Identification and analysis of the TIFY gene family in Gossypium raimondii

Abstract

ABSTRACT. The highly conserved TIFY domain is included in the TIFY protein family of transcription factors, which is important in plant development. Here, 28 TIFY family genes were identified in the Gossypium raimondii genome and classified into JAZ (15 genes), ZML (8), PPD (3), and TIFY (2). The normal (TIF[F/Y]XG) motif was dominant in the TIFY family, excluding the ZML subfamily, in which TLSFXG was prevalent. TIFY family genes were unevenly distributed in the G. raimondii genome, with TIFY clusters present on chromosome 9. Phylogenetic analysis indicated abundant variations in the G. raimondii TIFY family, which were most closely related to those in Theobroma cacao among 5 species. Exon-intron organization and intron phases were homologous within each subfamily, correlating with their phylogeny. Intra-species synteny analyses indicated that genomic duplication contributed to the expansion of the TIFY family. Inter-species synteny analyses indicated that synteny regions involved in G. raimondii TIFY family genes were also present in the comparison of G. raimondii vs Arabidopsis thaliana or T. cacao, signifying that these genes had common ancestors and play the same or similar roles in biological processes. Greater synteny was present in the comparison of G. raimondii vs T. cacao than of G. raimondii vs A. thaliana. The expression patterns of TIFY family genes were characterized and most TIFY family genes were indicated to be involved in fiber development. Our study provides new data related to the evolution of TIFYs and their role as important regulators of transcription; these data can be useful for fiber development.

Genome-wide identification and characterization of JAZ gene family in upland cotton (Gossypium hirsutum)

“…JAZ family proteins, as the important transcription factors, have been identified in some plant species, like rice 46 , Chickpea 54 , grape 55 , soybean 47 , rubber tree 48 , Salvia miltiorrhiza 56 , G . ramondii 43 and maize 57 . Until more recently, Zhao et al .…”

“…Recently, 28 TIFY genes were identified in a diploid cotton species Gossypium raimondii , and some of JAZs are expressed in cotton fibers 43 . Another study reported 21, 28 and 50 TIFY family members in three cotton species ( G .…”

Identification of TIFY Family Genes and Analysis of Their Expression Profiles in Response to Phytohormone Treatments and Melampsora larici-populina Infection in Poplar

“…(Sirhindi et al, 2016); 30 TIFY genes were found in apple ( Malus × domestica Borkh.) (Li et al, 2014); 19 TIFY genes were found in grape ( Vitis vinifera ) (Zhang et al, 2012); 28 TIFY genes were found in the Gossypium raimondii genome (He et al, 2015); 21 TIFY genes were found in Brachypodium distachyon (Zhang et al, 2015); and 34 TIFY genes in found in wild soybean ( Glycine soja ) (Zhu et al, 2013). In these studies, the expression profiles of TIFY genes were investigated and their functions were predicted based on their preferentially transcriptional abundance in a given tissue or under a given stress condition.…”

Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses

“…Such work has been performed in several genome-sequenced plant species, such as Arabidopsis (Vanholme et al, 2007), Oryza sativa (Ye et al, 2009), grape (Zhang et al, 2012), Phaseolus vulgaris (Aparicio-Fabre et al, 2013), Glycine soja (Zhu et al, 2013), apple (Li et al, 2015), Gossypium raimondii (He et al, 2015) and Brachypodium distachyon (Zhang, You & Chan, 2015), etc.…”