Global Methylome and gene expression analysis during early Peanut pod development
Abstract Background Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. Results To investig...
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-018-1546-4 |
| _version_ | 1818299896486166528 |
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| author | Pengfei Wang Suhua Shi Junjie Ma Hui Song Ye Zhang Chao Gao Chuanzhi Zhao Shuzhen Zhao Lei Hou Javier Lopez-Baltazar Shoujin Fan Han Xia Xingjun Wang |
| author_facet | Pengfei Wang Suhua Shi Junjie Ma Hui Song Ye Zhang Chao Gao Chuanzhi Zhao Shuzhen Zhao Lei Hou Javier Lopez-Baltazar Shoujin Fan Han Xia Xingjun Wang |
| author_sort | Pengfei Wang |
| collection | DOAJ |
| description | Abstract Background Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. Results To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. Conclusion A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development. |
| first_indexed | 2024-12-13T04:58:30Z |
| format | Article |
| id | doaj.art-dfbd839964104879a662b1e7fac6240d |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-13T04:58:30Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj.art-dfbd839964104879a662b1e7fac6240d2022-12-21T23:58:50ZengBMCBMC Plant Biology1471-22292018-12-0118111310.1186/s12870-018-1546-4Global Methylome and gene expression analysis during early Peanut pod developmentPengfei Wang0Suhua Shi1Junjie Ma2Hui Song3Ye Zhang4Chao Gao5Chuanzhi Zhao6Shuzhen Zhao7Lei Hou8Javier Lopez-Baltazar9Shoujin Fan10Han Xia11Xingjun Wang12Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyLife Science College of Shandong Normal UniversityLife Science College of Shandong UniversityBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyInstituto Tecnologico del Valle de OaxacaLife Science College of Shandong Normal UniversityBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyBiotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyAbstract Background Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. Results To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. Conclusion A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.http://link.springer.com/article/10.1186/s12870-018-1546-4PeanutGynophorePod developmentMethylomeSmall RNA |
| spellingShingle | Pengfei Wang Suhua Shi Junjie Ma Hui Song Ye Zhang Chao Gao Chuanzhi Zhao Shuzhen Zhao Lei Hou Javier Lopez-Baltazar Shoujin Fan Han Xia Xingjun Wang Global Methylome and gene expression analysis during early Peanut pod development BMC Plant Biology Peanut Gynophore Pod development Methylome Small RNA |
| title | Global Methylome and gene expression analysis during early Peanut pod development |
| title_full | Global Methylome and gene expression analysis during early Peanut pod development |
| title_fullStr | Global Methylome and gene expression analysis during early Peanut pod development |
| title_full_unstemmed | Global Methylome and gene expression analysis during early Peanut pod development |
| title_short | Global Methylome and gene expression analysis during early Peanut pod development |
| title_sort | global methylome and gene expression analysis during early peanut pod development |
| topic | Peanut Gynophore Pod development Methylome Small RNA |
| url | http://link.springer.com/article/10.1186/s12870-018-1546-4 |
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