Origin,Evolution And Function Analysis Of Intronless Sub-family Genes In Rosaceae Fruit Trees

Eukaryotic genes can be classified into intronless（no introns）,intron-poor（three or fewer introns per gene）,or intron-rich.Early eukaryotic genes were all intron-rich,and their alternative splicing into multiple transcripts,giving rise to different proteins,might have played pivotal roles in adaptation and evolution.Interestingly,extant plant genomes contain many gene families with one or sometimes few sub-families with genes that are intron-poor or intronless.Previous studies found the intronless genes responsed to abiotic stresses.However,it remains unknown how these intron-poor or intronless genes have originated and evolved and what their possible functions are.The Rosaceae family is an economically-important family throughout the world,and comprises many important fruits,such as strawberries,apples,pears,peaches,meis and apricots,as well as flowers and ornamental trees such as roses and rowans.Understanding the microevolution of intron-poor sub-families in Rosaceae species,provides further insight into evolutionary mechanisms in angiosperms and plant genome evolution and functional divergence.Strawberry is an important horticultural crop grown in many tropical,subtropical,and temperate areas throughout the world.However,more extreme temperatures and droughts,serious fungal infections and secondary salinization have strongly limited the growth,development,reproduction,and yield of strawberry plants in recent years.The sequenced diploid woodland strawberry Fragaria vesca with a small genome（240 Mb genome,2n=2x=14）as a model for the fruit trees offers the opportunity to study intron-poor subfamily genes.1.In this study,we selected seven genomes representative for the tree of plant life（the green alga Chlamydomonas reinhardtii,the moss Physcomitrella patens,the the early vascular plant Selaginella moellendorffii,the gymnosperm Ginkgo biloba,the early diverging angiosperm Amborella trichopoda,the monocot Oryza sativa,and the eudicot Arahaliana）.For resolving the following:in a given species,how many gene families may contain such intronless or intron-poor sub-families?When did these originate?Did they evolve once or multiple times?How did they evolve?What are their potential functions?What were the mechanisms responsible for their origin and expansion?Did intronless and/or intron poor genes face the same or different selection pressures as the intronrich genes?We identified 33 such gene families that contained intronless and intron-poor sub-families.The identified intronless genes from the different gene sub-families were distributed over all chromosomes in both Arabidopsis and rice and uneven.Intronless genes seemed to have first emerged in early land plant evolution,while intron-poor sub-families seemed first to have appeared in green algae.The results illustrate that both WGD/segmental and tandem duplications played an important role in the expansion of intronless genes in the intron-poor sub-families.In contrast to intron-rich genes,intronless genes in intron-poor subfamilies occurred later,and were subject to stronger functional constraints by duplication time and selection pressure analysis.Based on large-scale RNA-seq analyses and GO enrichment in Arabidopsis and rice,intronless or intron-poor genes in AP2,EF-hand₇,bZIP,FAD_binding₄,STE_STE11,CAMK_CAMKL-CHK1,and C2 gene families were more likely to play a role in response to drought and salt stress,compared to intron-rich genes in the same gene families,whereas intronless genes in the B_lectin and S_locus_glycop gene family were more likely to participate in epigenetic processes and plant development.Understanding the origin and evolutionary trajectory,as well as the potential functions,of intronless and intron-poor sub-families provides further insight into plant genome evolution and the functional divergence of genes.2.The sequenced genomes of the Rosaceae species offer the opportunity to study the microevolution of these intron-poor sub-families.In present study,we added grape as outgroup,analyzed the 33 gene families contained intronless and intron-poor sub-families in Prunus dulcis,Prunus domestica,Prunus persica,Pyrus communis,Malus×domestica,Rosa chinensis,Rubus occidentailis and Fragaria vesca.These species belong to Maloideae,Prunoideae,and Rosoideae.It was found that very few intron-rich genes appeared in intronpoor sub-families in Rosaceae species.We counted the gene duplication and gene loss events in intron-poor sub-family genes,the gene loss events occurred randomly.In contrast to intron-rich genes,intronless genes in intron-poor sub-families occurred later,were subject to weaker functional constraints and faster evolutionary processes.3.Based on the two parts studies,we further analysis the phylogenetic,chromosomal locations,duplication,selection pressure and functions of intronless genes in intron-poor subfamilies of woodland strawberry.All the identified strawberry genes were mapped to the seven strawberry chromosomes and were not distributed evenly in these seven chromosomes.The both WGD/segmental and transposed duplications played an important role in the expansion of strawberry intronless genes in the intron-poor sub-families.Furthermore,in contrast to intron-rich genes,the intronless duplicates in intron-poor sub-families occurred later,which were subject to stronger functional constraints and slower evolutionary processes according to the analysis of Ks and selective pressure.The functional analysis revealed that strawberry intronless genes played more important roles in responding to plant diseases and drought stresses than intron-rich genes.Understanding the evolution of intronless and intronpoor sub-families,as well as the potential functions,provides further insight into plant genome evolution and functional divergence.