Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data
2016
Chen, Xin | Ma, Qin | Rao, Xiaolan | Tang, Yuhong | Wang, Yan | Li, Gaoyang | Zhang, Chi | Mao, Xizeng | Dixon, Richard A. | Xu, Ying
Large numbers of plant cell-wall (CW)-related genes have been identified or predicted in several plant genomes such as Arabidopsis thaliana, Oryza sativa (rice), and Zea mays (maize), as results of intensive studies of these organisms in the past 2 decades. However, no such gene list has been identified in switchgrass (Panicum virgatum), a key bioenergy crop. Here, we present a computational study for prediction of CW genes in switchgrass using a two-step procedure: (i) homology mapping of all annotated CW genes in the fore-mentioned species to switchgrass, giving rise to a total of 991 genes, and (ii) candidate prediction of CW genes based on switchgrass genes co-expressed with the 991 genes under a large number of experimental conditions. Specifically, our co-expression analyses using the 991 genes as seeds led to the identification of 104 large clusters of co-expressed genes, each referred to as a co-expression module (CEM), covering 830 of the 991 genes plus 823 additional genes that are strongly co-expressed with some of the 104 CEMs. These 1653 genes represent our prediction of CW genes in switchgrass, 112 of which are homologous to predicted CW genes in Arabidopsis. Functional inference of these genes is conducted to derive the possible functional relations among these predicted CW genes. Overall, these data may offer a highly useful information source for cell-wall biologists of switchgrass as well as plants in general.
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