Abstract
The three-amino-acid-loop-extension (TALE) superfamily genes broadly existed in plants, which played important roles in plant growth, development and abiotic stress responses. In this study, we identified 68 Glycine max TALE (GmTALE) superfamily members. Phylogenetic analysis divided the GmTALE superfamily into the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Moreover, the KNOX subfamily could be further categorized into three clades (KNOX Class I, KNOX Class II and KNOX Class III). The GmTALE genes showed similarities in the gene structures in the same subfamily or clade, whose coding proteins exhibited analogous motif and conserved domain compositions. Besides, synteny analyses and evolutionary constraint evaluations of the TALE members among soybean and different species provided more clues for GmTALE superfamily evolution. The cis-element analyses in gene promoter regions and relevant gene expression profiling revealed different regulating roles of GmTALE genes during soybean plant development, saline and dehydration stresses. Genome-wide characterization, evolution, and expression profile analyses of GmTALE genes can pave the way for future gene functional research and facilitate their roles for applications in genetic improvement on soybean in saline and dehydration stresses.
Highlights
The homeobox genes broadly exist in eukaryotes and play an important role in plant growth and development [1]
68 Glycine max TALE (GmTALE) genes were identified from the soybean Wm82.a2.v1 genome on JGI Phytozome 13, and referring to the nomenclature of TALE genes in poplar [1], we named them GmTALE1 to GmTALE68 according to their gene coordinate (Table S1)
We identified 68 TALE superfamily members in soybean, which were unevenly distributed on 20 chromosomes and two scaffolds of the soybean genome
Summary
The homeobox genes broadly exist in eukaryotes and play an important role in plant growth and development [1]. There were four genes in the Arabidopsis KNOX Class I clade, AtSTM, AtKNAT1, AtKNAT2 and AtKNAT6, which displayed distinct expression patterns and functions in the meristems [8,9,10]. The KNOX Class II genes, AtKNAT7, PoptrKNAT7, GhKNAT7-A03 and OsKNAT7 were reported to be crucial for cell elongation and secondary cell wall (SCW) biosynthesis in Arabidopsis, poplar, cotton and rice, respectively [13,14,15]. The KNOX Class III clade of Arabidopsis only contained one gene (AtKNATM) that affected the leaf polarity and leaf development [16]. BEL1-like proteins played important roles in plant growth and development. In Arabidopsis, there were 13 BEL1-like members and large-scale yeast two-hybrid experiments showed they generally were able to interact and form heterodimers with at least one KNOX protein [17,18]. The TALE superfamilies exhibited functional and regulating roles in plant development and different biological processes
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