Genome-Wide Identification, Evolution, and Expression of GDSL-Type Esterase/Lipase Gene Family in Soybean

Abstract

GDSL-type esterase/lipase proteins (GELPs) belong to the SGNH hydrolase superfamily and contain a conserved GDSL motif at their N-terminus. GELPs are widely distributed in nature, from microbes to plants, and play crucial roles in growth and development, stress responses and pathogen defense. However, the identification and functional analysis of GELP genes are hardly explored in soybean. This study describes the identification of 194 GELP genes in the soybean genome and their phylogenetic classification into 11 subfamilies (A–K). GmGELP genes are disproportionally distributed on 20 soybean chromosomes. Large-scale WGD/segmental duplication events contribute greatly to the expansion of the soybean GDSL gene family. The Ka/Ks ratios of more than 70% of duplicated gene pairs ranged from 0.1–0.3, indicating that most GmGELP genes were under purifying selection pressure. Gene structure analysis indicate that more than 74% of GmGELP genes are interrupted by 4 introns and composed of 5 exons in their coding regions, and closer homologous genes in the phylogenetic tree often have similar exon-intron organization. Further statistics revealed that approximately 56% of subfamily K members contain more than 4 introns, and about 28% of subfamily I members consist of less than 4 introns. For this reason, the two subfamilies were used to simulate intron gain and loss events, respectively. Furthermore, a new model of intron position distribution was established in current study to explore whether the evolution of multi-gene families resulted from the diversity of gene structure. Finally, RNA-seq data were used to investigate the expression profiles of GmGELP gene under different tissues and multiple abiotic stress treatments. Subsequently, 7 stress-responsive GmGELP genes were selected to verify their expression levels by RT-qPCR, the results were consistent with RNA-seq data. Among 7 GmGELP genes, GmGELP28 was selected for further study owing to clear responses to drought, salt and ABA treatments. Transgenic Arabidopsis thaliana and soybean plants showed drought and salt tolerant phenotype. Overexpression of GmGELP28 resulted in the changes of several physiological indicators, which allowed plants to adapt adverse conditions. In all, GmGELP28 is a potential candidate gene for improving the salinity and drought tolerance of soybean.

Genomic-Wide Analysis of the PLC Family and Detection of GmPI-PLC7 Responses to Drought and Salt Stresses in Soybean

“…Identification of the soybean PLC gene family was performed according to the method described previously ( Amarjeet et al, 2013 ; Su et al, 2020 ), with some revisions. The putative GmPLC gene family members were identified in the soybean gene family databases Phytozome v12 and SoyBase ( Goodstein et al, 2012 ), using keywords such as “phospholipase C,” “phosphatidylinositol phospholipase C,” and “phosphoesterase.” We verified identifications using the phospholipase C domain in the SMART database ( Letunic et al, 2012 ).…”

Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification of GmDUF4228–70 in Response to Drought and Salt Stresses

“…For salt stress, the roots of seedlings were placed in a 200 mM NaCl solution. Samples were also collected at 0, 0.5, 1, 2, 4, 8, 12, and 24 h after treatment (Su et al, 2020). The collected samples were quickly moved into liquid nitrogen and then stored at −80 • C for later use.…”

High-Throughput Sequencing-Based Identification of miRNAs and Their Target mRNAs in Wheat Variety Qing Mai 6 Under Salt Stress Condition

“…In alkali-tolerant SR4 wheat, tae-miR1122a was found to inhibit ROS accumulation and enhance alkaline stress tolerance by regulating its target gene Rboh expression ( Han et al, 2018 ). GDSL esterase also plays a vital role in abiotic stress, pathogen defense, seed development, and lipid metabolism ( Tan et al, 2014 ; Su et al, 2020 ). However, there is no report about the effect of GDSL esterase on wheat salt tolerance.…”