respectively) were compared with those of flowers, ovaries, and sepals with deciduous calyx (TL_hua, TL_ep, and TL_zf, respectively). Temporal changes in the expression of selected genes in floral organs with either persistent or deciduous calyx were compared using real-time quantitative PCR (qRT-PCR).</p></sec><sec><title>Results</title><p>Comparison of the transcriptome sequences for SC_hua and TL_hua indicated 26 differentially expressed genes (DEGs) with known relationship to abscission and 10 DEGs with unknown function. We identified 98 MYB and 21 SPL genes from the assembled unigenes. From SC_zf vs TL_zf, we identified 21 DEGs with known relationship to abscission and 18 DEGs with unknown function. From SC_ep vs TL_ep, 12 DEGs with known relationship to abscission were identified along with 11 DEGs with unknown function. Ten DEGs were identified by both transcriptome sequencing and DGE sequencing.</p></sec><sec><title>Conclusions</title><p>More than 50 DEGs were observed that were related to calyx persistence in Korla fragrant pear. Some of the genes were related to cell wall degradation, plant hormone signal transduction, and stress response. Other DEGs were identified as zinc finger protein genes and lipid transfer protein genes. Further analysis showed that calyx persistence in Korla fragment pear was a metabolic process regulated by many genes related to cell wall degradation and plant hormones.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-2470-3) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gao, Qm" uniqKey="Gao Q">QM Gao</name></author><author><name sortKey="Li, J" uniqKey="Li J">J Li</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liang, Sw" uniqKey="Liang S">SW Liang</name></author><author><name sortKey="Wang, Wl" uniqKey="Wang W">WL Wang</name></author><author><name sortKey="Zhang, Jh" uniqKey="Zhang J">JH 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<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-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26911295</article-id><article-id pub-id-type="pmc">4765163</article-id><article-id pub-id-type="publisher-id">2470</article-id><article-id pub-id-type="doi">10.1186/s12864-016-2470-3</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Identification and expression analysis of genes related to calyx persistence in Korla fragrant pear</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Pei</surname><given-names>Maosong</given-names></name><address><email>1185248506@qq.com</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Niu</surname><given-names>Jianxin</given-names></name><address><email>njx105@163.com</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Chenjing</given-names></name><address><email>1429994796@qq.com</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Cao</surname><given-names>Fujun</given-names></name><address><email>528296410@qq.com</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Quan</surname><given-names>Shaowen</given-names></name><address><email>731982806@qq.com</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><aff id="Aff1"><label></label>Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang China</aff><aff id="Aff2"><label></label>Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang China</aff></contrib-group><pub-date pub-type="epub"><day>24</day><month>2</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>24</day><month>2</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>17</volume><elocation-id>132</elocation-id><history><date date-type="received"><day>9</day><month>7</month><year>2015</year></date><date date-type="accepted"><day>12</day><month>2</month><year>2016</year></date></history><permissions><copyright-statement>© Pei et al. 2016</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold>This article is distributed under the terms of the Creative Commons Attribution 4.0 International 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 you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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>The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (<italic>Pyrus brestschneideri</italic> Rehd). Flowers were collected at early bloom, full bloom, and late bloom. The RNA was extracted from the flowers and then combined according to calyx type. Transcriptome and digital gene expression (DGE) profiles of flowers, ovaries, and sepals with persistent calyx (SC_hua, SC_ep, and SC_zf, respectively) were compared with those of flowers, ovaries, and sepals with deciduous calyx (TL_hua, TL_ep, and TL_zf, respectively). Temporal changes in the expression of selected genes in floral organs with either persistent or deciduous calyx were compared using real-time quantitative PCR (qRT-PCR).</p></sec><sec><title>Results</title><p>Comparison of the transcriptome sequences for SC_hua and TL_hua indicated 26 differentially expressed genes (DEGs) with known relationship to abscission and 10 DEGs with unknown function. We identified 98 MYB and 21 SPL genes from the assembled unigenes. From SC_zf vs TL_zf, we identified 21 DEGs with known relationship to abscission and 18 DEGs with unknown function. From SC_ep vs TL_ep, 12 DEGs with known relationship to abscission were identified along with 11 DEGs with unknown function. Ten DEGs were identified by both transcriptome sequencing and DGE sequencing.</p></sec><sec><title>Conclusions</title><p>More than 50 DEGs were observed that were related to calyx persistence in Korla fragrant pear. Some of the genes were related to cell wall degradation, plant hormone signal transduction, and stress response. Other DEGs were identified as zinc finger protein genes and lipid transfer protein genes. Further analysis showed that calyx persistence in Korla fragment pear was a metabolic process regulated by many genes related to cell wall degradation and plant hormones.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-2470-3) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Persistent calyx</kwd><kwd>Deciduous calyx</kwd><kwd>Transcriptome sequencing</kwd><kwd>DGE sequencing</kwd></kwd-group><funding-group><award-group><funding-source><institution>The National Natural Science Foundation of China</institution></funding-source><award-id>31360474</award-id><principal-award-recipient><name><surname>Niu</surname><given-names>Jianxin</given-names></name></principal-award-recipient></award-group><award-group><funding-source><institution>The Specialized Research Fund for the Doctoral Program of Higher Education</institution></funding-source><award-id>2013651810002</award-id><principal-award-recipient><name><surname>Niu</surname><given-names>Jianxin</given-names></name></principal-award-recipient></award-group><award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/http://dx.doi.org/10.13039/501100004052</institution-id><institution>King Abdullah University of Science and Technology (SA)</institution></institution-wrap></funding-source></award-group><award-group><funding-source><institution>The International Scientific and Technological Cooperation Projects</institution></funding-source><award-id>2009YD32</award-id><principal-award-recipient><name><surname>Niu</surname><given-names>Jianxin</given-names></name></principal-award-recipient></award-group></funding-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Cao, Fujun" sort="Cao, Fujun" uniqKey="Cao F" first="Fujun" last="Cao">Fujun Cao</name><name sortKey="Li, Chenjing" sort="Li, Chenjing" uniqKey="Li C" first="Chenjing" last="Li">Chenjing Li</name><name sortKey="Niu, Jianxin" sort="Niu, Jianxin" uniqKey="Niu J" first="Jianxin" last="Niu">Jianxin Niu</name><name sortKey="Pei, Maosong" sort="Pei, Maosong" uniqKey="Pei M" first="Maosong" last="Pei">Maosong Pei</name><name sortKey="Quan, Shaowen" sort="Quan, Shaowen" uniqKey="Quan S" first="Shaowen" last="Quan">Shaowen Quan</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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