The Effect Of TEs And SRNA On Genes Related With Cotton Fiber Early Development

Cotton is an important natural fiber crop in the world.It is also regarded as a model plant for studying fiber cell differentiation,evolution of polyploidy and repeated sequences in the genome.Allotetraploid cotton derived from hybridization and polyploidization between the primitive ancestors of diploid A genome cotton species and diploid D genome cotton species.There is great divergence about fiber quality and fiber yield among the three Gossypium species.In the study,mRNA-seq and s RNA-seq were done from early developmental ovules of G.hirsutum(AD₁),G.arboreum(A₂)and G.raimondii(D₅).Transposable elements(TEs)and orthologous genes were identified from the reference genome of the three Gossypium species with the same pipeline.We analyzed the response of TEs to polyploidy,the effect of TEs on the gene expression and the orthologs expression pattern during early fiber development of the three Gossypium species.The main findings are:1.Identification and analysis of TEs in the genomes of G.hirsutum,G.arboreum and G.raimondiiUsing the same TEs discovery pipeline,there are 1,632,693 TE insertions in the genome of G.arboreum,1,006,042 in G.raimondii and 1,362,500 in the A-subgenome and 928,002in the D-subgenome of G.hirsutum.TEs in the genome of G.arboreum are the most abundant and the coverage rate is 82%.Gypsy elements are the most abundant of all TE types in all three Gossypium genomes,going through all the chromosomes with high coverage rate on the middle of the chromosomes.However,most of other TEs distribute on the end of the chromosomes.The number of full-length Gypsy is the largest in G.arboreum and the fewest in the G.raimondii.The copies of most types of TE are fewer in each subgenome of G.hirsutum than in their diploid progenitors.Therefore,no large-scale TE transposition burst is detected in G.hirsutum after allotetraploidization.TEs evolved independently in the three Gossypium genome.2.The distance between TEs and genesThere are a lot of TEs in the three Gossypium genomes.These TEs are the most abundant at 0?500 bp from genes,especially in diploid D genome.It is also the most abundant when TEs insert into genes in G.raimondii.In G.hirsutum,36.5%of genes harbor TEs,which is lower than G.arboreum and G.raimondii.When TEs insert into genes or away 0?500bp from genes,the proportion of Gypsy elements decline relative to the proportion in the whole genome,and LARD and MITE increase.This illustrates that high frequency of recombination and exchange,and TEs suffered strong purified selection in the vicinity of genes.3.The effect of TEs on gene expressionTEs associated with 24-nt siRNA are about 50%of total TEs in the three Gossypium genome.The proportion of TEs associated with 24-nt and 24-nt siRNAs associated with TEs are both the highest in G.hirsutum.The average gene expression level decline when TEs insert into genes or within the vicinity of genes,especially for siRNA+TEs.But the trends of gene expression differ not entirely the same,which are caused by the difference of transposon activity in the three Gossypium genome.Moreover,TEs not only bring down gene expression level but also increase them.So,the effect of TEs on genes are diverse,which are possibly involved in fiber early development.4.Identification of orthologs among the three Gossypium genomesBased on chromosome co-linear relation and gene sequence similarity,we obtained37,062 orthologs between two Gossypium genomes,and 23,690 orthologs among the three Gossypium genome.Orthologs are separated into 16 types,some of them show novel expression or gene silencing.As a whole,silenced genes are more than genes with novel expression in allotetraploidy.Meanwhile,both of them in Dt-subgenome are more than At-subgenome,which may influence the early development of fiber.The number of orthologs with differential expression is the highest when compare between two diploid progenitors.It is the fewest when compare between G.hirsutum and G.arboreum.The number of orthologs with differential expression is similar in the different time of early ovule development.Therefore,the global expression pattern is closer to A₂ progenitor than D₅progenitor in tetraploid cotton.The orthologs with differential expression are related to fatty acid related process,flavonoid biosynthesis process and plant hormone signal transduction,which closely related to fiber development.5.Expression level dominance of orthologs in G.hirsutumThe proportion of genes with non-additive expression is 16.68%on the average for four periods in G.hirsutum,which is far higher than genes with additive expression.The ELD-A genes are more than ELD-D genes.Most orthologs show up-regulated expression or down-regulated expression in Dt-subgenome for ELD-A genes and vice versa.More transgressive regulation orthologs represent up-regulated expression than down-regulated expression in all times in allotertraploidy,and they show no differential expression between two diploid progenitors.Several orthologs are not the same.These orthologs expression probably changed after allopolyploidy,which associate with regulatory factor or epigenetic modifications.6.Function divergence of orthologs in G.hirsutumThe expression patterns of orthologs changed after allotertraploidy and artificial domestication(The expression models of GA/GR and At/Dt are different).The differential expression of many orthologs lose in allotertraploidy.Orthologs silence in one of subgenomes,which is one of the major ways of ortholog's function divergence.Fiber character in G.hirsutum mainly inherited from diploid A genome progenitor.However,genes from diploid D genome progenitor show high expression or novel expression,which take chances for allotertraploidy to optimize fiber yield and fiber quality.