De novo assembly and analysis of the transcriptome of Rumex patientia L. during cold stress
Rumex patientia L. is consumed as a green vegetable in several parts of the world, and can withstand extremely low temperatures (-35°C). However, little or no available genomic data for this species has been reported to date. Here, we used Illumina Hiseq technology for transcriptome assembly in R. p...
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| description | Rumex patientia L. is consumed as a green vegetable in several parts of the world, and can withstand extremely low temperatures (-35°C). However, little or no available genomic data for this species has been reported to date. Here, we used Illumina Hiseq technology for transcriptome assembly in R. patientia under normal and cold conditions to evaluate how it responds to cold stress.
After an in-depth RNA-Seq analysis, 115,589 unigenes were produced from the assembled transcripts. Based on similarity search analysis with seven databases, we obtained and annotated 60,157 assembled unigenes to at least one database. In total, 1,179 unigenes that were identified as differentially expressed genes (DEGs), including up-regulated (925) and down-regulated ones (254), were successfully assigned GO annotations and classified into three major metabolic pathways. Ribosome, carbon metabolism, oxidative phosphorylation and biosynthesis of amino acids were the most highly enriched pathways according to KEGG analysis. Overall, 66 up-regulated genes were identified as putatively involved in the response to cold stress, including members of MYB, AP2/ERF, CBF, Znf, bZIP, NAC and COR families.
To our knowledge, this investigation was the first to provide a cold-responsive (COR) transcriptome assembly in R. patientia. A large number of potential COR genes were identified, suggesting that this species is suitable for cultivation in northern China. In summary, these data provide valuable information for future research and genomic studies in R. patientia. |
| doi_str_mv | 10.1371/journal.pone.0186470 |
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After an in-depth RNA-Seq analysis, 115,589 unigenes were produced from the assembled transcripts. Based on similarity search analysis with seven databases, we obtained and annotated 60,157 assembled unigenes to at least one database. In total, 1,179 unigenes that were identified as differentially expressed genes (DEGs), including up-regulated (925) and down-regulated ones (254), were successfully assigned GO annotations and classified into three major metabolic pathways. Ribosome, carbon metabolism, oxidative phosphorylation and biosynthesis of amino acids were the most highly enriched pathways according to KEGG analysis. Overall, 66 up-regulated genes were identified as putatively involved in the response to cold stress, including members of MYB, AP2/ERF, CBF, Znf, bZIP, NAC and COR families.
To our knowledge, this investigation was the first to provide a cold-responsive (COR) transcriptome assembly in R. patientia. A large number of potential COR genes were identified, suggesting that this species is suitable for cultivation in northern China. In summary, these data provide valuable information for future research and genomic studies in R. patientia.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0186470</identifier><identifier>PMID: 29023590</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Acetylcysteine ; Amino acids ; Analysis ; Annotations ; Arabidopsis ; Assembly ; Biology and life sciences ; Biosynthesis ; Cerebral blood flow ; Cold ; Cold Temperature ; Cultivation ; Databases, Genetic ; Down-Regulation ; Ecology and Environmental Sciences ; Gene expression ; Genes ; Genetic engineering ; Genomics ; Life sciences ; Low temperature ; Membrane lipids ; Metabolic pathways ; Metabolism ; Oxidative metabolism ; Oxidative phosphorylation ; Pathways ; Phosphorylation ; Physical Sciences ; Physiology ; Plant biology ; Plant Proteins - classification ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Polygonaceae ; Proteins ; Real-Time Polymerase Chain Reaction ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; RNA sequencing ; RNA, Plant - chemistry ; RNA, Plant - isolation & purification ; RNA, Plant - metabolism ; Rumex - genetics ; Rumex - metabolism ; Rumex patientia ; Sequence Analysis, DNA ; Stress ; Stress, Physiological ; Stresses ; Technology application ; Transcription Factors - classification ; Transcription Factors - genetics ; Transcription Factors - metabolism ; Transcriptome ; Up-Regulation</subject><ispartof>PloS one, 2017-10, Vol.12 (10), p.e0186470-e0186470</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (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>2017 Liu et al 2017 Liu et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-8737ba8c273abfe15e7e9f5eefcdbd21ae286dfeea6bbc58e09f2c657a4b9a293</citedby><cites>FETCH-LOGICAL-c692t-8737ba8c273abfe15e7e9f5eefcdbd21ae286dfeea6bbc58e09f2c657a4b9a293</cites><orcidid>0000-0001-9612-227X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638559/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638559/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29023590$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Min, Xiang Jia</contributor><creatorcontrib>Liu, Jianxin</creatorcontrib><creatorcontrib>Xu, Yongqing</creatorcontrib><creatorcontrib>Zhang, Liguo</creatorcontrib><creatorcontrib>Li, Wei</creatorcontrib><creatorcontrib>Cai, Zhenxue</creatorcontrib><creatorcontrib>Li, Fei</creatorcontrib><creatorcontrib>Peng, Mu</creatorcontrib><creatorcontrib>Li, Fenglan</creatorcontrib><creatorcontrib>Hu, Baozhong</creatorcontrib><title>De novo assembly and analysis of the transcriptome of Rumex patientia L. during cold stress</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Rumex patientia L. is consumed as a green vegetable in several parts of the world, and can withstand extremely low temperatures (-35°C). However, little or no available genomic data for this species has been reported to date. Here, we used Illumina Hiseq technology for transcriptome assembly in R. patientia under normal and cold conditions to evaluate how it responds to cold stress.
After an in-depth RNA-Seq analysis, 115,589 unigenes were produced from the assembled transcripts. Based on similarity search analysis with seven databases, we obtained and annotated 60,157 assembled unigenes to at least one database. In total, 1,179 unigenes that were identified as differentially expressed genes (DEGs), including up-regulated (925) and down-regulated ones (254), were successfully assigned GO annotations and classified into three major metabolic pathways. Ribosome, carbon metabolism, oxidative phosphorylation and biosynthesis of amino acids were the most highly enriched pathways according to KEGG analysis. Overall, 66 up-regulated genes were identified as putatively involved in the response to cold stress, including members of MYB, AP2/ERF, CBF, Znf, bZIP, NAC and COR families.
To our knowledge, this investigation was the first to provide a cold-responsive (COR) transcriptome assembly in R. patientia. A large number of potential COR genes were identified, suggesting that this species is suitable for cultivation in northern China. In summary, these data provide valuable information for future research and genomic studies in R. patientia.</description><subject>Abiotic stress</subject><subject>Acetylcysteine</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Annotations</subject><subject>Arabidopsis</subject><subject>Assembly</subject><subject>Biology and life sciences</subject><subject>Biosynthesis</subject><subject>Cerebral blood flow</subject><subject>Cold</subject><subject>Cold Temperature</subject><subject>Cultivation</subject><subject>Databases, Genetic</subject><subject>Down-Regulation</subject><subject>Ecology and Environmental Sciences</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic engineering</subject><subject>Genomics</subject><subject>Life sciences</subject><subject>Low temperature</subject><subject>Membrane lipids</subject><subject>Metabolic pathways</subject><subject>Metabolism</subject><subject>Oxidative metabolism</subject><subject>Oxidative phosphorylation</subject><subject>Pathways</subject><subject>Phosphorylation</subject><subject>Physical Sciences</subject><subject>Physiology</subject><subject>Plant biology</subject><subject>Plant Proteins - classification</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Polygonaceae</subject><subject>Proteins</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>RNA, Plant - chemistry</subject><subject>RNA, Plant - isolation & purification</subject><subject>RNA, Plant - metabolism</subject><subject>Rumex - genetics</subject><subject>Rumex - metabolism</subject><subject>Rumex patientia</subject><subject>Sequence Analysis, DNA</subject><subject>Stress</subject><subject>Stress, Physiological</subject><subject>Stresses</subject><subject>Technology application</subject><subject>Transcription Factors - classification</subject><subject>Transcription Factors - genetics</subject><subject>Transcription Factors - metabolism</subject><subject>Transcriptome</subject><subject>Up-Regulation</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</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>eNqNk0tr3DAQx01padK036C0hkJpD7vVw7KtSyGkr4WFQPq49CBkebSrRba2khyy375ydhPWJYcihMToN__RjDRZ9hKjOaYV_rBxg--lnW9dD3OE67Ko0KPsFHNKZiVB9PHR_iR7FsIGIUbrsnyanRCOCGUcnWa_P0Heu2uXyxCga-wul32bprS7YELudB7XkEcv-6C82UbXwWi8Gjq4ybcyGuijkflynreDN_0qV862eYgeQniePdHSBnhxWM-yn18-_7j4Nltefl1cnC9nquQkzuqKVo2sFamobDRgBhVwzQC0apuWYAmkLlsNIMumUawGxDVRJatk0XBJOD3LXu91t9YFcahLEJgzVKCqKqpELPZE6-RGbL3ppN8JJ424NTi_EtJHoyyIVlOOKC8KJuuCYNxoxYGhhreKoxrGaB8P0Yamg1alAnhpJ6LTk96sxcpdC1bSmrFR4N1BwLs_A4QoOhMUWCt7cMPtvVmJCGZFQt_8gz6c3YFayZSA6bVLcdUoKs4Z4oRxXtJEzR-g0mihMyp9Im2SfeLwfuKQmAg3cSWHEMTi-9X_s5e_puzbI3YN0sZ1cHaIxvVhChZ7UHkXggd9X2SMxNgDd9UQYw-IQw8kt1fHD3TvdPfp6V8eygKN</recordid><startdate>20171012</startdate><enddate>20171012</enddate><creator>Liu, 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novo assembly and analysis of the transcriptome of Rumex patientia L. during cold stress</title><author>Liu, Jianxin ; Xu, Yongqing ; Zhang, Liguo ; Li, Wei ; Cai, Zhenxue ; Li, Fei ; Peng, Mu ; Li, Fenglan ; Hu, Baozhong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-8737ba8c273abfe15e7e9f5eefcdbd21ae286dfeea6bbc58e09f2c657a4b9a293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Abiotic stress</topic><topic>Acetylcysteine</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Annotations</topic><topic>Arabidopsis</topic><topic>Assembly</topic><topic>Biology and life sciences</topic><topic>Biosynthesis</topic><topic>Cerebral blood flow</topic><topic>Cold</topic><topic>Cold Temperature</topic><topic>Cultivation</topic><topic>Databases, Genetic</topic><topic>Down-Regulation</topic><topic>Ecology and Environmental Sciences</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genetic engineering</topic><topic>Genomics</topic><topic>Life sciences</topic><topic>Low temperature</topic><topic>Membrane lipids</topic><topic>Metabolic pathways</topic><topic>Metabolism</topic><topic>Oxidative metabolism</topic><topic>Oxidative phosphorylation</topic><topic>Pathways</topic><topic>Phosphorylation</topic><topic>Physical Sciences</topic><topic>Physiology</topic><topic>Plant biology</topic><topic>Plant Proteins - classification</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Polygonaceae</topic><topic>Proteins</topic><topic>Real-Time Polymerase Chain Reaction</topic><topic>Research and Analysis Methods</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA sequencing</topic><topic>RNA, Plant - chemistry</topic><topic>RNA, Plant - isolation & purification</topic><topic>RNA, Plant - metabolism</topic><topic>Rumex - genetics</topic><topic>Rumex - 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stress</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-10-12</date><risdate>2017</risdate><volume>12</volume><issue>10</issue><spage>e0186470</spage><epage>e0186470</epage><pages>e0186470-e0186470</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Rumex patientia L. is consumed as a green vegetable in several parts of the world, and can withstand extremely low temperatures (-35°C). However, little or no available genomic data for this species has been reported to date. Here, we used Illumina Hiseq technology for transcriptome assembly in R. patientia under normal and cold conditions to evaluate how it responds to cold stress.
After an in-depth RNA-Seq analysis, 115,589 unigenes were produced from the assembled transcripts. Based on similarity search analysis with seven databases, we obtained and annotated 60,157 assembled unigenes to at least one database. In total, 1,179 unigenes that were identified as differentially expressed genes (DEGs), including up-regulated (925) and down-regulated ones (254), were successfully assigned GO annotations and classified into three major metabolic pathways. Ribosome, carbon metabolism, oxidative phosphorylation and biosynthesis of amino acids were the most highly enriched pathways according to KEGG analysis. Overall, 66 up-regulated genes were identified as putatively involved in the response to cold stress, including members of MYB, AP2/ERF, CBF, Znf, bZIP, NAC and COR families.
To our knowledge, this investigation was the first to provide a cold-responsive (COR) transcriptome assembly in R. patientia. A large number of potential COR genes were identified, suggesting that this species is suitable for cultivation in northern China. In summary, these data provide valuable information for future research and genomic studies in R. patientia.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29023590</pmid><doi>10.1371/journal.pone.0186470</doi><tpages>e0186470</tpages><orcidid>https://orcid.org/0000-0001-9612-227X</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | PloS one, 2017-10, Vol.12 (10), p.e0186470-e0186470 |
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| source | PubMed Central Free; MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Acetylcysteine Amino acids Analysis Annotations Arabidopsis Assembly Biology and life sciences Biosynthesis Cerebral blood flow Cold Cold Temperature Cultivation Databases, Genetic Down-Regulation Ecology and Environmental Sciences Gene expression Genes Genetic engineering Genomics Life sciences Low temperature Membrane lipids Metabolic pathways Metabolism Oxidative metabolism Oxidative phosphorylation Pathways Phosphorylation Physical Sciences Physiology Plant biology Plant Proteins - classification Plant Proteins - genetics Plant Proteins - metabolism Polygonaceae Proteins Real-Time Polymerase Chain Reaction Research and Analysis Methods Ribonucleic acid RNA RNA sequencing RNA, Plant - chemistry RNA, Plant - isolation & purification RNA, Plant - metabolism Rumex - genetics Rumex - metabolism Rumex patientia Sequence Analysis, DNA Stress Stress, Physiological Stresses Technology application Transcription Factors - classification Transcription Factors - genetics Transcription Factors - metabolism Transcriptome Up-Regulation |
| title | De novo assembly and analysis of the transcriptome of Rumex patientia L. during cold stress |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T01%3A07%3A46IST&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=De%20novo%20assembly%20and%20analysis%20of%20the%20transcriptome%20of%20Rumex%20patientia%20L.%20during%20cold%20stress&rft.jtitle=PloS%20one&rft.au=Liu,%20Jianxin&rft.date=2017-10-12&rft.volume=12&rft.issue=10&rft.spage=e0186470&rft.epage=e0186470&rft.pages=e0186470-e0186470&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0186470&rft_dat=%3Cgale_plos_%3EA509259963%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=1950407747&rft_id=info:pmid/29023590&rft_galeid=A509259963&rft_doaj_id=oai_doaj_org_article_df39039445a84211bfc9e50b9dc908e9&rfr_iscdi=true |