Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.)
MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail...
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| creator | Muthamilarasan, Mehanathan Khandelwal, Rohit Yadav, Chandra Bhan Bonthala, Venkata Suresh Khan, Yusuf Prasad, Manoj |
| description | MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I-X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli. |
| doi_str_mv | 10.1371/journal.pone.0109920 |
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Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I-X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0109920</identifier><identifier>PMID: 25279462</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Arabidopsis ; Biodiesel fuels ; Biology and Life Sciences ; Cell division ; Chromosome Mapping ; Chromosomes ; Chromosomes, Plant ; Corn ; Crops ; Deoxyribonucleic acid ; DNA ; Environmental effects ; Evolution, Molecular ; Gene duplication ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene mapping ; Gene Ontology ; Genes ; Genomes ; Genomics ; Graphical representations ; Identification ; Millet ; Multigene Family ; MYB protein ; Orthology ; Oryza ; Panicum virgatum ; Pennisetum glaucum ; Pennisetum purpureum ; Phylogenetics ; Phylogeny ; Plant Proteins - chemistry ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Promoter Regions, Genetic - genetics ; Proteins ; Proto-Oncogene Proteins c-myb - chemistry ; Proto-Oncogene Proteins c-myb - genetics ; Proto-Oncogene Proteins c-myb - metabolism ; Real-Time Polymerase Chain Reaction ; Renewable energy ; Reproduction (copying) ; Reverse Transcriptase Polymerase Chain Reaction ; Rice ; RNA polymerase ; RNA, Messenger - genetics ; Setaria italica ; Setaria Plant - genetics ; Setaria Plant - growth & development ; Setaria Plant - metabolism ; Signal transduction ; Sorghum ; Tissue analysis ; Transcription factors ; Transcription Factors - chemistry ; Transcription Factors - genetics ; Transcription Factors - metabolism</subject><ispartof>PloS one, 2014-10, Vol.9 (10), p.e109920-e109920</ispartof><rights>2014 Muthamilarasan 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>2014 Muthamilarasan et al 2014 Muthamilarasan et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-f1239d322a76daed18cc8d99676c867d9a9807211b329f509b23e398b40bf7ca3</citedby><cites>FETCH-LOGICAL-c526t-f1239d322a76daed18cc8d99676c867d9a9807211b329f509b23e398b40bf7ca3</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/PMC4184890/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184890/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,2096,2915,23847,27905,27906,53772,53774,79349,79350</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25279462$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Pandey, Girdhar K.</contributor><creatorcontrib>Muthamilarasan, Mehanathan</creatorcontrib><creatorcontrib>Khandelwal, Rohit</creatorcontrib><creatorcontrib>Yadav, Chandra Bhan</creatorcontrib><creatorcontrib>Bonthala, Venkata Suresh</creatorcontrib><creatorcontrib>Khan, Yusuf</creatorcontrib><creatorcontrib>Prasad, Manoj</creatorcontrib><title>Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.)</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I-X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.</description><subject>Arabidopsis</subject><subject>Biodiesel fuels</subject><subject>Biology and Life Sciences</subject><subject>Cell division</subject><subject>Chromosome Mapping</subject><subject>Chromosomes</subject><subject>Chromosomes, Plant</subject><subject>Corn</subject><subject>Crops</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Environmental effects</subject><subject>Evolution, Molecular</subject><subject>Gene duplication</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene mapping</subject><subject>Gene Ontology</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Graphical representations</subject><subject>Identification</subject><subject>Millet</subject><subject>Multigene Family</subject><subject>MYB protein</subject><subject>Orthology</subject><subject>Oryza</subject><subject>Panicum virgatum</subject><subject>Pennisetum glaucum</subject><subject>Pennisetum purpureum</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Proteins - chemistry</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Promoter Regions, Genetic - genetics</subject><subject>Proteins</subject><subject>Proto-Oncogene Proteins c-myb - chemistry</subject><subject>Proto-Oncogene Proteins c-myb - genetics</subject><subject>Proto-Oncogene Proteins c-myb - metabolism</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Renewable energy</subject><subject>Reproduction (copying)</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>Rice</subject><subject>RNA polymerase</subject><subject>RNA, Messenger - genetics</subject><subject>Setaria italica</subject><subject>Setaria Plant - genetics</subject><subject>Setaria Plant - growth & development</subject><subject>Setaria Plant - metabolism</subject><subject>Signal transduction</subject><subject>Sorghum</subject><subject>Tissue analysis</subject><subject>Transcription factors</subject><subject>Transcription Factors - 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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>Muthamilarasan, Mehanathan</au><au>Khandelwal, Rohit</au><au>Yadav, Chandra Bhan</au><au>Bonthala, Venkata Suresh</au><au>Khan, Yusuf</au><au>Prasad, Manoj</au><au>Pandey, Girdhar K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-10-03</date><risdate>2014</risdate><volume>9</volume><issue>10</issue><spage>e109920</spage><epage>e109920</epage><pages>e109920-e109920</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I-X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25279462</pmid><doi>10.1371/journal.pone.0109920</doi><oa>free_for_read</oa></addata></record> |
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| recordid | cdi_plos_journals_1582255359 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Arabidopsis Biodiesel fuels Biology and Life Sciences Cell division Chromosome Mapping Chromosomes Chromosomes, Plant Corn Crops Deoxyribonucleic acid DNA Environmental effects Evolution, Molecular Gene duplication Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Gene mapping Gene Ontology Genes Genomes Genomics Graphical representations Identification Millet Multigene Family MYB protein Orthology Oryza Panicum virgatum Pennisetum glaucum Pennisetum purpureum Phylogenetics Phylogeny Plant Proteins - chemistry Plant Proteins - genetics Plant Proteins - metabolism Promoter Regions, Genetic - genetics Proteins Proto-Oncogene Proteins c-myb - chemistry Proto-Oncogene Proteins c-myb - genetics Proto-Oncogene Proteins c-myb - metabolism Real-Time Polymerase Chain Reaction Renewable energy Reproduction (copying) Reverse Transcriptase Polymerase Chain Reaction Rice RNA polymerase RNA, Messenger - genetics Setaria italica Setaria Plant - genetics Setaria Plant - growth & development Setaria Plant - metabolism Signal transduction Sorghum Tissue analysis Transcription factors Transcription Factors - chemistry Transcription Factors - genetics Transcription Factors - metabolism |
| title | Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-20T20%3A17%3A39IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Identification%20and%20molecular%20characterization%20of%20MYB%20Transcription%20Factor%20Superfamily%20in%20C4%20model%20plant%20foxtail%20millet%20(Setaria%20italica%20L.)&rft.jtitle=PloS%20one&rft.au=Muthamilarasan,%20Mehanathan&rft.date=2014-10-03&rft.volume=9&rft.issue=10&rft.spage=e109920&rft.epage=e109920&rft.pages=e109920-e109920&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0109920&rft_dat=%3Cproquest_plos_%3E3451347461%3C/proquest_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1582255359&rft_id=info:pmid/25279462&rft_doaj_id=oai_doaj_org_article_224bd98ecd754b25915b62dbf4d4e94d&rfr_iscdi=true |