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Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.)

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Title Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.)
 
Creator Puranik, Swati
Sahu, Pranav Pankaj
Mandal, Sambhu Nath
Suresh B., Venkata
Parida, Swarup K.
Prasad, Manoj
 
Subject Foxtail Millet
Setaria italica
Expression Profiling
NAC
Transcription Factor
 
Description Accepted date: April 16, 2013
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.
The authors work in this area was supported by the core grant from National Institute of Plant Genome Research (NIPGR), New Delhi, India. SP acknowledges the award of Research Associateship from NIPGR. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
 
Date 2015-11-13T09:58:15Z
2015-11-13T09:58:15Z
2013
 
Type Article
 
Identifier PLoS One, 8(5): e64594
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/357
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064594
10.1371/journal.pone.0064594
 
Language en_US
 
Publisher PLOS