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.
Highlights
In eukaryotes, precursor mRNAs become mature mRNAs through fundamental processes of splicing, 5 capping, 3 polyadenylation, etc
By BLASTP and HMMER software searching, 57 SSM/SLSM genes were found in the wheat (TaSSM/SLSMs)
From the result of dN/dS, we found that most SM genes wwheeraetp. uFrreolymsethleectreedsudlut roinf gdNpo/lydpSl,owideizfaotuionndetxhcaetpmt inostthSeMfirsgtesnteasgewoefrpeoplyuprelolyidsizealetciotend dSuMriDn1g pwoelryeplpooidsiitzivateiloynseexleccetpetdinanthdeifinrstht estasgeceoonfdpostlaygpelooidf ipzaotliyopnloSiMdiDza1tiwonerSeMpoBsiwtivereely speolescitievdelaynsdelienctehde,swechoinledssptlaicgeeoosof mpoalyLpSloMidgizenateisonmSoMstlBy wunedreerpgoosiptiovseitliyveseslelcetcetdio, nwehxi-le scpelpictefoosromLSaMl L3SaMndgeLnSeMs 7mgoesntleys.uTnhdeeregvoolpuotsioitnivareysetrleceticoonnsetxrcuecptetdfofrorLSSMM3Da2ngdenLeSMis7 gsehnoews.nThine eFvioglurteion3a.ryCtoremepcaornesdtruwctiethd fToraSSMMDD22-3gDen, eTisaSsMhoDw2n-3iBn FaignudreT3a.SCMoDm2p-3aAre,d wTiatShMTaDS2M-5DA2,3thDe, TeavSoMluDti2o-n3aBryandreTlaatSioMnDsh2i-p3Ab,eTtwaSeMenD2T-a5SAM, tDh2e-e4vDoluantidonTaraySMreDla2ti-o4nBshisip bcelotwseere. n TaSMD2-4D and TaSMD2-4B is closer
Summary
Precursor mRNAs (pre-mRNAs) become mature mRNAs through fundamental processes of splicing, 5 capping, 3 polyadenylation, etc. Pre-mRNA splicing is catalyzed by the spliceosome, a highly dynamic ribonucleoprotein machinery containing small nuclear ribonucleo-proteins (snRNPs) and non-snRNP proteins [1,2]. For the U6 snRNP, the binding proteins were replaced with seven SM-like proteins (LSM) named as LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, and LSM8 (SLSM gene family) [7,8,9,10]. These 14 genes are directly binding with the spliceosome, they are collectively referred to as SSM/SLSM (spliceosomal SM/LSM) gene family
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