Gene Expression Analysis of Pak Choi in Response to Vernalization
Pak choi is a seed vernalization-type plant whose vernalization mechanism is currently unclear. Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after l...
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| description | Pak choi is a seed vernalization-type plant whose vernalization mechanism is currently unclear. Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after low temperature treatment using high-throughput RNA sequencing technology. The results showed that there are 1,664 and 1,192 differentially expressed genes (DEGs) in pak choi in cold treatment ending and before flower bud differentiation, respectively, including 42 genes that exhibited similar expression trend at both stages. Detailed annotation revealed that the proteins encoded by the DEGs are located in the extracellular region, cell junction and extracellular matrix. These proteins exhibit activity such as antioxidant activity and binding protein/transcription factor activity, and they are involved in signal transduction and the immune system/biological processes. Among the DEGs, Bra014527 was up-regulated in low temperature treatment ending, Bra024097 was up-regulated before flower bud differentiation and Bra035940 was down-regulated at both stages in low temperature-treated shoot apices. Homologues of these genes in A. thaliana, AT3G59790, AT4G30200 and AT5G61150, are involved in flowering and vernalization, suggesting that they take part in the vernalization process in pak choi. Further pathway enrichment analysis revealed that most genes were enriched in the tryptophan metabolism and glucosinolate biosynthesis pathways. However, the functions of tryptophan and glucosinolate in vernalization are not yet clear and require further analysis. |
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Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after low temperature treatment using high-throughput RNA sequencing technology. The results showed that there are 1,664 and 1,192 differentially expressed genes (DEGs) in pak choi in cold treatment ending and before flower bud differentiation, respectively, including 42 genes that exhibited similar expression trend at both stages. Detailed annotation revealed that the proteins encoded by the DEGs are located in the extracellular region, cell junction and extracellular matrix. These proteins exhibit activity such as antioxidant activity and binding protein/transcription factor activity, and they are involved in signal transduction and the immune system/biological processes. Among the DEGs, Bra014527 was up-regulated in low temperature treatment ending, Bra024097 was up-regulated before flower bud differentiation and Bra035940 was down-regulated at both stages in low temperature-treated shoot apices. Homologues of these genes in A. thaliana, AT3G59790, AT4G30200 and AT5G61150, are involved in flowering and vernalization, suggesting that they take part in the vernalization process in pak choi. Further pathway enrichment analysis revealed that most genes were enriched in the tryptophan metabolism and glucosinolate biosynthesis pathways. However, the functions of tryptophan and glucosinolate in vernalization are not yet clear and require further analysis.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0141446</identifier><identifier>PMID: 26517271</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Annotations ; Antioxidants ; Arabidopsis - genetics ; Arabidopsis - growth & development ; Arabidopsis thaliana ; Biological activity ; Biosynthesis ; Brassica oleracea ; Brassica rapa - genetics ; Brassica rapa - growth & development ; Brassica rapa chinensis ; Carbohydrate Metabolism - genetics ; Cellular signal transduction ; Cold Temperature ; Cold treatment ; Differentiation ; DNA, Complementary - genetics ; DNA, Plant - genetics ; Extracellular matrix ; Flowering ; Flowers & plants ; Flowers - growth & development ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Library ; Gene sequencing ; Genes ; Genes, Plant ; Genetic aspects ; Genomes ; Glucosinolates - metabolism ; High-Throughput Nucleotide Sequencing ; Homology ; Horticulture ; Immune system ; Kinases ; Low temperature ; Metabolic Networks and Pathways - genetics ; Metabolism ; Molecular Sequence Annotation ; Physiology ; Plant growth ; Plant Growth Regulators - metabolism ; Plant Shoots - growth & development ; Plant Shoots - metabolism ; Proteins ; Real-Time Polymerase Chain Reaction ; Ribonucleic acid ; RNA ; RNA sequencing ; RNA, Messenger - biosynthesis ; RNA, Messenger - genetics ; Science ; Seeds ; Signal processing ; Species Specificity ; Studies ; Temperature ; Temperature effects ; Transduction ; Tryptophan ; Tryptophan - metabolism ; Vernalization</subject><ispartof>PloS one, 2015-10, Vol.10 (10), p.e0141446</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Sun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Sun et al 2015 Sun et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-f34f27ff3ab75443f684c85c7f542f2a901992ae9e3dc58aff002ee95bc952343</citedby><cites>FETCH-LOGICAL-c758t-f34f27ff3ab75443f684c85c7f542f2a901992ae9e3dc58aff002ee95bc952343</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627790/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627790/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23868,27926,27927,53793,53795</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26517271$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Fu, Binying</contributor><creatorcontrib>Sun, Mengxia</creatorcontrib><creatorcontrib>Qi, Xianhui</creatorcontrib><creatorcontrib>Hou, Leiping</creatorcontrib><creatorcontrib>Xu, Xiaoyong</creatorcontrib><creatorcontrib>Zhu, Zhujun</creatorcontrib><creatorcontrib>Li, Meilan</creatorcontrib><title>Gene Expression Analysis of Pak Choi in Response to Vernalization</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Pak choi is a seed vernalization-type plant whose vernalization mechanism is currently unclear. Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after low temperature treatment using high-throughput RNA sequencing technology. The results showed that there are 1,664 and 1,192 differentially expressed genes (DEGs) in pak choi in cold treatment ending and before flower bud differentiation, respectively, including 42 genes that exhibited similar expression trend at both stages. Detailed annotation revealed that the proteins encoded by the DEGs are located in the extracellular region, cell junction and extracellular matrix. These proteins exhibit activity such as antioxidant activity and binding protein/transcription factor activity, and they are involved in signal transduction and the immune system/biological processes. Among the DEGs, Bra014527 was up-regulated in low temperature treatment ending, Bra024097 was up-regulated before flower bud differentiation and Bra035940 was down-regulated at both stages in low temperature-treated shoot apices. Homologues of these genes in A. thaliana, AT3G59790, AT4G30200 and AT5G61150, are involved in flowering and vernalization, suggesting that they take part in the vernalization process in pak choi. Further pathway enrichment analysis revealed that most genes were enriched in the tryptophan metabolism and glucosinolate biosynthesis pathways. However, the functions of tryptophan and glucosinolate in vernalization are not yet clear and require further analysis.</description><subject>Analysis</subject><subject>Annotations</subject><subject>Antioxidants</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis - growth & development</subject><subject>Arabidopsis thaliana</subject><subject>Biological activity</subject><subject>Biosynthesis</subject><subject>Brassica oleracea</subject><subject>Brassica rapa - genetics</subject><subject>Brassica rapa - growth & development</subject><subject>Brassica rapa chinensis</subject><subject>Carbohydrate Metabolism - genetics</subject><subject>Cellular signal transduction</subject><subject>Cold Temperature</subject><subject>Cold treatment</subject><subject>Differentiation</subject><subject>DNA, Complementary - genetics</subject><subject>DNA, Plant - genetics</subject><subject>Extracellular matrix</subject><subject>Flowering</subject><subject>Flowers & plants</subject><subject>Flowers - growth & development</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene Library</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Glucosinolates - metabolism</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Homology</subject><subject>Horticulture</subject><subject>Immune system</subject><subject>Kinases</subject><subject>Low temperature</subject><subject>Metabolic Networks and Pathways - genetics</subject><subject>Metabolism</subject><subject>Molecular Sequence Annotation</subject><subject>Physiology</subject><subject>Plant growth</subject><subject>Plant Growth Regulators - metabolism</subject><subject>Plant Shoots - growth & development</subject><subject>Plant Shoots - metabolism</subject><subject>Proteins</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>RNA, Messenger - biosynthesis</subject><subject>RNA, Messenger - genetics</subject><subject>Science</subject><subject>Seeds</subject><subject>Signal processing</subject><subject>Species Specificity</subject><subject>Studies</subject><subject>Temperature</subject><subject>Temperature effects</subject><subject>Transduction</subject><subject>Tryptophan</subject><subject>Tryptophan - metabolism</subject><subject>Vernalization</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl9v0zAUxSMEYmPwDRBEQkLw0OL_Tl6QqmqMSpOGBuzVcpzr1iWNOztBG58ed82mBu0B-cGW_Tvn-tony15jNMVU4k9r34dWN9Otb2GKMMOMiSfZMS4pmQiC6NOD9VH2IsY1QpwWQjzPjojgWBKJj7PZGbSQn95sA8TofJvPkudtdDH3Nv-mf-XzlXe5a_NLiKlShLzz-RXsKrs_ukuKl9kzq5sIr4b5JPv55fTH_Ovk_OJsMZ-dT4zkRTexlFkiraW6kpwxakXBTMGNtJwRS3SJcFkSDSXQ2vBCW4sQASh5ZUpOKKMn2du977bxUQ3dR5X6KBhCiOFELPZE7fVabYPb6HCrvHbqbsOHpdKhc6YBVTBuqWSi0iCYEEhbXleVQDVYUdPCJK_PQ7W-2kBtoO2Cbkam45PWrdTS_1ZMEClLlAw-DAbBX_cQO7Vx0UDT6BZ8f3fvknJEC5LQd_-gj3c3UEudGnCt9amu2ZmqGaMUC4mkSNT0ESqNGjbOpKhYl_ZHgo8jQWI6uOmWuo9RLb5f_j97cTVm3x-wK9BNt4q-6XeRiWOQ7UETfIwB7MMjY6R2Sb9_DbVLuhqSnmRvDj_oQXQfbfoXlIn3JQ</recordid><startdate>20151030</startdate><enddate>20151030</enddate><creator>Sun, Mengxia</creator><creator>Qi, Xianhui</creator><creator>Hou, Leiping</creator><creator>Xu, Xiaoyong</creator><creator>Zhu, Zhujun</creator><creator>Li, Meilan</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20151030</creationdate><title>Gene Expression Analysis of Pak Choi in Response to Vernalization</title><author>Sun, Mengxia ; Qi, Xianhui ; Hou, Leiping ; Xu, Xiaoyong ; Zhu, Zhujun ; Li, Meilan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-f34f27ff3ab75443f684c85c7f542f2a901992ae9e3dc58aff002ee95bc952343</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Analysis</topic><topic>Annotations</topic><topic>Antioxidants</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis - growth & development</topic><topic>Arabidopsis thaliana</topic><topic>Biological activity</topic><topic>Biosynthesis</topic><topic>Brassica oleracea</topic><topic>Brassica rapa - genetics</topic><topic>Brassica rapa - growth & development</topic><topic>Brassica rapa chinensis</topic><topic>Carbohydrate Metabolism - genetics</topic><topic>Cellular signal transduction</topic><topic>Cold Temperature</topic><topic>Cold treatment</topic><topic>Differentiation</topic><topic>DNA, Complementary - genetics</topic><topic>DNA, Plant - genetics</topic><topic>Extracellular matrix</topic><topic>Flowering</topic><topic>Flowers & plants</topic><topic>Flowers - growth & development</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene Library</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Glucosinolates - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sun, Mengxia</au><au>Qi, Xianhui</au><au>Hou, Leiping</au><au>Xu, Xiaoyong</au><au>Zhu, Zhujun</au><au>Li, Meilan</au><au>Fu, Binying</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Gene Expression Analysis of Pak Choi in Response to Vernalization</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-10-30</date><risdate>2015</risdate><volume>10</volume><issue>10</issue><spage>e0141446</spage><pages>e0141446-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Pak choi is a seed vernalization-type plant whose vernalization mechanism is currently unclear. Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after low temperature treatment using high-throughput RNA sequencing technology. The results showed that there are 1,664 and 1,192 differentially expressed genes (DEGs) in pak choi in cold treatment ending and before flower bud differentiation, respectively, including 42 genes that exhibited similar expression trend at both stages. Detailed annotation revealed that the proteins encoded by the DEGs are located in the extracellular region, cell junction and extracellular matrix. These proteins exhibit activity such as antioxidant activity and binding protein/transcription factor activity, and they are involved in signal transduction and the immune system/biological processes. Among the DEGs, Bra014527 was up-regulated in low temperature treatment ending, Bra024097 was up-regulated before flower bud differentiation and Bra035940 was down-regulated at both stages in low temperature-treated shoot apices. Homologues of these genes in A. thaliana, AT3G59790, AT4G30200 and AT5G61150, are involved in flowering and vernalization, suggesting that they take part in the vernalization process in pak choi. Further pathway enrichment analysis revealed that most genes were enriched in the tryptophan metabolism and glucosinolate biosynthesis pathways. However, the functions of tryptophan and glucosinolate in vernalization are not yet clear and require further analysis.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26517271</pmid><doi>10.1371/journal.pone.0141446</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Annotations Antioxidants Arabidopsis - genetics Arabidopsis - growth & development Arabidopsis thaliana Biological activity Biosynthesis Brassica oleracea Brassica rapa - genetics Brassica rapa - growth & development Brassica rapa chinensis Carbohydrate Metabolism - genetics Cellular signal transduction Cold Temperature Cold treatment Differentiation DNA, Complementary - genetics DNA, Plant - genetics Extracellular matrix Flowering Flowers & plants Flowers - growth & development Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Gene Library Gene sequencing Genes Genes, Plant Genetic aspects Genomes Glucosinolates - metabolism High-Throughput Nucleotide Sequencing Homology Horticulture Immune system Kinases Low temperature Metabolic Networks and Pathways - genetics Metabolism Molecular Sequence Annotation Physiology Plant growth Plant Growth Regulators - metabolism Plant Shoots - growth & development Plant Shoots - metabolism Proteins Real-Time Polymerase Chain Reaction Ribonucleic acid RNA RNA sequencing RNA, Messenger - biosynthesis RNA, Messenger - genetics Science Seeds Signal processing Species Specificity Studies Temperature Temperature effects Transduction Tryptophan Tryptophan - metabolism Vernalization |
| title | Gene Expression Analysis of Pak Choi in Response to Vernalization |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-17T18%3A19%3A05IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Gene%20Expression%20Analysis%20of%20Pak%20Choi%20in%20Response%20to%20Vernalization&rft.jtitle=PloS%20one&rft.au=Sun,%20Mengxia&rft.date=2015-10-30&rft.volume=10&rft.issue=10&rft.spage=e0141446&rft.pages=e0141446-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0141446&rft_dat=%3Cgale_plos_%3EA433167076%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1728400041&rft_id=info:pmid/26517271&rft_galeid=A433167076&rft_doaj_id=oai_doaj_org_article_845f3746bae64660af5dbb60def6d38c&rfr_iscdi=true |