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 ( ) 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 amo...
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Published in | Frontiers in genetics Vol. 9; p. 574 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
Published |
Switzerland
Frontiers Media S.A
27.11.2018
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Subjects | |
Online Access | Get full text |
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Summary: | Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (
) 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
-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. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 This article was submitted to Bioinformatics and Computational Biology, a section of the journal Frontiers in Genetics These authors have contributed equally to this work Reviewed by: Hamed Bostan, North Carolina State University, United States; Dinesh Kumar, Indian Council of Agricultural Research (ICAR), India Edited by: Vinicius Maracaja-Coutinho, Universidad de Chile, Chile |
ISSN: | 1664-8021 1664-8021 |
DOI: | 10.3389/fgene.2018.00574 |