Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress
The enzyme myo-inositol oxygenase (MIOX) catalyzes the myo-inositol into glucuronic acid. In this study, 6 MIOX genes were identified from all of the three diploid cotton species (Gossypium arboretum, Gossypium herbaceum and Gossypium raimondii) and Gossypioides kirkii, 12 MIOX genes were identified...
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| creator | Li, Zhaoguo Liu, Zhen Wei, Yangyang Liu, Yuling Xing, Linxue Liu, Mengjie Li, Pengtao Lu, Quanwei Peng, Renhai |
| description | The enzyme myo-inositol oxygenase (MIOX) catalyzes the myo-inositol into glucuronic acid. In this study, 6 MIOX genes were identified from all of the three diploid cotton species (Gossypium arboretum, Gossypium herbaceum and Gossypium raimondii) and Gossypioides kirkii, 12 MIOX genes were identified from two domesticated tetraploid cottons Gossypium hirsutum, Gossypium barbadense, and 11 MIOX genes were identified from three wild tetraploid cottons Gossypium tomentosum, Gossypium mustelinum and Gossypium darwinii. The number of MIOX genes in tetraploid cotton genome is roughly twice that of diploid cotton genome. Members of MIOX family were classified into six groups based on the phylogenetic analysis. Integrated analysis of collinearity events and chromosome locations suggested that both whole genome duplication and segmental duplication events contributed to the expansion of MIOX genes during cotton evolution. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates revealed that purifying selection was the main force driving the evolution of MIOX genes. Numerous cis-acting elements related to light responsive element, defense and stress responsive element were identified in the promoter of the MIOX genes. Expression analyses of MIOX genes based on RNA-seq data and quantitative real time PCR showed that MIOX genes within the same group shared similar expression patterns with each other. All of these results provide the foundation for further study of the biological functions of MIOX genes in cotton environmental adaptability. |
| doi_str_mv | 10.1371/journal.pone.0254111 |
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In this study, 6 MIOX genes were identified from all of the three diploid cotton species (Gossypium arboretum, Gossypium herbaceum and Gossypium raimondii) and Gossypioides kirkii, 12 MIOX genes were identified from two domesticated tetraploid cottons Gossypium hirsutum, Gossypium barbadense, and 11 MIOX genes were identified from three wild tetraploid cottons Gossypium tomentosum, Gossypium mustelinum and Gossypium darwinii. The number of MIOX genes in tetraploid cotton genome is roughly twice that of diploid cotton genome. Members of MIOX family were classified into six groups based on the phylogenetic analysis. Integrated analysis of collinearity events and chromosome locations suggested that both whole genome duplication and segmental duplication events contributed to the expansion of MIOX genes during cotton evolution. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates revealed that purifying selection was the main force driving the evolution of MIOX genes. Numerous cis-acting elements related to light responsive element, defense and stress responsive element were identified in the promoter of the MIOX genes. Expression analyses of MIOX genes based on RNA-seq data and quantitative real time PCR showed that MIOX genes within the same group shared similar expression patterns with each other. All of these results provide the foundation for further study of the biological functions of MIOX genes in cotton environmental adaptability.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0254111</identifier><identifier>PMID: 34242283</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Abiotic stress ; Adaptability ; Amino acids ; Analysis ; Arboreta ; Biological evolution ; Biology ; Biology and Life Sciences ; Biosynthesis ; Chromosomes ; Collinearity ; Computer and Information Sciences ; Cotton ; Diploids ; Ecology and Environmental Sciences ; Ecosystem components ; Engineering and Technology ; Enzymes ; Evolution ; Evolutionary genetics ; Gene expression ; Genes ; Genomes ; Gossypium hirsutum ; Inositol ; Inositol oxygenase ; Laboratories ; Oxygenase ; Phylogenetics ; Phylogeny ; Proteins ; R&D ; Regulatory sequences ; Reproduction (copying) ; Research & development</subject><ispartof>PloS one, 2021-07, Vol.16 (7), p.e0254111-e0254111</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 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>2021 Li et al 2021 Li et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c669t-ae39836e5eca41146f04b48fc14b9ca4b9bd07c7609c56adae365a88bf78e7183</citedby><cites>FETCH-LOGICAL-c669t-ae39836e5eca41146f04b48fc14b9ca4b9bd07c7609c56adae365a88bf78e7183</cites><orcidid>0000-0002-4791-5537</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/PMC8270170/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8270170/$$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></links><search><contributor>Atif, Rana Muhammad</contributor><creatorcontrib>Li, Zhaoguo</creatorcontrib><creatorcontrib>Liu, Zhen</creatorcontrib><creatorcontrib>Wei, Yangyang</creatorcontrib><creatorcontrib>Liu, Yuling</creatorcontrib><creatorcontrib>Xing, Linxue</creatorcontrib><creatorcontrib>Liu, Mengjie</creatorcontrib><creatorcontrib>Li, Pengtao</creatorcontrib><creatorcontrib>Lu, Quanwei</creatorcontrib><creatorcontrib>Peng, Renhai</creatorcontrib><title>Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress</title><title>PloS one</title><description>The enzyme myo-inositol oxygenase (MIOX) catalyzes the myo-inositol into glucuronic acid. In this study, 6 MIOX genes were identified from all of the three diploid cotton species (Gossypium arboretum, Gossypium herbaceum and Gossypium raimondii) and Gossypioides kirkii, 12 MIOX genes were identified from two domesticated tetraploid cottons Gossypium hirsutum, Gossypium barbadense, and 11 MIOX genes were identified from three wild tetraploid cottons Gossypium tomentosum, Gossypium mustelinum and Gossypium darwinii. The number of MIOX genes in tetraploid cotton genome is roughly twice that of diploid cotton genome. Members of MIOX family were classified into six groups based on the phylogenetic analysis. Integrated analysis of collinearity events and chromosome locations suggested that both whole genome duplication and segmental duplication events contributed to the expansion of MIOX genes during cotton evolution. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates revealed that purifying selection was the main force driving the evolution of MIOX genes. Numerous cis-acting elements related to light responsive element, defense and stress responsive element were identified in the promoter of the MIOX genes. Expression analyses of MIOX genes based on RNA-seq data and quantitative real time PCR showed that MIOX genes within the same group shared similar expression patterns with each other. All of these results provide the foundation for further study of the biological functions of MIOX genes in cotton environmental adaptability.</description><subject>Abiotic stress</subject><subject>Adaptability</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Arboreta</subject><subject>Biological evolution</subject><subject>Biology</subject><subject>Biology and Life Sciences</subject><subject>Biosynthesis</subject><subject>Chromosomes</subject><subject>Collinearity</subject><subject>Computer and Information Sciences</subject><subject>Cotton</subject><subject>Diploids</subject><subject>Ecology and Environmental Sciences</subject><subject>Ecosystem components</subject><subject>Engineering and Technology</subject><subject>Enzymes</subject><subject>Evolution</subject><subject>Evolutionary genetics</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genomes</subject><subject>Gossypium 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identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress</title><author>Li, Zhaoguo ; Liu, Zhen ; Wei, Yangyang ; Liu, Yuling ; Xing, Linxue ; Liu, Mengjie ; Li, Pengtao ; Lu, Quanwei ; Peng, Renhai</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c669t-ae39836e5eca41146f04b48fc14b9ca4b9bd07c7609c56adae365a88bf78e7183</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Abiotic stress</topic><topic>Adaptability</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Arboreta</topic><topic>Biological evolution</topic><topic>Biology</topic><topic>Biology and Life Sciences</topic><topic>Biosynthesis</topic><topic>Chromosomes</topic><topic>Collinearity</topic><topic>Computer and Information Sciences</topic><topic>Cotton</topic><topic>Diploids</topic><topic>Ecology and Environmental Sciences</topic><topic>Ecosystem components</topic><topic>Engineering and Technology</topic><topic>Enzymes</topic><topic>Evolution</topic><topic>Evolutionary genetics</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genomes</topic><topic>Gossypium hirsutum</topic><topic>Inositol</topic><topic>Inositol oxygenase</topic><topic>Laboratories</topic><topic>Oxygenase</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Proteins</topic><topic>R&D</topic><topic>Regulatory sequences</topic><topic>Reproduction (copying)</topic><topic>Research & development</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Zhaoguo</creatorcontrib><creatorcontrib>Liu, Zhen</creatorcontrib><creatorcontrib>Wei, Yangyang</creatorcontrib><creatorcontrib>Liu, Yuling</creatorcontrib><creatorcontrib>Xing, Linxue</creatorcontrib><creatorcontrib>Liu, Mengjie</creatorcontrib><creatorcontrib>Li, Pengtao</creatorcontrib><creatorcontrib>Lu, 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stress</atitle><jtitle>PloS one</jtitle><date>2021-07-09</date><risdate>2021</risdate><volume>16</volume><issue>7</issue><spage>e0254111</spage><epage>e0254111</epage><pages>e0254111-e0254111</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The enzyme myo-inositol oxygenase (MIOX) catalyzes the myo-inositol into glucuronic acid. In this study, 6 MIOX genes were identified from all of the three diploid cotton species (Gossypium arboretum, Gossypium herbaceum and Gossypium raimondii) and Gossypioides kirkii, 12 MIOX genes were identified from two domesticated tetraploid cottons Gossypium hirsutum, Gossypium barbadense, and 11 MIOX genes were identified from three wild tetraploid cottons Gossypium tomentosum, Gossypium mustelinum and Gossypium darwinii. The number of MIOX genes in tetraploid cotton genome is roughly twice that of diploid cotton genome. Members of MIOX family were classified into six groups based on the phylogenetic analysis. Integrated analysis of collinearity events and chromosome locations suggested that both whole genome duplication and segmental duplication events contributed to the expansion of MIOX genes during cotton evolution. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates revealed that purifying selection was the main force driving the evolution of MIOX genes. Numerous cis-acting elements related to light responsive element, defense and stress responsive element were identified in the promoter of the MIOX genes. Expression analyses of MIOX genes based on RNA-seq data and quantitative real time PCR showed that MIOX genes within the same group shared similar expression patterns with each other. All of these results provide the foundation for further study of the biological functions of MIOX genes in cotton environmental adaptability.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34242283</pmid><doi>10.1371/journal.pone.0254111</doi><tpages>e0254111</tpages><orcidid>https://orcid.org/0000-0002-4791-5537</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Abiotic stress Adaptability Amino acids Analysis Arboreta Biological evolution Biology Biology and Life Sciences Biosynthesis Chromosomes Collinearity Computer and Information Sciences Cotton Diploids Ecology and Environmental Sciences Ecosystem components Engineering and Technology Enzymes Evolution Evolutionary genetics Gene expression Genes Genomes Gossypium hirsutum Inositol Inositol oxygenase Laboratories Oxygenase Phylogenetics Phylogeny Proteins R&D Regulatory sequences Reproduction (copying) Research & development |
| title | Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress |
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