Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development
Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes....
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00574/full |
| _version_ | 1819054371291267072 |
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| author | Xuelian Ma Hansheng Zhao Wenying Xu Qi You Hengyu Yan Zhimin Gao Zhen Su |
| author_facet | Xuelian Ma Hansheng Zhao Wenying Xu Qi You Hengyu Yan Zhimin Gao Zhen Su |
| author_sort | Xuelian Ma |
| collection | DOAJ |
| description | Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amounts of bamboo transcriptome data have become available, including data on the multiple growth stages of tissues. It is now feasible for us to construct co-expression networks to improve bamboo gene annotation and reveal the relationships between gene expression and growth traits. We integrated the genome sequence of moso bamboo and 78 transcriptome data sets to build genome-wide global and conditional co-expression networks. We overlaid the gene expression results onto the network with multiple dimensions (different development stages). Through combining the co-expression network, module classification and function enrichment tools, we identified 1,896 functional modules related to bamboo development, which covered functions such as photosynthesis, hormone biosynthesis, signal transduction, and secondary cell wall biosynthesis. Furthermore, an online database (http://bioinformatics.cau.edu.cn/bamboo) was built for searching the moso bamboo co-expression network and module enrichment analysis. Our database also includes cis-element analysis, gene set enrichment analysis, and other tools. In summary, we integrated public and in-house bamboo transcriptome data sets and carried out co-expression network analysis and functional module identification. Through data mining, we have yielded some novel insights into the regulation of growth and development. Our established online database might be convenient for the bamboo research community to identify functional genes or modules with important traits. |
| first_indexed | 2024-12-21T12:50:34Z |
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| id | doaj.art-a0e1fe9cb62e42e9adf2a9de6b5ef6ed |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-21T12:50:34Z |
| publishDate | 2018-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-a0e1fe9cb62e42e9adf2a9de6b5ef6ed2022-12-21T19:03:30ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-11-01910.3389/fgene.2018.00574415160Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and DevelopmentXuelian Ma0Hansheng Zhao1Wenying Xu2Qi You3Hengyu Yan4Zhimin Gao5Zhen Su6State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, ChinaState Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, ChinaState Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, ChinaState Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, ChinaState Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, ChinaState Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, ChinaState Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, ChinaBamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amounts of bamboo transcriptome data have become available, including data on the multiple growth stages of tissues. It is now feasible for us to construct co-expression networks to improve bamboo gene annotation and reveal the relationships between gene expression and growth traits. We integrated the genome sequence of moso bamboo and 78 transcriptome data sets to build genome-wide global and conditional co-expression networks. We overlaid the gene expression results onto the network with multiple dimensions (different development stages). Through combining the co-expression network, module classification and function enrichment tools, we identified 1,896 functional modules related to bamboo development, which covered functions such as photosynthesis, hormone biosynthesis, signal transduction, and secondary cell wall biosynthesis. Furthermore, an online database (http://bioinformatics.cau.edu.cn/bamboo) was built for searching the moso bamboo co-expression network and module enrichment analysis. Our database also includes cis-element analysis, gene set enrichment analysis, and other tools. In summary, we integrated public and in-house bamboo transcriptome data sets and carried out co-expression network analysis and functional module identification. Through data mining, we have yielded some novel insights into the regulation of growth and development. Our established online database might be convenient for the bamboo research community to identify functional genes or modules with important traits.https://www.frontiersin.org/article/10.3389/fgene.2018.00574/fullbamboogene network analysisfunctional modulegene expression viewsgrowth and development |
| spellingShingle | Xuelian Ma Hansheng Zhao Wenying Xu Qi You Hengyu Yan Zhimin Gao Zhen Su Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development Frontiers in Genetics bamboo gene network analysis functional module gene expression views growth and development |
| title | Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development |
| title_full | Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development |
| title_fullStr | Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development |
| title_full_unstemmed | Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development |
| title_short | Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development |
| title_sort | co expression gene network analysis and functional module identification in bamboo growth and development |
| topic | bamboo gene network analysis functional module gene expression views growth and development |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00574/full |
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