Genome-wide identification and expression analysis of expansin gene family in common wheat (Triticum aestivum L.)

Abstract

BackgroundExpansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). In this work, we performed a comprehensive study on the molecular characterization, phylogenetic relationship and expression profiling of common wheat (Triticum aestivum) expansin gene family using the recently released wheat genome database (IWGSC RefSeq v1.1 with a coverage rate of 94%).ResultsGenome-wide analysis identified 241 expansin genes in the wheat genome, which were grouped into three subfamilies (EXPA, EXPB and EXLA) by phylogenetic tree. Molecular structure analysis showed that wheat expansin gene family showed high evolutionary conservation although some differences were present in different subfamilies. Some key amino acid sites that contribute to functional divergence, positive selection, and coevolution were detected. Evolutionary analysis revealed that wheat expansin gene superfamily underwent strong positive selection. The transcriptome map and qRT-PCR analysis found that wheat expansin genes had tissue/organ expression specificity and preference, and generally highly expressed in the roots. The expression levels of some expansin genes were significantly induced by NaCl and polyethylene glycol stresses, which was consistent with the differential distribution of the cis-elements in the promoter region.ConclusionsWheat expansin gene family showed high evolutionary conservation and wide range of functional divergence. Different selection constraints may influence the evolution of the three expansin subfamilies. The different expression patterns demonstrated that expansin genes could play important roles in plant growth and abiotic stress responses. This study provides new insights into the structures, evolution and functions of wheat expansin gene family.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5455-1) contains supplementary material, which is available to authorized users.

Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

“…Multiple sequence alignment of the amino acid sequences of Dof proteins were performed based on MUSCLE program (http://www.ebi.ac.uk/Tools/msa/ muscle/) [75,76]. Subsequently, the Bayesian and N-J phylogenetic trees were constructed based on the method by Han et al [77]. Furthermore, maximum likelihood and minimal evolution methods were applied for the tree construction to validate the results of the N-J method in MEGA5.0.…”

“…The Chinese wheat cultivar Zhongmai 175 seedlings were cultivated into two leaves and one heart stage according to the culture conditions of Han et al [77]. Then seedlings were treated with the following conditions: heavy metal stress with 300 μM CrCl 3 and CdCl 2 , drought stress with 20% (w/v) PEG 6000, salinity stress with 200 mM NaCl, oxidative stress with 15 mM H 2 O 2 , hormone stress with 100 μM ABA (abscisic acid) and SA (salicylic acid), and 10 μM IAA (indole-3-acetic acid), cold stress under 4°C) and heat stress under 42°C.…”

Transcription strategies related to photosynthesis and nitrogen metabolism of wheat in response to nitrogen deficiency

“…In the pathway of extracellular region (Fig. 10c), expansin gene family can increase the extensibility of cell wall [41][42][43]. Previous studies have shown that overexpression of expansin family members can cause the changes in crop morphology and improve the crop adaptability of stress resistance or low nutrition conditions [44,45].…”

Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

“…The Chinese wheat cultivar Zhongmai 175 seedlings were cultivated into two leaves and one heart stage according to the culture conditions of Han et al [77]. Then seedlings were treated with the…”