title: Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.).
abstract: The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet) that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI), with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants.
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Swati
authors.initials: S
authors.lastname: Puranik
authors.forename: Pranav Pankaj
authors.initials: PP
authors.lastname: Sahu
authors.forename: Sambhu Nath
authors.initials: SN
authors.lastname: Mandal
authors.forename: Venkata Suresh
authors.initials: VS
authors.lastname: B
authors.forename: Swarup Kumar
authors.initials: SK
authors.lastname: Parida
authors.forename: Manoj
authors.initials: M
authors.lastname: Prasad
mesh_terms: D000595:Amino Acid Sequence; D032461:Chromosomes, Plant; D020869:Gene Expression Profiling; D017343:Genes, Plant; D008969:Molecular Sequence Data; D008897:Panicum / Q000235:genetics*; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics*
chemical_list: D014157:Transcription Factors