Systematic identification of cell-wall related genes in Populus based on analysis of functional modules in co-expression network.

Bin Cai,Jian Huang,Cheng-Hui Li,Ken Mills

doi:10.1371/journal.pone.0095176

Bin Cai, Jian Huang + Show 2 more

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https://doi.org/10.1371/journal.pone.0095176

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Abstract

The identification of novel genes relevant to plant cell wall (PCW) biosynthesis in Populus is a highly important and challenging problem. We surveyed candidate Populus cell wall genes using a non-targeted approach. First, a genome-wide Populus gene co-expression network (PGCN) was constructed using microarray data available in the public domain. Module detection was then performed, followed by gene ontology (GO) enrichment analysis, to assign the functional category to these modules. Based on GO annotation, the modules involved in PCW biosynthesis were then selected and analyzed in detail to annotate the candidate PCW genes in these modules, including gene annotation, expression of genes in different tissues, and so on. We examined the overrepresented cis-regulatory elements (CREs) in the gene promoters to understand the possible transcriptionally co-regulated relationships among the genes within the functional modules of cell wall biosynthesis. PGCN contains 6,854 nodes (genes) with 324,238 edges. The topological properties of the network indicate scale-free and modular behavior. A total of 435 modules were identified; among which, 67 modules were identified by overrepresented GO terms. Six modules involved in cell wall biosynthesis were identified. Module 9 was mainly involved in cellular polysaccharide metabolic process in the primary cell wall, whereas Module 4 comprises genes involved in secondary cell wall biogenesis. In addition, we predicted and analyzed 10 putative CREs in the promoters of the genes in Module 4 and Module 9. The non-targeted approach of gene network analysis and the data presented here can help further identify and characterize cell wall related genes in Populus.

Highlights

Populus represents the fast-growing temperate tree species in the world
To identify plant cell wall (PCW) genes using co-expression data sets, we developed a computational pipeline (Figure 1)
The pipeline consists of the following steps: (1) construction of a genome-wide gene co-expression network; (2) identification of co-expression modules based on the connectivity of nodes in the network; (3) enrichment analysis of gene ontology (GO) terms in functional modules; (4) selection and analysis of the modules related to cell wall biology

Summary

Introduction

Populus represents the fast-growing temperate tree species in the world. The perennial growth habit and wide-ranging habitat of Populus makes it an important model woody crop for economic and ecological applications [1]. The development of high throughput biological data collection techniques has led to the accumulation of a vast amount of ‘omics’ data, including complete genome sequences, transcript profiles, and so on. These data sets have been used to reconstruct networks and pathways to infer functional relationships among genes, proteins, and metabolites [2]. Several microarray analyses of Populus have been conducted using an Affymetrix Poplar GeneChip platform. These experiments were conducted under biotic, abiotic, and developmental conditions. The compendium of Populus microarray data has allowed the construction of a co-expression network

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