Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress
A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgras...
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| description | A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research. |
| doi_str_mv | 10.1371/journal.pone.0131153 |
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Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0131153</identifier><identifier>PMID: 26115186</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Abscisic acid ; Acclimatization - genetics ; Arabidopsis ; Ascorbic acid ; Ascorbic acid metabolism ; Biosynthesis ; Breeding ; Cold ; Cold Temperature ; Cold treatment ; Cultivars ; Desiccation ; DNA sequencing ; Drying ; Environmental science ; Enzymes ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes ; Genes, Plant ; Genomes ; Genomics ; High-Throughput Nucleotide Sequencing ; Kinases ; Metabolism ; Methionine ; Molecular Sequence Annotation ; Oxidative stress ; Photosynthesis ; Physiology ; Poaceae - genetics ; Poaceae - physiology ; Proline ; Proteins ; Ribonucleic acid ; RNA ; Signal transduction ; Starch ; Stress, Physiological - genetics ; Superoxide dismutase ; Temperate zones ; Transcriptome ; Variance analysis ; Zoysia</subject><ispartof>PloS one, 2015-06, Vol.10 (6), p.e0131153-e0131153</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Wei 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 Wei et al 2015 Wei et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-7272ae010c9f48bac3995a5f889ad74e8cca5cd1328d5012aab890c5f6c89b313</citedby><cites>FETCH-LOGICAL-c758t-7272ae010c9f48bac3995a5f889ad74e8cca5cd1328d5012aab890c5f6c89b313</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/PMC4482698/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482698/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,729,782,786,866,887,2104,2930,23873,27931,27932,53798,53800</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26115186$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Chen, Zhong-Hua</contributor><creatorcontrib>Wei, Shanjun</creatorcontrib><creatorcontrib>Du, Zhenlin</creatorcontrib><creatorcontrib>Gao, Fei</creatorcontrib><creatorcontrib>Ke, Xiang</creatorcontrib><creatorcontrib>Li, Jing</creatorcontrib><creatorcontrib>Liu, Jianxiu</creatorcontrib><creatorcontrib>Zhou, Yijun</creatorcontrib><title>Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.</description><subject>Abiotic stress</subject><subject>Abscisic acid</subject><subject>Acclimatization - genetics</subject><subject>Arabidopsis</subject><subject>Ascorbic acid</subject><subject>Ascorbic acid metabolism</subject><subject>Biosynthesis</subject><subject>Breeding</subject><subject>Cold</subject><subject>Cold Temperature</subject><subject>Cold treatment</subject><subject>Cultivars</subject><subject>Desiccation</subject><subject>DNA sequencing</subject><subject>Drying</subject><subject>Environmental science</subject><subject>Enzymes</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genomes</subject><subject>Genomics</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Kinases</subject><subject>Metabolism</subject><subject>Methionine</subject><subject>Molecular Sequence Annotation</subject><subject>Oxidative stress</subject><subject>Photosynthesis</subject><subject>Physiology</subject><subject>Poaceae - genetics</subject><subject>Poaceae - physiology</subject><subject>Proline</subject><subject>Proteins</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Signal transduction</subject><subject>Starch</subject><subject>Stress, Physiological - genetics</subject><subject>Superoxide dismutase</subject><subject>Temperate zones</subject><subject>Transcriptome</subject><subject>Variance analysis</subject><subject>Zoysia</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>eNqNkl1v0zAUhiMEYh_wDxBEQmJw0WLH-bBvkKYKRqWhom1wwY114py0rty42MlE_z3Omk0N2gXyhS37Oe_58BtFryiZUlbQj2vbuQbMdGsbnBLKKM3Yk-iYCpZM8oSwpwfno-jE-zUhGeN5_jw6SvJAU54fR4sLY0sw8Y2Dxiunt63dYPzd2Vob9LGt47NvuEN3Fv-yO69h6cD7WDfxFfqQ2WPc2nhmTRVftw69fxE9q8F4fDnsp9GPL59vZl8nl4uL-ez8cqKKjLeTIikSQEKJEnXKS1BMiAyymnMBVZEiVwoyVVGW8CojNAEouSAqq3PFRckoO43e7HW3xno5zMJLmguaEl4UPTHfE5WFtdw6vQG3kxa0vLuwbinBtVoZlKLOKTCBvAzV1JSWWNK8VJxWnIkaedD6NGTryg1WCpvWgRmJjl8avZJLeyvTlCe56AXeDwLO_u7Qt3KjvUJjoEHb3dWdJIJlggX07T_o490N1BJCA7qpbcirelF5nlKRkZwWIlDTR6iwKtxoFYzT__I44MMoIDAt_mmX0Hkv59dX_88ufo7ZdwfsCsG0K29N1-rgoTGY7kHlrPcO64chUyJ7399PQ_a-l4PvQ9jrww96CLo3OvsLDtv8tA</recordid><startdate>20150626</startdate><enddate>20150626</enddate><creator>Wei, Shanjun</creator><creator>Du, Zhenlin</creator><creator>Gao, Fei</creator><creator>Ke, Xiang</creator><creator>Li, Jing</creator><creator>Liu, Jianxiu</creator><creator>Zhou, Yijun</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>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150626</creationdate><title>Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress</title><author>Wei, Shanjun ; Du, Zhenlin ; Gao, Fei ; Ke, Xiang ; Li, Jing ; Liu, Jianxiu ; Zhou, Yijun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-7272ae010c9f48bac3995a5f889ad74e8cca5cd1328d5012aab890c5f6c89b313</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Abiotic stress</topic><topic>Abscisic acid</topic><topic>Acclimatization - 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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>Wei, Shanjun</au><au>Du, Zhenlin</au><au>Gao, Fei</au><au>Ke, Xiang</au><au>Li, Jing</au><au>Liu, Jianxiu</au><au>Zhou, Yijun</au><au>Chen, Zhong-Hua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-06-26</date><risdate>2015</risdate><volume>10</volume><issue>6</issue><spage>e0131153</spage><epage>e0131153</epage><pages>e0131153-e0131153</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>A long green period is essential for a turfgrass species with high ornamental value and a wide area of use. Zoysiagrasses (Zoysia spp. Willd.) are perennial turfgrass species popular in tropical, subtropical and temperate zones, possessing many properties necessary to be economically useful turfgrass. They do not have a long green period because of cold sensitivity. A main focus in zoysiagrass research is to develop cold tolerant cultivars. Understanding the cold response in zoysiagrass is a fundamental area of research. In the present study, 'Meyer' zoysiagrass (Zoysia japonica), a widely cultivated variety in the genus, is used. We employed RNA-Seq to investigate genome-wide gene expression profiles in leaves under cold stress (4°C). Using the Illumina sequencing platform, we obtained approximately 206 million high-quality paired-end reads from three libraries (0 h, 2 h, and 72 h cold treatment at 4°C). After de novo assembly and quantitative assessment, 46,412 unigenes were generated with an average length of 998 bp and an N50 of 1,522 bp. A total of 25,644 (55.2%) unigenes were annotated by alignment with public protein databases including NR, SwissProt, KEGG and KOG. Differentially expressed genes (DEGs) were investigated using the RPKM method. A total of 756 DEGs were identified between 0 h and 2 h-cold treatment, with 522 up-regulated and 234 down-regulated; and 5327 DEGs were identified between 0 h and 72 h-cold treatment, with 2453 up-regulated and 2874 down-regulated. The expression profile of 15 DEGs selected randomly was confirmed with qRT-PCR. The results suggest that cold stress can induce desiccation and oxidative stress, inhibit photosynthesis and substance transport. In response to the stress, genes involved in proline synthesis, in starch hydrolysis, in methionine and ascorbic acid metabolism, in SOD activity, and in DREBs response pathway were up-regulated. GA metabolism, ABA and JA stimulus response were affected under cold exposure. This is the first transcriptome sequencing of Z. japonica, providing a large set of sequence data as well as gene expression profiles under cold stress. It will improve our current understanding of the cold response of zoysiagrass and be beneficial in breeding research.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26115186</pmid><doi>10.1371/journal.pone.0131153</doi><oa>free_for_read</oa></addata></record> |
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| recordid | cdi_plos_journals_1691408771 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS) Journals Open Access; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Abscisic acid Acclimatization - genetics Arabidopsis Ascorbic acid Ascorbic acid metabolism Biosynthesis Breeding Cold Cold Temperature Cold treatment Cultivars Desiccation DNA sequencing Drying Environmental science Enzymes Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Genes Genes, Plant Genomes Genomics High-Throughput Nucleotide Sequencing Kinases Metabolism Methionine Molecular Sequence Annotation Oxidative stress Photosynthesis Physiology Poaceae - genetics Poaceae - physiology Proline Proteins Ribonucleic acid RNA Signal transduction Starch Stress, Physiological - genetics Superoxide dismutase Temperate zones Transcriptome Variance analysis Zoysia |
| title | Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-09T17%3A20%3A23IST&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=Global%20Transcriptome%20Profiles%20of%20'Meyer'%20Zoysiagrass%20in%20Response%20to%20Cold%20Stress&rft.jtitle=PloS%20one&rft.au=Wei,%20Shanjun&rft.date=2015-06-26&rft.volume=10&rft.issue=6&rft.spage=e0131153&rft.epage=e0131153&rft.pages=e0131153-e0131153&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0131153&rft_dat=%3Cgale_plos_%3EA419506179%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=1691408771&rft_id=info:pmid/26115186&rft_galeid=A419506179&rft_doaj_id=oai_doaj_org_article_9f61a39e8b9f4f11beb16bc81d839fe8&rfr_iscdi=true |