Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Abstract

BackgroundNAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.

Genome-Wide Identification and Characterization of the <i>Dof</i> Transcription Factor Gene Family in <i>Phaseolus vulgaris</i> L.

“…The number of PvDof homologs identified in this study was similar to that found previously in Arabidopsis, rice, This domain is indicative to be considered a functional TF pertaining to the Dof gene family [40] [44]. Although the same number of Dof genes was found in Arabidopsis (36) and common bean (36), the common bean genome, at 650 Mb [45], is considerably larger than the Arabidopsis genome, at 145 Mb [46]. As shown in Table 1, Cai et al [9] found 34 genes in tomato (with a genome size of 950 Mb), indicating that genome size is not proportional to the number of genes.…”

SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

“…The NAC gene is Ptr-SND1-L-2, an SND1-like NAC domain protein that shares 47% sequence identity with Ptr-SND1-B1 (Li et al, 2012). Phylogenetically, the protein sequence of Ptr-SND1-L-2 is in the same clade as the SND1s and VNDs, both involved in the regulation of secondary cell wall thickening (Hu et al, 2010). The four MYBs include a pair of paralogs, Ptr-MYB002 and Ptr-MYB021 (Li et al, 2012), and two other MYB related TFs (DEG004 and 005).…”

A structural view of the conserved domain of rice stress-responsive NAC1

“…NAC (named as NAM, ATAF1, 2, and CUC2) transcription factors, which are unique to plants, constitute one of the largest plant transcription factor families, of which 105, 138 and 163 putative NAC members have been identified in Arabidopsis, rice and Populus genomes respectively (Ooka et al, 2003;Fang et al, 2008;Hu et al, 2010). Among the three members, after which this family is named, NAM (No Apical Meristem) from petunia is important for shoot apical meristem formation (Souer et al, 1996), CUC2 (cup-shaped cotyledon) is involved in controlling the formation of boundary cells of the meristem (Aida et al, 1997), and ATAF1, 2 show dual function in biotic and abiotic stress responses (Collinge and Boller, 2001;Delessert et al, 2005;Jensen et al, 2007;Lu et al, 2007;Jensen et al, 2008;Wang et al, 2009;Wu et al, 2009).…”