Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patt...
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| description | The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs. |
| doi_str_mv | 10.1371/journal.pone.0197392 |
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Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0197392</identifier><identifier>PMID: 29768506</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adenosine ; Analysis ; Arboreta ; Biology and Life Sciences ; Classification ; Collinearity ; Computer and Information Sciences ; Cotton ; Cotton (Plant) ; Cyclin-dependent kinases ; Ecology and Environmental Sciences ; Evolution ; Evolutionary genetics ; Expansion ; Ferns ; Flowers & plants ; Funding ; Gene expression ; Genes ; Genetic aspects ; Genomes ; Genomics ; Gossypium ; Gossypium barbadense ; Identification ; Information science ; Kinases ; Life sciences ; Phylogenetics ; Phylogeny ; Pk gene ; Protein kinase ; Proteins ; Reproduction (copying) ; Research and Analysis Methods ; Rice ; Soybeans ; Stress ; Stress response ; Stresses ; Synteny</subject><ispartof>PloS one, 2018-05, Vol.13 (5), p.e0197392-e0197392</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Yan 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>2018 Yan et al 2018 Yan et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-139d43154be05af56feca2a8039918f6c16199301e9636ce162e8a2eca47ad6c3</citedby><cites>FETCH-LOGICAL-c758t-139d43154be05af56feca2a8039918f6c16199301e9636ce162e8a2eca47ad6c3</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/PMC5955557/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955557/$$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/29768506$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Fang, David D</contributor><creatorcontrib>Yan, Jun</creatorcontrib><creatorcontrib>Li, Guilin</creatorcontrib><creatorcontrib>Guo, Xingqi</creatorcontrib><creatorcontrib>Li, Yang</creatorcontrib><creatorcontrib>Cao, Xuecheng</creatorcontrib><title>Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs.</description><subject>Adenosine</subject><subject>Analysis</subject><subject>Arboreta</subject><subject>Biology and Life Sciences</subject><subject>Classification</subject><subject>Collinearity</subject><subject>Computer and Information Sciences</subject><subject>Cotton</subject><subject>Cotton (Plant)</subject><subject>Cyclin-dependent kinases</subject><subject>Ecology and Environmental Sciences</subject><subject>Evolution</subject><subject>Evolutionary genetics</subject><subject>Expansion</subject><subject>Ferns</subject><subject>Flowers & plants</subject><subject>Funding</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Gossypium</subject><subject>Gossypium barbadense</subject><subject>Identification</subject><subject>Information 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expression</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Gossypium</topic><topic>Gossypium barbadense</topic><topic>Identification</topic><topic>Information science</topic><topic>Kinases</topic><topic>Life sciences</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Pk gene</topic><topic>Protein kinase</topic><topic>Proteins</topic><topic>Reproduction (copying)</topic><topic>Research and Analysis Methods</topic><topic>Rice</topic><topic>Soybeans</topic><topic>Stress</topic><topic>Stress response</topic><topic>Stresses</topic><topic>Synteny</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yan, Jun</creatorcontrib><creatorcontrib>Li, Guilin</creatorcontrib><creatorcontrib>Guo, Xingqi</creatorcontrib><creatorcontrib>Li, Yang</creatorcontrib><creatorcontrib>Cao, Xuecheng</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In 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One</addtitle><date>2018-05-16</date><risdate>2018</risdate><volume>13</volume><issue>5</issue><spage>e0197392</spage><epage>e0197392</epage><pages>e0197392-e0197392</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29768506</pmid><doi>10.1371/journal.pone.0197392</doi><tpages>e0197392</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adenosine Analysis Arboreta Biology and Life Sciences Classification Collinearity Computer and Information Sciences Cotton Cotton (Plant) Cyclin-dependent kinases Ecology and Environmental Sciences Evolution Evolutionary genetics Expansion Ferns Flowers & plants Funding Gene expression Genes Genetic aspects Genomes Genomics Gossypium Gossypium barbadense Identification Information science Kinases Life sciences Phylogenetics Phylogeny Pk gene Protein kinase Proteins Reproduction (copying) Research and Analysis Methods Rice Soybeans Stress Stress response Stresses Synteny |
| title | Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium |
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