Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i>
WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (<i>Citrus sinensis</i>) accounts for a large proportion of the world’s citrus industry, which has high economic value, whil...
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MDPI AG
2023-02-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/45/2/82 |
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| author | Dengxian Xi Tuo Yin Peichen Han Xiuyao Yang Mengjie Zhang Chaojin Du Hanyao Zhang Xiaozhen Liu |
| author_facet | Dengxian Xi Tuo Yin Peichen Han Xiuyao Yang Mengjie Zhang Chaojin Du Hanyao Zhang Xiaozhen Liu |
| author_sort | Dengxian Xi |
| collection | DOAJ |
| description | WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (<i>Citrus sinensis</i>) accounts for a large proportion of the world’s citrus industry, which has high economic value, while <i>Penicillium digitatum</i> is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after <i>P. digitatum</i> infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each <i>CsWRKY</i> gene under <i>P. digitatum</i> stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of <i>WRKY</i> genes were involved in the transcriptional regulation of sweet orange in response to <i>P. digitatum</i> infection. We obtained 15 differentially expressed genes and used the reported function of <i>AtWRKY</i> genes as references. They may be involved in defense against <i>P. digitatum</i> and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, <i>CsWRKY2</i> and <i>CsWRKY14</i>, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to <i>P. digitatum</i> infection and provides a vital reference for molecular breeding. |
| first_indexed | 2024-03-11T08:59:06Z |
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| spelling | doaj.art-8d0e394332564184a2ec20346f5fa9192023-11-16T19:50:52ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452023-02-014521250127110.3390/cimb45020082Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i>Dengxian Xi0Tuo Yin1Peichen Han2Xiuyao Yang3Mengjie Zhang4Chaojin Du5Hanyao Zhang6Xiaozhen Liu7Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, ChinaKey Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, ChinaWRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (<i>Citrus sinensis</i>) accounts for a large proportion of the world’s citrus industry, which has high economic value, while <i>Penicillium digitatum</i> is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after <i>P. digitatum</i> infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each <i>CsWRKY</i> gene under <i>P. digitatum</i> stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of <i>WRKY</i> genes were involved in the transcriptional regulation of sweet orange in response to <i>P. digitatum</i> infection. We obtained 15 differentially expressed genes and used the reported function of <i>AtWRKY</i> genes as references. They may be involved in defense against <i>P. digitatum</i> and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, <i>CsWRKY2</i> and <i>CsWRKY14</i>, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to <i>P. digitatum</i> infection and provides a vital reference for molecular breeding.https://www.mdpi.com/1467-3045/45/2/82sweet orangeWRKY transcription factorbiological stress<i>Penicillium digitatum</i>genome-wide analysis |
| spellingShingle | Dengxian Xi Tuo Yin Peichen Han Xiuyao Yang Mengjie Zhang Chaojin Du Hanyao Zhang Xiaozhen Liu Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> Current Issues in Molecular Biology sweet orange WRKY transcription factor biological stress <i>Penicillium digitatum</i> genome-wide analysis |
| title | Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_full | Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_fullStr | Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_full_unstemmed | Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_short | Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by <i>Penicillium digitatum</i> |
| title_sort | genome wide identification of sweet orange wrky transcription factors and analysis of their expression in response to infection by i penicillium digitatum i |
| topic | sweet orange WRKY transcription factor biological stress <i>Penicillium digitatum</i> genome-wide analysis |
| url | https://www.mdpi.com/1467-3045/45/2/82 |
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