A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production

NAM, ATAF, and CUC2 (NAC) proteins are encoded by one of the largest plant-specific transcription factor gene families. The functions of many NAC proteins relate to different aspects of lignocellulosic biomass production, and a small group of NAC transcription factors has been characterized as master regulators of plant cell wall development. In the present study, a total of 1,232 NAC protein sequences from 11 different organisms were analyzed by sequence phylogeny based on protein DNA-binding domains. We included eight whole genomes (Arabidopsis, rice, poplar, grape, sorghum, soybean, moss (Physcomitrella patens), and spike moss (Selaginella moellendorffii)) and three not yet fully sequenced genomes (maize, switchgrass, and Medicago truncatula) in our analyses. Ninety-two potential PvNAC genes from switchgrass and 148 PtNAC genes from poplar were identified. The 1,232 NAC proteins were phylogenetically classified into eight subfamilies, each of which was further divided into subgroups according to their tree topology. The phylogenetic subgroups were then grouped into different clades each sharing conserved motif patterns in the C-terminal sequences, and those that may function in plant cell wall development were further identified through motif grouping and gene expression pattern analysis using publicly available microarray data. Our results provide a bioinformatic baseline for further functional analyses of candidate NAC genes for improving cell wall and environmental tolerance traits in the bioenergy crops switchgrass and poplar.