Genome-Wide Identification and Characterisation of Wheat MATE Genes Reveals Their Roles in Aluminium Tolerance

Abstract

The Multidrug and toxin efflux (MATE) gene family plays crucial roles in plant growth and development and response to adverse stresses. This work investigated the structural and evolutionary characteristics, expression profiling and potential functions involved in aluminium (Al) tolerance from a genome-wide level. In total, 211 wheat MATE genes were identified, which were classified into four subfamilies and unevenly distributed on chromosomes. Duplication analysis showed that fragments and tandem repeats played the main roles in the amplification of TaMATEs, and Type II functional disproportionation had a leading role in the differentiation of TaMATEs. TaMATEs had abundant Al resistance and environmental stress-related elements, and generally had a high expression level in roots and leaves and in response to Al stress. The 3D structure prediction by AlphaFold and molecular docking showed that six TaMATE proteins localised in the plasmalemma could combine with citrate via amino acids in the citrate exuding motif and other sites, and then transport citrate to soil to form citrate aluminium. Meanwhile, citrate aluminium formed in root cells might be transported to leaves by TaMATEs to deposit in vacuoles, thereby alleviating Al toxicity.

Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses

“…The GFF3 file in the whole genome information of tomato ABF/AREB was visualized and analyzed by TBtools software. ABF/AREB gene members were renamed according to their chromosomal distribution ( Duan et al, 2022 ). The CDS sequences of tomato ABF/AREB genes were further used to calculate the relationship between Ka (non-synonymous substitution rate) and Ks (synonymous substitution rate) among family members by calculating Ka and Ks values by Simple Ka/Ks calculator (NG) of TBtools software ( Liu et al, 2022b ).…”

Genome Wide Identification and Characterization of Wheat GH9 Genes Reveals Their Roles in Pollen Development and Anther Dehiscence

“…The total RNA of all samples was extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufactures’ instructions, and approximately 1 µg RNA was reverse transcribed with PrimerScript 1st Strand cDNA synthesis kit (TaKaRa, Shiga, Japan) and miRcute Plus miRNA cDNA T (Tingen, Beijing, China) for genes and miRNAs, respectively, according to the manufacturer protocol. qRT-RCR assays for TaGH9 and miRNAs were conducted on an Eco Real-time PCR system (Illumina, CA, USA) using TB Green Premix Ex Taq (Tli RNaseH Plus) kit (TaKaRa, Shiga, Japan) and SYBR ® miRcute Plus miRNA PreMix (Tingen, Beijing, China), respectively, as described previously [ 28 , 75 ]. Wheat 18S gene served as the reference gene for TaGH9 analysis, and U6 was used as a reference gene for miRNA analysis.…”

Genome-wide identification of wheat ABC1K gene family and functional dissection of TaABC1K3 and TaABC1K6 involved in drought tolerance

“…The three-dimensional (3D) structures of TaABC1K proteins from different clades were predicted using the online Alphafold2 website according to Duan et al (2022) . As the latest developed protein predicting tool, Alphafold has high accuracy and easy-to-use ( Jumper et al, 2021 ).…”