Comprehensive analysis of NAC transcription factors in diploid Gossypium: sequence conservation and expression analysis uncover their roles during fiber development

Abstract

Determining how function evolves following gene duplication is necessary for understanding gene expansion. Transcription factors (TFs) are a class of proteins that regulate gene expression by binding to specific cis-acting elements in the promoters of target genes, subsequently activating or repressing their transcription. In the present study, we systematically examined the functional diversification of the NAC transcription factor (NAC-TFs) family by analyzing their chromosomal location, structure, phylogeny, and expression pattern in Gossypium raimondii (Gr) and G. arboreum (Ga). The 145 and 141 NAC genes identified in the Gr and Ga genomes, respectively, were annotated and divided into 18 subfamilies, which showed distinct divergence in gene structure and expression patterns during fiber development. In addition, when the functional parameters were examined, clear divergence was observed within tandem clusters, which suggested that subfunctionalization had occurred among duplicate genes. The expression patterns of homologous gene pairs also changed, suggestive of the diversification of gene function during the evolution of diploid cotton. These findings provide insights into the mechanisms underlying the functional differentiation of duplicated NAC-TFs genes in two diploid cotton species. cotton, NAC gene family, phylogeny, expression patterns Citation:Shang, H., Wang, Z., Zou, C., Zhang, Z., Li, W., Li, J., Shi, Y., Gong, W., Chen, T., Liu, A., Gong, J., Ge, Q., Yuan, Y. (2016). Comprehensive analysis of NAC transcription factors in diploid Gossypium: sequence conservation and expression analysis uncover their roles during fiber development. Sci China Life Sci 59, 142 -153.

Transcriptome Analysis of Ten Days Post Anthesis Elongating Fiber in the Upland Cotton (<i>Gossypium hirsutum</i>) Chromosome Substitution Line CS-B25

“…Among them, more than 30 had been shown to have higher expression levels in 10 -20 DPA fiber. NAC genes had been shown to control secondary cell wall thickening during fiber development [69]. Our transcript profile observations during fiber development are similar to those of Al-Ghazi et al [70].…”

“…Many NAC transcription factors were also highly expressed in CS-B25 10-DPA fibers. A total of 143 and 145 NAC genes have been identified in the genomes of the two diploid cottons G. arboretum and G. raimondii, respectively [69].…”

“…This observation is consistent with the results of Dou et al [73], in that many GhWRKY transcription factors had high expression levels at 0, 20, and 25 DPA fiber and they are involved in fiber initiation and secondary wall synthesis. Using the homologous alignment method, 143 genes for NAC-transcription factors in the G. arboretum genome were identified [69]. Many of them were highly expressed in 15 DPA fiber cells and might be involved in the fiber secondary wall thickening.…”

Asymmetric Evolution and Expansion of the NAC Transcription Factor in Polyploidized Cotton

“…A comprehensive analysis of the NAC family during allopolyploidization is expected to accelerate molecular breeding in cotton. Previous studies conducted whole-genome annotation of the NAC family in G. arboreum and G. raimondii (Shang et al, 2013 , 2016 ) but only identified the NAC family in G. hirsutum by using EST scanning (Meng et al, 2009 ; Huang et al, 2013 ; Shah et al, 2013 , 2014 ). Thus, a systematic research of the molecular evolution of the NAC family in cotton is needed.…”

Cotton genome: challenge into the polyploidy

“…Secondly, these cotton genome references are available to the genome-wide analysis and expression profiling of the specific gene family, such as phospholipase D gene family in G. arboreum [11], NAC transcription factors gene family in diploid Gossypium [12] and a mass of secondary metabolites such as gossypol, the cotton phytoalexins against pathogens and herbivores [6,13].…”