Genome-wide Identification And Expression Profiling Of The SlHsp20 Gene Family In Tomato

The sHsp20 genes are involved in the response of plants to environment stresses including heat shock and also play a vital role in plant growth and development.Small heat shock proteins(sHsps)are crucial molecular chaperones that have been found in all the living organisms.In plant,they represent the most abundant and widespread class among the HSPs.Small Hsps comprised a conserved alpha-crystallin domain(ACD)which is flanked by variable C-terminal and N-terminal regions.These proteins participated in multiple essential processes of cellular activities and could respond to abiotic and biotic stresses,such as heat,drought,pathogens,etc.Although there are a lot of studies on the evolutionary origins and expression regulation of the small heat shock proteins(sHsps)in plants,little is known about this family in tomato,an important vegetable crop in the world.In the present study,we characterized heat shock protein 20(SlHsp20)gene family in tomato(Solanum lycopersicum)through integration of gene structure,chromosome location,phylogenetic relationship and comprehensive expression profile by means of the bioinformatics methods.The salient features of current study are as follows:1.Identification and feature analysis of SlHsp20 family members in tomato.Using bio informatics-based methods,we identified at least 42 putative SlHsp20 genes in tomato.Sequence analysis revealed that most of SlHsp20 genes possessed no intron or a relatively short intron in length.Chromosome mapping showed SlHsp20 genes were randomly distributed across the 12 tomato chromosomes,indicating that inter-arm and intra-chromosome duplication events contributed remarkably to the expansion of sHsp20 genes in tomato.2.Evolution pattern of SlHsp20 gene family.Based on the phylogentic tree of sHsp20 genes from tomato and other plant species(Arabidopsis,rice,soybean,barley,common wheat),all these sHsp20 genes were distributed into 17 subfamilies(CI-CXII,ER,MI,MII,P,Px).SlHsp20 genes were grouped into 13 out of 17 subfamilies.Each subfamily contained several members from diverse species,indicating that these genes may have a common ancestor that generated diverse subfamilies prior to the mono-dicot split.Phylogenetic analysis revealed that the diverse subfamilies of sHsps in plant might go through divergent evolutionary processes.Primary evolutionary forces,like gene duplication,sequence divergence and gene conversion,played important roles in shaping these subfamilies.3.Differential expression analysis of SlHsp20 genes in cultivated tomato and the wild relative Solanum pimpinellifolium.Expression analysis of SlHsp20 genes by using RNA-Seq data in various tissues and developmental stages revealed that 73.8%and 81.0%of the 42 SIHsp20 genes were expressed in at least one stage(tissue)of tomato cultivar and the wild species,respectively.Four genes(SlHsp17.7A?SIHsp17.6B?SlHsp17.6C?SlHsp24.5)were expressed constitutively in almost all the tissues analyzed(leaf,root,flower,flower bud,fruit,cotyledon and hypocotyl),implying that these genes might have specific housekeeping function in tomato cell under normal growth conditions.Two SlHsp20 genes(SlHsp25.7B and SlHsp17.6A)were not expressed in root,leaf,flower in cultivated tomato whereas high expression levels were found in the wild relative.This differential expression levels between tomato cultivar and the wild suggested inter-species diversification for functional specialization during the process of domestication.4.Tissue-specific expression analysis of SlHsp20 gene in cultivated tomato.The results revealed that 19 SlHsp20 genes were preferentially expressed in reproductive organs(flower and fruit)and only 4 were preferentially expressed in vegetative organs(root and leaf).One third(14)SlHsp20 genes were preferentially expressed in B10(ten days after breaker)fruit,indicating their higher activity at the late stage of fruit development.The expression of SlHsp20 genes in different tissues showed specificity among subfamilies.Genes from CI,CVII and CIX subfamilies were expressed in all the tested tissues(root,leaf,flower and fruit).CII,CIII,MI and Px subfamily members were expressed only in reproductive organs.Genes from CV family were expressed only in vegetative organs.Expression analysis of SlHsp20 genes during fruits ripening showed that twenty genes were expressed in at least one fruit development stage.Genes from seven subfamilies(fifteen genes)were expressed at three fruit development stages(mature green,breaker,ten days after breaker).5.Expression analysis of SlHsp20 genes under various stresses and hormone treatment.To further investigate whether the SlHsp20 genes regulated by fruit maturation were induced under environment stresses,quantitative real-time PCR(qRT-PCR)were performed to analyze the expression profiles of SlHsp20 genes under abiotic stresses and hormones.The results revealed that all of the SlHsp20 genes expressed in fruits were regulated under heat stress and most(85%)were up-regulated.And the heat stress inducibility in tolerant plants was stronger than that in susceptible plants.Only one and four SlHsp20 genes were up-regulated under high salinity and drought and more than half were down-regulated.Most genes(95%)expressed in fruit were regulated by various hormones and were mainly down-regulated.In conclusion,we reported the characteristics of SlHsp20 gene family in tomato,including the composition,structure,expression profiles,as well as the origin and evolution.These results provide valuable information that can be implicated in elucidating the evolutionary relationship of sHsp20 gene family in higher plants and functional characterization of the SlHsp20 gene family in the future.Moreover,it might provide deeper insights into sHsps and valuable references for practical applications.