Genome-wide Identification And Characterization Of Expansin Genes In Gossypium(G.Raimondii And G.hirsutum)

Cotton(Gossypium spp.)is an important economic crop and provides the pleasing natural fiber for spinning industry.The releases of Gossypium(G.raimondii,G.arboreum and G.hirsutum)genome sequence provide much important information for identification of genes controlling high yield and excellent quality,and for exploration of loci responding to disease and stress.And the sequences of Gossypium have laid a good foundation for the cotton genetic improvement.Expansin is the first protein which has been shown to loosen the components of rigid plant cell walls and thereby allow cell expansion.Expansins are able to weaken the linkage between cellulose microfibrils,thereby allowing extension of the wall through polymer creep in response to the mechanical forces generated by cell turgor pressure,which could result in the plant cell growth.Although many molecular research progresses in Arabidopsis thaliana have been reported,the information of Expansin in Gossypium is necessary to explore.To get insight into Expansin genes in Gossypium,genome-wide exploration and comprehensive characterization of the G.raimondii and G.hirsutum Expansin gene family members were conducted.The evolutionary history was evaluated by means of phylogenetic tree construction and collinearity analyses on Expansin genes.Based on the expression microarray and RNA-seq data,the expression profile of Gossypium Expansin genes was detected in different development stage of fiber and other tissues(including leaf,petal,ovule,etc),so as to identify the Expansin genes controlling fiber development.The results are as follows:1.Thirty-nine and 72 Expansin genes were identified in G.raimondii and G.hirsutum,respectively.A phylogenetic analysis of Gossypium Expansin amino acid sequences has been performed(using Expansins from A.thaliana and O.sativa as outgroup)to classify Expansin families.To naming Expansin families members,protein subfamily root symbols(EXPA,EXPB,EXLA,EXLB)were followed by a subfamily designator(1,2,3,4 etc.)concluding with the individual gene number(based on chromosomal position within each subfamily).Therefore,26 GrEXPA,4 GrEXPB,3 GrEXLA and 6 GrEXLB are including in G.raimondii,and 46 GhEXPA,8 GhEXPB,6 GhEXLA and 12 GhEXLB are including in G.hirsutum genome.Every subfamily of Expansin possessed diversity exon-intron structures.2.Dispersed chromosome segmental duplications and tandem duplications were also important factors facilitating gene family expansion.Collinearity analysis indicated that the tandem duplications and segmental duplications resulted in the expansion of Expansins in G.raimondii.The Expansin family experienced an abrupt threefold ploidy increase,resulted from three genomic duplication contributed to the expansion,followed by purifying selection(negative selection)of selective pressure.The Expansin family of G.raimondii followed by purifying selectionMeanwhile,in the tetraploidy G.hirsutum,the abundance of Expansin members also results from polyploidizaion,although gene loss and dysfunctional were observed.3.Collinearity analyses between Gossypium and A.thaliana indicated that most Expansin genes were located in the collinear chromosome regions.The collinearity information indicated that the Expansins in Gossypium and A.thaliana evolved from the common ancestors.Most functions of Expansins in A.thaliana have been explored and discovered,so we can predict the role of collinear orthologous Expansin genes in Gossypium so as to further characterise and validate the functions of Expansin genes in G.hirsutum.4.Comparsion of expression profile among G.raimondii different stage of fiber development,different tissue including leaf and petal based on RNA-seq and microarray indicated that most Expansin genes were involved in the physiology procceedure and development,and diversity expression level among different spatio-temporal domain.GrEXLA1,GrEXLA2 and GrEXPA16 exhibited the highest expression in petal.GrEXPA23 and GrEXPA24 exhibited the highest expression in leaf.It was speculated that the five genes were involved in the development of petal and leaf.The remained genes exhibited different transcript accumulation at different stages of fiber development,indicated some roles relating to fiber.5.Expansin genes in G.hirsutum were involved in the development of fiber and others.RNA-seq data indicated that the transcript abundance of every Expansin gene increased significantly at special spatio-temporal domain.The high level transcript of GhEXPA07 and GhEXLB11 were observed in root,activity expression of GhEXPA26 and GhEXLB01 were detected in stem,abundant mRNA transcripted from GhEXPA24 was observed in young leaves.GhEXPA18 transcribed actively in 0 dpa ovule.The expression profile of Expansins indicated that the unique role of Expansin at special developmental stage and/or special tissue.Especially,the transcript level of GhEXPA14 and GhEXPA36 were unusually high in the10~20 dpa ovlue/fiber,of which the orthologous GrEXPA19 samely transcripted actively.So,GhEXPA14 and GhEXPA36 were speculated to play an important role in the formation of fiber quality.