Abstract
The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and performed a comprehensive investigation for gene and protein structural properties, phylogeny, expression patterns, and multilevel gene regulations. The identified TaTALE proteins were further classified into two groups, TaBLHs and TaKNOXs, which were tightly clustered into the phylogeny. The negative Ka/Ks ratio of duplicated genes suggested purifying selection pressure with confined functional divergence. Various signature domains and motifs were found conserved in both groups of proteins. The occurrence of diverse cis-regulatory elements and modulated expression during various developmental stages and in the presence of abiotic (heat, drought, salt) and two different fungal stresses suggested their roles in development and stress response, as well. The interaction of TaTALEs with the miRNAs and other development-related homeobox proteins also suggested their roles in growth and development and stress response. The present study revealed several important aspects of TaTALEs that will be useful in further functional validation of these genes in future studies.
Highlights
The growth and developmental processes of an organism are directed by a group of genes, known as homeobox genes
The identified sequences were further searched for the occurrence of signature domains, including HD, knotted-like homeobox (KNOX), POX domains as described in the Materials and Methods section, which resulted in the identification of a total of
Based on the sequence similarity (≥90%), the TaTALE genes were clustered into 21 homeologous groups, and each group embodied to A, B, and D subgenomes
Summary
The growth and developmental processes of an organism are directed by a group of genes, known as homeobox genes. These genes encode 60 amino acids residues (AA). Long homeodomain (HD) that consists of three helical structures. The first two helices are connected by a loop, while the helix-turn-helix structure is formed between the second and third helices [1]. The first plant homeobox genes, known as knotted-like homeobox, were discovered in maize [2]. The three amino acid loop extension (TALE) superclass of atypical HD has three extra AAs between the first and second helices [3]. TALE superclass has been further classified into two classes; BEL-like homeobox (BLH) and knotted-like homeobox (KNOX) in plants
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