Alternative Splicing during Fiber Development in <i>G. hirsutum</i>
Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory pro...
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MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/14/11812 |
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| author | Jing Zheng Shuhan Wen Zhipeng Yu Keyan Luo Junkang Rong Mingquan Ding |
| author_facet | Jing Zheng Shuhan Wen Zhipeng Yu Keyan Luo Junkang Rong Mingquan Ding |
| author_sort | Jing Zheng |
| collection | DOAJ |
| description | Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in <i>Gossypium hirsutum</i>. Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon–intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process. |
| first_indexed | 2024-03-11T00:59:30Z |
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| id | doaj.art-396e30e9a4434d02ae42952b297d04bf |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T00:59:30Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-396e30e9a4434d02ae42952b297d04bf2023-11-18T19:45:25ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-07-0124141181210.3390/ijms241411812Alternative Splicing during Fiber Development in <i>G. hirsutum</i>Jing Zheng0Shuhan Wen1Zhipeng Yu2Keyan Luo3Junkang Rong4Mingquan Ding5The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, ChinaCotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in <i>Gossypium hirsutum</i>. Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon–intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process.https://www.mdpi.com/1422-0067/24/14/11812<i>Gossypium hirsutum</i>alternative splicingtranscriptomefiber developmentGO enrichmentmethylation |
| spellingShingle | Jing Zheng Shuhan Wen Zhipeng Yu Keyan Luo Junkang Rong Mingquan Ding Alternative Splicing during Fiber Development in <i>G. hirsutum</i> International Journal of Molecular Sciences <i>Gossypium hirsutum</i> alternative splicing transcriptome fiber development GO enrichment methylation |
| title | Alternative Splicing during Fiber Development in <i>G. hirsutum</i> |
| title_full | Alternative Splicing during Fiber Development in <i>G. hirsutum</i> |
| title_fullStr | Alternative Splicing during Fiber Development in <i>G. hirsutum</i> |
| title_full_unstemmed | Alternative Splicing during Fiber Development in <i>G. hirsutum</i> |
| title_short | Alternative Splicing during Fiber Development in <i>G. hirsutum</i> |
| title_sort | alternative splicing during fiber development in i g hirsutum i |
| topic | <i>Gossypium hirsutum</i> alternative splicing transcriptome fiber development GO enrichment methylation |
| url | https://www.mdpi.com/1422-0067/24/14/11812 |
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