Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses
WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study,...
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| Veröffentlicht in: | PloS one 2020-12, Vol.15 (12), p.e0241965-e0241965, Article 0241965 |
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| creator | Li, Juanjuan Islam, Faisal Huang, Qian Wang, Jian Zhou, Weijun Xu, Ling Yang, Chong |
| description | WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop. |
| doi_str_mv | 10.1371/journal.pone.0241965 |
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Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0241965</identifier><identifier>PMID: 33270651</identifier><language>eng</language><publisher>SAN FRANCISCO: Public Library Science</publisher><subject>Abiotic stress ; Bioengineering ; Biology and Life Sciences ; Botanical research ; Breeding ; Chromosomes ; Chromosomes, Plant - genetics ; Computer and Information Sciences ; Crop science ; Deoxyribonucleic acid ; DNA ; DNA-Binding Proteins - genetics ; Environmental aspects ; Evolutionary genetics ; Flowering ; Flowering plants ; Gene duplication ; Gene expression ; Gene Expression Regulation, Plant - genetics ; Gene families ; Genes ; Genetic aspects ; Genome, Plant - genetics ; Genome-Wide Association Study ; Genomes ; Helianthus ; Helianthus - genetics ; Helianthus annuus ; Kinases ; Life sciences ; Metabolism ; Multidisciplinary Sciences ; Multigene Family - genetics ; Phylogenetics ; Phylogeny ; Physiological effects ; Plant breeding ; Plant Proteins - genetics ; Plant tissues ; Plant tolerance ; Plants (botany) ; Polyethylene glycol ; Proteins ; Quality control ; Reproduction (copying) ; Research and Analysis Methods ; Science & Technology ; Science & Technology - Other Topics ; Seeds ; Senescence ; Spectrum analysis ; Stress (Physiology) ; Stress response ; Stress, Physiological - genetics ; Stresses ; Subgroups ; Sunflowers ; Synteny ; Tobacco ; Transcription factors ; Transcription Factors - genetics ; Vegetable oils</subject><ispartof>PloS one, 2020-12, Vol.15 (12), p.e0241965-e0241965, Article 0241965</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Li 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>2020 Li et al 2020 Li et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>18</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000597149100096</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c692t-5e34e8acd798ca9d2e166283fc849b6a57e1e96f93dbf4eb841738db62e325ad3</citedby><cites>FETCH-LOGICAL-c692t-5e34e8acd798ca9d2e166283fc849b6a57e1e96f93dbf4eb841738db62e325ad3</cites><orcidid>0000-0003-0749-6195</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/PMC7714227/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714227/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2115,2929,23871,27929,27930,28253,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33270651$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ali, Basharat</contributor><creatorcontrib>Li, Juanjuan</creatorcontrib><creatorcontrib>Islam, Faisal</creatorcontrib><creatorcontrib>Huang, Qian</creatorcontrib><creatorcontrib>Wang, Jian</creatorcontrib><creatorcontrib>Zhou, Weijun</creatorcontrib><creatorcontrib>Xu, Ling</creatorcontrib><creatorcontrib>Yang, Chong</creatorcontrib><title>Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses</title><title>PloS one</title><addtitle>PLOS ONE</addtitle><addtitle>PLoS One</addtitle><description>WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.</description><subject>Abiotic stress</subject><subject>Bioengineering</subject><subject>Biology and Life Sciences</subject><subject>Botanical research</subject><subject>Breeding</subject><subject>Chromosomes</subject><subject>Chromosomes, Plant - genetics</subject><subject>Computer and Information Sciences</subject><subject>Crop science</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA-Binding Proteins - genetics</subject><subject>Environmental aspects</subject><subject>Evolutionary genetics</subject><subject>Flowering</subject><subject>Flowering plants</subject><subject>Gene duplication</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant - genetics</subject><subject>Gene families</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genome, Plant - genetics</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Helianthus</subject><subject>Helianthus - genetics</subject><subject>Helianthus annuus</subject><subject>Kinases</subject><subject>Life sciences</subject><subject>Metabolism</subject><subject>Multidisciplinary Sciences</subject><subject>Multigene Family - genetics</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physiological effects</subject><subject>Plant breeding</subject><subject>Plant Proteins - genetics</subject><subject>Plant tissues</subject><subject>Plant tolerance</subject><subject>Plants (botany)</subject><subject>Polyethylene glycol</subject><subject>Proteins</subject><subject>Quality control</subject><subject>Reproduction (copying)</subject><subject>Research and Analysis Methods</subject><subject>Science & Technology</subject><subject>Science & Technology - Other Topics</subject><subject>Seeds</subject><subject>Senescence</subject><subject>Spectrum analysis</subject><subject>Stress (Physiology)</subject><subject>Stress response</subject><subject>Stress, Physiological - genetics</subject><subject>Stresses</subject><subject>Subgroups</subject><subject>Sunflowers</subject><subject>Synteny</subject><subject>Tobacco</subject><subject>Transcription factors</subject><subject>Transcription Factors - genetics</subject><subject>Vegetable oils</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>AOWDO</sourceid><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>eNqNk11rFDEUhgdRbK3-A9EBQRTZdSbJ5ONGKIu2i4VC_cKrkMmc2U2ZTdYkY1t_gT_bzO60dKUXJRc5JM95k5yTN8uel8W0xKx8f-56b1U3XTsL0wKRUtDqQbZfCowmFBX44a14L3sSwnlRVJhT-jjbwxixglblfvb3CKxbweTCNJDrpfJKR_Dmj4rG2dy1-Y-zzz_zBVjIW7Uy3VVubH4MnVE2LvuQK2v7NJ1MU9TkcQnG53C59hDCILD2rjUdhLy3Dfi8Ni4avUHVGIc4sBCeZo9a1QV4Ns4H2bdPH7_Ojicnp0fz2eHJRFOB4qQCTIAr3TDBtRINgpJSxHGrORE1VRWDEgRtBW7qlkDNSckwb2qKAKNKNfgge7nVXXcuyLGIQSJCKWOEFzQR8y3ROHUu196slL-SThm5WXB-IZVPV-9AFqzmnLcgoAZCKFO1EhUimjOhsUAkaX0YT-vrFTQabPSq2xHd3bFmKRfut2SsJAixJPBmFPDuVw8hypUJGrpOWXD95t6MloxglNBX_6F3v26kFio9wNjWpXP1ICoPKcGU4VLwRE3voNJoYGV0-nFDV3cT3u4kJCbCZVyoPgQ5_3J2f_b0-y77-ha7BNXFZXBdP3zPsAuSLai9C8FDe1PkspCDYa6rIQfDyNEwKe3F7QbdJF07JAHvtsAF1K4N2oDVcIMVyVMitUqUKRJDdfn96ZmJG5vNXG8j_gf8FjMM</recordid><startdate>20201203</startdate><enddate>20201203</enddate><creator>Li, Juanjuan</creator><creator>Islam, Faisal</creator><creator>Huang, Qian</creator><creator>Wang, Jian</creator><creator>Zhou, Weijun</creator><creator>Xu, Ling</creator><creator>Yang, Chong</creator><general>Public Library Science</general><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>AOWDO</scope><scope>BLEPL</scope><scope>DTL</scope><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><orcidid>https://orcid.org/0000-0003-0749-6195</orcidid></search><sort><creationdate>20201203</creationdate><title>Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses</title><author>Li, Juanjuan ; Islam, Faisal ; Huang, Qian ; Wang, Jian ; Zhou, Weijun ; Xu, Ling ; Yang, Chong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-5e34e8acd798ca9d2e166283fc849b6a57e1e96f93dbf4eb841738db62e325ad3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Abiotic stress</topic><topic>Bioengineering</topic><topic>Biology and Life Sciences</topic><topic>Botanical research</topic><topic>Breeding</topic><topic>Chromosomes</topic><topic>Chromosomes, Plant - 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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>Li, Juanjuan</au><au>Islam, Faisal</au><au>Huang, Qian</au><au>Wang, Jian</au><au>Zhou, Weijun</au><au>Xu, Ling</au><au>Yang, Chong</au><au>Ali, Basharat</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses</atitle><jtitle>PloS one</jtitle><stitle>PLOS ONE</stitle><addtitle>PLoS One</addtitle><date>2020-12-03</date><risdate>2020</risdate><volume>15</volume><issue>12</issue><spage>e0241965</spage><epage>e0241965</epage><pages>e0241965-e0241965</pages><artnum>0241965</artnum><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.</abstract><cop>SAN FRANCISCO</cop><pub>Public Library Science</pub><pmid>33270651</pmid><doi>10.1371/journal.pone.0241965</doi><tpages>18</tpages><orcidid>https://orcid.org/0000-0003-0749-6195</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2020-12, Vol.15 (12), p.e0241965-e0241965, Article 0241965 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_gale_healthsolutions_A643673198 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS) Journals Open Access; Web of Science - Science Citation Index Expanded - 2020<img src="https://exlibris-pub.s3.amazonaws.com/fromwos-v2.jpg" />; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Abiotic stress Bioengineering Biology and Life Sciences Botanical research Breeding Chromosomes Chromosomes, Plant - genetics Computer and Information Sciences Crop science Deoxyribonucleic acid DNA DNA-Binding Proteins - genetics Environmental aspects Evolutionary genetics Flowering Flowering plants Gene duplication Gene expression Gene Expression Regulation, Plant - genetics Gene families Genes Genetic aspects Genome, Plant - genetics Genome-Wide Association Study Genomes Helianthus Helianthus - genetics Helianthus annuus Kinases Life sciences Metabolism Multidisciplinary Sciences Multigene Family - genetics Phylogenetics Phylogeny Physiological effects Plant breeding Plant Proteins - genetics Plant tissues Plant tolerance Plants (botany) Polyethylene glycol Proteins Quality control Reproduction (copying) Research and Analysis Methods Science & Technology Science & Technology - Other Topics Seeds Senescence Spectrum analysis Stress (Physiology) Stress response Stress, Physiological - genetics Stresses Subgroups Sunflowers Synteny Tobacco Transcription factors Transcription Factors - genetics Vegetable oils |
| title | Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses |
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