Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression
The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7–52.9%, and the effect of photoperiod treatment is more significant under low temperature than under hi...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2018-12-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.118.200755 |
| _version_ | 1818618764037455872 |
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| author | Yun-Song Lai Wei Zhang Xiaohui Zhang Di Shen Haiping Wang Yang Qiu Jiangping Song Xixiang Li |
| author_facet | Yun-Song Lai Wei Zhang Xiaohui Zhang Di Shen Haiping Wang Yang Qiu Jiangping Song Xixiang Li |
| author_sort | Yun-Song Lai |
| collection | DOAJ |
| description | The cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7–52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes. Nevertheless, there was significant enrichment of CG- and CHG-types of DNA methylation changes nearing transcription start sites (TSSs)/transcription end sites (TESs) and gene bodies, respectively. Predominantly negative association between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were observed which implied epiregulation of DEGs. Two MADS-box genes that were significantly downregulated by long photoperiod showed significant hypermethylation in promoter regions that is essentially TE-rich. This study indicates MADS-box genes which are partially regulated by promoter methylation state may mediate photoperiod-dependent regulation of cucumber sex expression. |
| first_indexed | 2024-12-16T17:26:46Z |
| format | Article |
| id | doaj.art-076bf4fe76ba4043a459169f8f649b60 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-16T17:26:46Z |
| publishDate | 2018-12-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-076bf4fe76ba4043a459169f8f649b602022-12-21T22:23:02ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362018-12-018123981399110.1534/g3.118.20075522Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex ExpressionYun-Song LaiWei ZhangXiaohui ZhangDi ShenHaiping WangYang QiuJiangping SongXixiang LiThe cucumber (Cucumis sativus) is characterized by its diversity and seasonal plasticity in sexual type. A long day length condition significantly decreased the cucumber female flower ratio by 17.7–52.9%, and the effect of photoperiod treatment is more significant under low temperature than under high temperature. Transcriptome analysis indicates that the photoperiod treatment preferentially significantly influenced flower development processes, particularly MADS-box genes in shoot apices. The long-day treatment resulted in predominantly transposable element (TE)- and gene-associated CHH-types of DNA methylation changes. Nevertheless, there was significant enrichment of CG- and CHG-types of DNA methylation changes nearing transcription start sites (TSSs)/transcription end sites (TESs) and gene bodies, respectively. Predominantly negative association between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) were observed which implied epiregulation of DEGs. Two MADS-box genes that were significantly downregulated by long photoperiod showed significant hypermethylation in promoter regions that is essentially TE-rich. This study indicates MADS-box genes which are partially regulated by promoter methylation state may mediate photoperiod-dependent regulation of cucumber sex expression.http://g3journal.org/lookup/doi/10.1534/g3.118.200755CucumberPhotoperiodSex expressionDNA methylationTranscriptome |
| spellingShingle | Yun-Song Lai Wei Zhang Xiaohui Zhang Di Shen Haiping Wang Yang Qiu Jiangping Song Xixiang Li Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression G3: Genes, Genomes, Genetics Cucumber Photoperiod Sex expression DNA methylation Transcriptome |
| title | Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression |
| title_full | Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression |
| title_fullStr | Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression |
| title_full_unstemmed | Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression |
| title_short | Integrative Analysis of Transcriptomic and Methylomic Data in Photoperiod-Dependent Regulation of Cucumber Sex Expression |
| title_sort | integrative analysis of transcriptomic and methylomic data in photoperiod dependent regulation of cucumber sex expression |
| topic | Cucumber Photoperiod Sex expression DNA methylation Transcriptome |
| url | http://g3journal.org/lookup/doi/10.1534/g3.118.200755 |
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