Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots

Albero Cenci,Nicolas Roux,Valentin Guignon,Mathieu Rouard

doi:10.1007/s11103-013-0169-2

Abstract

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-013-0169-2) contains supplementary material, which is available to authorized users.

Highlights

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding
Five pseudogenes and a number of remnants were found in the M. acuminata genome
We refined the selection of NAC sequences for other species, taking into account previous publications dedicated to NAC transcription factors

Summary

Introduction

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. The NAC gene family is one of the largest groups of plant transcription factors (TFs), which is known to regulate biotic and abiotic stress-responses such as osmotic stress and various plant developmental processes. NAC proteins are plant-specific TFs, and the NAC family has been recently reviewed by Puranik et al (2012). Two parts can be distinguished in the structure of NAC proteins: the NAC domain (InterPro IPR003441), in the N-terminal region, subdivided in five well-conserved subdomains (A-E); and the transcription regulatory regions (TRRs), in the C-terminal region, which is very variable in sequence and in length. The NAC domain is involved in dimerization and DNA binding, whereas the TRR region plays the role of transcription activator or repressor (Puranik et al 2012). Evolutionary studies have been done on NAC genes for all major groups of land plants, and it has been shown that some NAC subfamilies were already present in early diverged land plants (Zhu et al 2012)

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