Abstract
Catharanthus roseus is a medicinal plant, which can produce monoterpene indole alkaloid (MIA) metabolites with biological activity and is rich in vinblastine and vincristine. With release of the scaffolded genome sequence of C. roseus, it is necessary to annotate gene functions on the whole-genome level. Recently, 53 RNA-seq datasets are available in public with different tissues (flower, root, leaf, seedling, and shoot) and different treatments (MeJA, PnWB infection and yeast elicitor). We used in-house data process pipeline with the combination of PCC and MR algorithms to construct a co-expression network exploring multi-dimensional gene expression (global, tissue preferential, and treat response) through multi-layered approaches. In the meanwhile, we added miRNA-target pairs, predicted PPI pairs into the network and provided several tools such as gene set enrichment analysis, functional module enrichment analysis, and motif analysis for functional prediction of the co-expression genes. Finally, we have constructed an online croFGD database (http://bioinformatics.cau.edu.cn/croFGD/). We hope croFGD can help the communities to study the C. roseus functional genomics and make novel discoveries about key genes involved in some important biological processes.
Highlights
Catharanthus roseus, a model plant of the Apocynaceae family, is best known for production of the bis-indole monoterpene indole alkaloids (MIAs)
We found that the gene: (I) was annotated with alkaloid biosynthetic process (GO: 0009821) and myricetin 3 -O-methyltransferase activity (GO: 0033799), etc.; (II) had two pfam domains: “Dimerisation (PF08100)” and “Methyltransf_2 (PF00891)” domains; (III) was mainly involved in vindoline and vinblastine biosynthesis; (IV) was relatively high in expression in leaf tissue (Figure 2A)
It could be applied to excavate important functional module related to agronomic traits, which would be beneficial for genetic breeding
Summary
Catharanthus roseus, a model plant of the Apocynaceae family, is best known for production of the bis-indole monoterpene indole alkaloids (MIAs). The biosynthesis of TIAs is regulated by several key transcription factors (TFs), such as ORCA3, ORCA2, WRKY, MYC, ZCT1, and BIS, which can enhance alkaloid production (Van Der Fits and Memelink, 2000; Suttipanta et al, 2011; Zhang et al, 2011; Li et al, 2013; Van Moerkercke et al, 2015; Rizvi et al, 2016) In addition to these key TFs, some hormones and transporters are essential for the regulation of TIA biosynthesis in C. roseus (Liu et al, 2017). The integration of co-expression network analysis and functional module identification can be used to improve C. roseus gene function annotation and helpful for the functional genomics research It can promote the research for the synthesis, metabolism of active substances and drug development
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