Genome-Wide Investigation of Spliceosomal SM/LSM Genes in Wheat (Triticum aestivum L.) and Its Progenitors

Abstract

The SSM/SLSM (spliceosomal Smith (SM)/SM-like (LSM)) genes are the central components of the spliceosome in eukaryotes, which play an important role in regulating RNA splicing, participating in diverse biological processes. Although it has been detected in Arabidopsis and rice etc. plants, the members and significance of the SSM/SLSM gene family in wheat are still not reported. In this study, we identified the SSM/SLSM genes in wheat and its progenitors at genome-scale, where 57 SSM/SLSM genes were identified in wheat, together with 41, 17and 19 found in Triticum dicoccoides, Triticum urartu, and Aegilops tauschii. Furthermore, their phylogenetic relationship, gene structures, conserved motifs, and cis-regulatory elements were systematically analyzed. By synteny analysis, good collinearity of SSM/SLSM genes was found among bread wheat and its progenitors’ genomes, and the distribution of SMD2 genes in wheat chromosome 5A, 4B and 4D located in the 4AL-5AL-7BS chromosome model, due to the translocation. Then, the positively selected genes were further investigated based on the non-synonymous to synonymous (dN/dS) analysis of the orthologous pairs. Finally, the expression profiles of the SSM/SLSM genes were detected using RNA-seq datasets, and eight stress-responsive candidate genes were selected to validate their expression through qPCR (real-time quantitative polymerase chain reaction). According to the co-expression network analysis, the correlation between the LSM7-7A gene and related genes was illustrated through Gene Ontology (GO) enrichment analysis. Furthermore, the LSM7-7A gene was related to the Arabidopsis homologous salt tolerance gene RCY1. This investigation systematically identified the complete candidates of SSM/SLSM genes and their characters in wheat and its progenitors, and provided clues to a better understanding of their contribution during the wheat polyploidy process.