Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat

Abstract

Background The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives. Results We identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu , 29 in Aegilops tauschii , and 31 in Brachypodium distachyon . We analyzed the chromosomal locations and orthology relations of the identified trihelix genes, and no trihelix gene was found to be located on chromosome 7A, 7B, or 7D of wheat, thereby reflecting the uneven distributions of wheat trihelix genes. Phylogenetic analysis indicated that the 186 identified trihelix proteins in wheat, rice, B. distachyon , and Arabidopsis were clustered into five major clades. The trihelix genes belonging to the same clades usually shared similar motif compositions and exon/intron structural patterns. Five pairs of tandem duplication genes and three pairs of segmental duplication genes were identified in the wheat trihelix gene family, thereby validating the supposition that more intrachromosomal gene duplication events occur in the genome of wheat than in that of other grass species. The tissue-specific expression and differential expression profiling of the identified genes under cold and drought stresses were analyzed by using RNA-seq data. qRT-PCR was also used to confirm the expression profiles of ten selected wheat trihelix genes under multiple abiotic stresses, and we found that these genes mainly responded to salt and cold stresses. Conclusions In this study, we identified trihelix genes in wheat and its close relatives and found that gene duplication events are the main driving force for trihelix gene evolution in wheat. Our expression profiling analysis demonstrated that wheat trihelix genes responded to multiple abiotic stresses, especially salt and cold stresses. The results of our study built a basis for further investigation of the functions of wheat trihelix genes and provided candidate genes for stress-resistant wheat breeding programs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5632-2) contains supplementary material, which is available to authorized users.

Genome-wide identification, characterization and expression pattern analysis of APYRASE family members in response to abiotic and biotic stresses in wheat

“…In wheat, transcription factors such as MYB (He et al, 2012; Zhang et al, 2012), WRKY (Ning et al, 2017; Niu et al, 2012), No Apical Meristem ( NAC ) (Xia et al, 2010) and Dehydration Response Element-Binding proteins ( DREB ) (Pellegrineschi et al, 2004) have been characterized as stress-related gene families. Meanwhile, many genes in wheat have shown specific responses under various stresses: for example, the TRIHELIX gene family under salt and cold stress (Xiao et al, 2019), Mitogen-activated protein kinase ( MAPK ) and Catlase ( CAT ) genes under osmotic stress (Dudziak et al, 2019), and Glucose-6-Phosphate Dehydrogenase ( G6PDH ) gene under salt stress (Nemoto & Sasakuma, 2000). Overexpression of stress-responsive genes from wheat could lead to a significant increase of stress tolerance, such as TaASR1 in drought stress (Hu et al, 2013), TaCIPK29 and TaAQP8 in salt stress (Deng et al, 2013; Hu et al, 2012), TaFER-5B in heat and other stresses (Zang et al, 2017), TaAQP7 in cold stress (Huang et al, 2014), and TaWRKY44 in multiple abiotic stress (Wang et al, 2015).…”

Peer Review #1 of "Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) (v0.1)"

“…These results reflected the diverse functions of tomato C2H2-ZFs and will be helpful for their future functional analysis. The tissue-specific expression of genes usually is preliminarily used to predict their corresponding functions (Xiao et al, 2019). Therefore, we assessed the expression profiles of the 104 C2H2-ZFs in various tomato tissues using published transcriptomic data (Zouine et al, 2017), revealing that the C2H2-ZF genes display a diversity of relative expression patterns in different organs ( Figure 6) and may therefore play differing roles in various tissues or biological processes.…”

Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression

“…In spite of their overall conservation with bacterial, archaeal, and animal RNase J-CPSF members, plant RNase Js are distinguished by a C-terminal extension with high homology to the GT-1 DNA-binding domain (Figure 1) [9,52]. The GT-1 domain was defined initially in pea and subsequently in about 30-member families of Arabidopsis, wheat, and rice transcription factors that regulate various developmental processes and are stress-responsive [58][59][60][61]. The DNA-binding domain of GT factors features a trihelix structure, which contains three conserved tryptophan residues and an amphipathic helix ( Figure 2).…”