AUTHOR=Wang Jiongliang , Ma Xuelian , Yang Jiaotong , Hui Yanan , She Jiajie , Tian Tian , Li Zhongqiu , Xu Wenying , Gao Zhimin , Su Zhen , Zhao Hansheng 

TITLE=Coexpression Analysis Reveals Dynamic Modules Regulating the Growth and Development of Cirri in the Rattans (Calamus simplicifolius and Daemonorops jenkinsiana)

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00378

DOI=10.3389/fgene.2020.00378

ISSN=1664-8021

ABSTRACT=<p>Rattan is regarded as one of the major non-timber forest products, second only to wood and bamboo, worldwide. Although the published genomes of <italic>Calamus simplicifolius</italic> and <italic>Daemonorops jenkinsiana</italic> have facilitated genome-wide gene functional analyses, coexpression networks (CENs) provide more comprehensive and complete annotations of gene function at the transcriptome level. Thus, we analyzed the CENs of the two rattans, <italic>C. simplicifolius</italic> and <italic>D. jenkinsiana</italic>, by integrating the genome sequences and analyzing in-house transcriptome data from different development stages of their cirri using a well-developed strategy. A total of 3,504 and 3,027 functional modules were identified in <italic>C. simplicifolius</italic> and <italic>D. jenkinsiana</italic>, respectively, based on a combination of CENs, gene family classification, and function enrichment tools. These modules covered the major developmental processes, including photosynthesis, lignin biosynthesis, flavonoid biosynthesis, and phenylpropanoid biosynthesis. Reference annotations were refined using CENs and functional modules. Moreover, we obtained novel insights into the regulation of cirrus growth and development in rattans. Furthermore, Rattan-NET (<ext-link ext-link-type="uri" xlink:href="http://rattan.bamboogdb.org/" xmlns:xlink="http://www.w3.org/1999/xlink">http://rattan.bamboogdb.org/</ext-link>), an online database with analysis tools for gene set enrichment analysis, module enrichment, network comparison analysis, and <italic>cis</italic>-element analysis, was constructed for the easy analysis of gene function and regulation modules involved in the growth and development of cirri in rattans.</p>