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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2018.00574

Co-expression gene network analysis and functional module identification in bamboo growth and development

 Xuelian Ma1,  Hansheng Zhao2, Wenying Xu1,  Qi You1, Hengyu Yan1, Zhimin Gao2 and  Zhen Su1*
  • 1China Agricultural University, China
  • 2Institute of Genetic Science for Bamboo and Rattan Resources, China

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.

Keywords: Bamboo, Gene network analysis, Functional Module, gene expression views, Growth and Development

Received: 21 Jul 2018; Accepted: 08 Nov 2018.

Edited by:

Vinicius Maracaja-Coutinho, Universidad de Chile, Chile

Reviewed by:

Hamed Bostan, North Carolina State University, United States
Dinesh Kumar, Indian Council of Agricultural Research (ICAR), India  

Copyright: © 2018 Ma, Zhao, Xu, You, Yan, Gao and Su. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Zhen Su, China Agricultural University, Beijing, China, zhensu@cau.edu.cn