Transcriptomic analysis reveals differential gene expressions for cell growth and functional secondary metabolites in induced autotetraploid of Chinese woad (Isatis indigotica Fort.)
The giant organs and enhanced concentrations of secondary metabolites realized by autopolyploidy are attractive for breeding the respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is n...
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| Veröffentlicht in: | PloS one 2015-03, Vol.10 (3), p.e0116392-e0116392 |
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| description | The giant organs and enhanced concentrations of secondary metabolites realized by autopolyploidy are attractive for breeding the respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x) were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents) and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53%) unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%)(2x vs 4x), 693(0.98%)(2x vs 3x), 1045(1.48%)(3x vs 4x) unigenes were detected to differentially expressed genes (DEGs), including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin), cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites. |
| doi_str_mv | 10.1371/journal.pone.0116392 |
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The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x) were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents) and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53%) unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%)(2x vs 4x), 693(0.98%)(2x vs 3x), 1045(1.48%)(3x vs 4x) unigenes were detected to differentially expressed genes (DEGs), including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin), cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0116392</identifier><identifier>PMID: 25739089</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Autopolyploidy ; Autotetraploid ; Bacteria ; Biosynthesis ; Brassicaceae ; Breeding ; Cell growth ; Cell Proliferation ; Cell walls ; Chromosomes ; Crops ; Deoxyribonucleic acid ; DNA ; DNA methylation ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Gene sequencing ; Genes, Plant ; Genetic aspects ; Genomes ; Genomics ; Isatis - cytology ; Isatis - genetics ; Isatis - metabolism ; Isatis indigotica ; Kinases ; Medicinal plants ; Meiosis ; Metabolic pathways ; Metabolites ; Molecular Sequence Annotation ; Morphology ; Organs ; Pectin ; Phenotypes ; Photosynthesis ; Photosynthesis - genetics ; Plant breeding ; Plant metabolites ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Plant sciences ; Plants (botany) ; Polyploidy ; Progeny ; Ribonucleic acid ; RNA ; Secondary Metabolism ; Secondary metabolites ; Transcriptome ; Viruses</subject><ispartof>PloS one, 2015-03, Vol.10 (3), p.e0116392-e0116392</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Zhou 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 Zhou et al 2015 Zhou et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-2a905129ee058c9b7bcfedd0cecad5e1da11a8584b19828b7fadf3f583e09da53</citedby><cites>FETCH-LOGICAL-c692t-2a905129ee058c9b7bcfedd0cecad5e1da11a8584b19828b7fadf3f583e09da53</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/PMC4349453/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349453/$$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/25739089$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Zhang, Jin-Song</contributor><creatorcontrib>Zhou, Yingying</creatorcontrib><creatorcontrib>Kang, Lei</creatorcontrib><creatorcontrib>Liao, Shiying</creatorcontrib><creatorcontrib>Pan, Qi</creatorcontrib><creatorcontrib>Ge, Xianhong</creatorcontrib><creatorcontrib>Li, Zaiyun</creatorcontrib><title>Transcriptomic analysis reveals differential gene expressions for cell growth and functional secondary metabolites in induced autotetraploid of Chinese woad (Isatis indigotica Fort.)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The giant organs and enhanced concentrations of secondary metabolites realized by autopolyploidy are attractive for breeding the respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x) were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents) and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53%) unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%)(2x vs 4x), 693(0.98%)(2x vs 3x), 1045(1.48%)(3x vs 4x) unigenes were detected to differentially expressed genes (DEGs), including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin), cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites.</description><subject>Autopolyploidy</subject><subject>Autotetraploid</subject><subject>Bacteria</subject><subject>Biosynthesis</subject><subject>Brassicaceae</subject><subject>Breeding</subject><subject>Cell growth</subject><subject>Cell Proliferation</subject><subject>Cell walls</subject><subject>Chromosomes</subject><subject>Crops</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA methylation</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation</subject><subject>Gene Ontology</subject><subject>Gene sequencing</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Isatis - cytology</subject><subject>Isatis - genetics</subject><subject>Isatis - metabolism</subject><subject>Isatis indigotica</subject><subject>Kinases</subject><subject>Medicinal plants</subject><subject>Meiosis</subject><subject>Metabolic pathways</subject><subject>Metabolites</subject><subject>Molecular Sequence Annotation</subject><subject>Morphology</subject><subject>Organs</subject><subject>Pectin</subject><subject>Phenotypes</subject><subject>Photosynthesis</subject><subject>Photosynthesis - genetics</subject><subject>Plant breeding</subject><subject>Plant metabolites</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Plant sciences</subject><subject>Plants (botany)</subject><subject>Polyploidy</subject><subject>Progeny</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Secondary Metabolism</subject><subject>Secondary metabolites</subject><subject>Transcriptome</subject><subject>Viruses</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>eNqNk99qFDEUxgdRbK2-gWhAkPZi12QyyUxuhFKsLhQKWr0NmeRkN2U2WZNM_7yYz2e23ZZd6YXMwAzJ7_tyzsk5VfWW4CmhLfl0Gcbo1TBdBQ9TTAinon5W7RNB6wmvMX2-9b9XvUrpEmNGO85fVns1a6nAndiv_lxE5ZOObpXD0mmkiuVtcglFuAI1JGSctRDBZ6cGNAcPCG5WEVJywSdkQ0QahrITw3VeFLlBdvQ6l93CJ9DBGxVv0RKy6sPgMiTkfHnNqMEgNeaQIUe1GoIzKFh0snAeEqDroAw6nCWV3Vph3DxkpxU6DTFPj15XL2yJDt5svgfVz9MvFyffJmfnX2cnx2cTzUWdJ7USmJFaAGDWadG3vbZgDNaglWFAjCJEdaxreiK6uutbq4yllnUUsDCK0YPq_b1viS_JTcmTJJxj3rSU8ULM7gkT1KVcRbcs6cqgnLxbCHEuVSyRDyBbLVjPCG9bbhpocYmts1TrniveatMVr8-b08Z-CUaXqkc17Jju7ni3kPNwJRvaiIbRYnC4MYjh9wgpy6VL6_tRHsJ4FzehdctYU9AP_6BPZ7eh5qok4LwN5Vy9NpXHTS26jjcdLtT0Cao8BkpPlf60rqzvCI52BIXJcJPnakxJzn58_3_2_Ncu-3GLXZQGzosUhnHdjmkXbO5BHUNKEexjkQmW6_F6qIZcj5fcjFeRvdu-oEfRwzzRvzw1JZM</recordid><startdate>20150304</startdate><enddate>20150304</enddate><creator>Zhou, 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analysis reveals differential gene expressions for cell growth and functional secondary metabolites in induced autotetraploid of Chinese woad (Isatis indigotica Fort.)</title><author>Zhou, Yingying ; Kang, Lei ; Liao, Shiying ; Pan, Qi ; Ge, Xianhong ; Li, Zaiyun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-2a905129ee058c9b7bcfedd0cecad5e1da11a8584b19828b7fadf3f583e09da53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Autopolyploidy</topic><topic>Autotetraploid</topic><topic>Bacteria</topic><topic>Biosynthesis</topic><topic>Brassicaceae</topic><topic>Breeding</topic><topic>Cell growth</topic><topic>Cell Proliferation</topic><topic>Cell walls</topic><topic>Chromosomes</topic><topic>Crops</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA methylation</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation</topic><topic>Gene Ontology</topic><topic>Gene sequencing</topic><topic>Genes, Plant</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Isatis - cytology</topic><topic>Isatis - genetics</topic><topic>Isatis - metabolism</topic><topic>Isatis indigotica</topic><topic>Kinases</topic><topic>Medicinal plants</topic><topic>Meiosis</topic><topic>Metabolic pathways</topic><topic>Metabolites</topic><topic>Molecular Sequence Annotation</topic><topic>Morphology</topic><topic>Organs</topic><topic>Pectin</topic><topic>Phenotypes</topic><topic>Photosynthesis</topic><topic>Photosynthesis - genetics</topic><topic>Plant breeding</topic><topic>Plant metabolites</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Plant sciences</topic><topic>Plants (botany)</topic><topic>Polyploidy</topic><topic>Progeny</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Secondary 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respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x) were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents) and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53%) unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%)(2x vs 4x), 693(0.98%)(2x vs 3x), 1045(1.48%)(3x vs 4x) unigenes were detected to differentially expressed genes (DEGs), including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin), cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25739089</pmid><doi>10.1371/journal.pone.0116392</doi><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2015-03, Vol.10 (3), p.e0116392-e0116392 |
| issn | 1932-6203 1932-6203 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Autopolyploidy Autotetraploid Bacteria Biosynthesis Brassicaceae Breeding Cell growth Cell Proliferation Cell walls Chromosomes Crops Deoxyribonucleic acid DNA DNA methylation Gene expression Gene Expression Profiling Gene Expression Regulation Gene Ontology Gene sequencing Genes, Plant Genetic aspects Genomes Genomics Isatis - cytology Isatis - genetics Isatis - metabolism Isatis indigotica Kinases Medicinal plants Meiosis Metabolic pathways Metabolites Molecular Sequence Annotation Morphology Organs Pectin Phenotypes Photosynthesis Photosynthesis - genetics Plant breeding Plant metabolites Plant Proteins - genetics Plant Proteins - metabolism Plant sciences Plants (botany) Polyploidy Progeny Ribonucleic acid RNA Secondary Metabolism Secondary metabolites Transcriptome Viruses |
| title | Transcriptomic analysis reveals differential gene expressions for cell growth and functional secondary metabolites in induced autotetraploid of Chinese woad (Isatis indigotica Fort.) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-28T16%3A02%3A15IST&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=Transcriptomic%20analysis%20reveals%20differential%20gene%20expressions%20for%20cell%20growth%20and%20functional%20secondary%20metabolites%20in%20induced%20autotetraploid%20of%20Chinese%20woad%20(Isatis%20indigotica%20Fort.)&rft.jtitle=PloS%20one&rft.au=Zhou,%20Yingying&rft.date=2015-03-04&rft.volume=10&rft.issue=3&rft.spage=e0116392&rft.epage=e0116392&rft.pages=e0116392-e0116392&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0116392&rft_dat=%3Cgale_plos_%3EA429886480%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=1660647356&rft_id=info:pmid/25739089&rft_galeid=A429886480&rft_doaj_id=oai_doaj_org_article_7c95b516776d4e709058f3ccb6a67cd8&rfr_iscdi=true |