Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton
<i>Oxidative Stress 3</i> (<i>OXS3</i>) encodes a plant-specific protein that makes great contributions to a plant’s stress tolerance. However, reports on genome-wide identification and expression pattern analyses of OXS3 were only found for <i>Arabidopsis</i>, wh...
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2024-11-01
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| author | Yu Chen Rui Yang Haojie Wang Xianghui Xiao Baoguang Xing Yanfang Li Qiankun Liu Quanwei Lu Renhai Peng Guodong Chen Yongbo Wang Pengtao Li |
| author_facet | Yu Chen Rui Yang Haojie Wang Xianghui Xiao Baoguang Xing Yanfang Li Qiankun Liu Quanwei Lu Renhai Peng Guodong Chen Yongbo Wang Pengtao Li |
| author_sort | Yu Chen |
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| description | <i>Oxidative Stress 3</i> (<i>OXS3</i>) encodes a plant-specific protein that makes great contributions to a plant’s stress tolerance. However, reports on genome-wide identification and expression pattern analyses of OXS3 were only found for <i>Arabidopsis</i>, wheat, and rice. The genus <i>Gossypium</i> (cotton) serves as an ideal model for studying allopolyploidy. Therefore, two diploid species (<i>G. raimondii</i> and <i>G. arboreum</i>) and two tetraploid species (<i>G. hirsutum</i> and <i>G. barbadense</i>) were chosen in this study for a bioinformatics analysis, resulting in 12, 12, 22, and 23 OXS3 members, respectively. A phylogenetic tree was constructed using 69 cotton <i>OXS3</i> genes alongside 8 <i>Arabidopsis</i>, 10 rice, and 9 wheat genes, which were classified into three groups (Group 1–3). A consistent evolutionary relationship with the phylogenetic tree was observed in our structural analysis of the cotton <i>OXS3</i> genes and the clustering of six conserved motifs. Gene duplication analysis across the four representative <i>Gossypium</i> species suggested that whole-genome duplication, segmental duplication, and tandem duplication might play significant roles in the expansion of the <i>OXS3</i> gene family. Some existing elements responsive to salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) were identified by cis-regulatory element analysis in the promoter regions, which could influence the expression levels of cotton <i>OXS3</i> genes. Furthermore, the expression patterns of the <i>GhOXS3</i> gene were examined in different tissues or organs, as well as in developing ovules and fibers, with the highest expression observed in ovules. <i>GhOXS3</i> genes exhibited a more pronounced regulatory response to abiotic stresses, of which ten <i>GhOXS3</i> genes showed similar expression patterns under cold, heat, salt, and drought treatments. These observations were verified by quantitative real-time PCR experiments. These findings enhance our understanding of the evolutionary relationships and expression patterns of the <i>OXS3</i> gene family and provide valuable insights for the identification of vital candidate genes for trait improvement in cotton breeding. |
| format | Article |
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| spelling | doaj-art-682d902fd39040d38dbff123d2234d742025-08-20T02:08:02ZengMDPI AGBiology2079-77372024-11-01131190310.3390/biology13110903Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in CottonYu Chen0Rui Yang1Haojie Wang2Xianghui Xiao3Baoguang Xing4Yanfang Li5Qiankun Liu6Quanwei Lu7Renhai Peng8Guodong Chen9Yongbo Wang10Pengtao Li11School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, ChinaCollege of Agriculture, Tarim University, Alar 843300, ChinaCotton Sciences Research Institute of Hunan, Changde 415101, ChinaSchool of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China<i>Oxidative Stress 3</i> (<i>OXS3</i>) encodes a plant-specific protein that makes great contributions to a plant’s stress tolerance. However, reports on genome-wide identification and expression pattern analyses of OXS3 were only found for <i>Arabidopsis</i>, wheat, and rice. The genus <i>Gossypium</i> (cotton) serves as an ideal model for studying allopolyploidy. Therefore, two diploid species (<i>G. raimondii</i> and <i>G. arboreum</i>) and two tetraploid species (<i>G. hirsutum</i> and <i>G. barbadense</i>) were chosen in this study for a bioinformatics analysis, resulting in 12, 12, 22, and 23 OXS3 members, respectively. A phylogenetic tree was constructed using 69 cotton <i>OXS3</i> genes alongside 8 <i>Arabidopsis</i>, 10 rice, and 9 wheat genes, which were classified into three groups (Group 1–3). A consistent evolutionary relationship with the phylogenetic tree was observed in our structural analysis of the cotton <i>OXS3</i> genes and the clustering of six conserved motifs. Gene duplication analysis across the four representative <i>Gossypium</i> species suggested that whole-genome duplication, segmental duplication, and tandem duplication might play significant roles in the expansion of the <i>OXS3</i> gene family. Some existing elements responsive to salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) were identified by cis-regulatory element analysis in the promoter regions, which could influence the expression levels of cotton <i>OXS3</i> genes. Furthermore, the expression patterns of the <i>GhOXS3</i> gene were examined in different tissues or organs, as well as in developing ovules and fibers, with the highest expression observed in ovules. <i>GhOXS3</i> genes exhibited a more pronounced regulatory response to abiotic stresses, of which ten <i>GhOXS3</i> genes showed similar expression patterns under cold, heat, salt, and drought treatments. These observations were verified by quantitative real-time PCR experiments. These findings enhance our understanding of the evolutionary relationships and expression patterns of the <i>OXS3</i> gene family and provide valuable insights for the identification of vital candidate genes for trait improvement in cotton breeding.https://www.mdpi.com/2079-7737/13/11/903cottonOXS3genome-wide identificationphylogenetic analysisabiotic stress response |
| spellingShingle | Yu Chen Rui Yang Haojie Wang Xianghui Xiao Baoguang Xing Yanfang Li Qiankun Liu Quanwei Lu Renhai Peng Guodong Chen Yongbo Wang Pengtao Li Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton Biology cotton OXS3 genome-wide identification phylogenetic analysis abiotic stress response |
| title | Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton |
| title_full | Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton |
| title_fullStr | Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton |
| title_full_unstemmed | Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton |
| title_short | Genome-Wide Identification of the <i>Oxidative Stress 3</i> (<i>OXS3</i>) Gene Family and Analysis of Its Expression Pattern During Ovule Development and Under Abiotic Stress in Cotton |
| title_sort | genome wide identification of the i oxidative stress 3 i i oxs3 i gene family and analysis of its expression pattern during ovule development and under abiotic stress in cotton |
| topic | cotton OXS3 genome-wide identification phylogenetic analysis abiotic stress response |
| url | https://www.mdpi.com/2079-7737/13/11/903 |
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