Studies Of DNA Composition And Evolution Of The Centromere In Saccharum Spontaneum

Centromere is one of the important functional elements of chromosomes in eukaryotes,which is responsible for precise regulation of the chromosome pairing,segregation and maintaining chromosome stability during mitosis and meiosis.Plant centromeric sequences are mainly composed of satellite DNAs and centromeric-specific retrotransposons.Although the function of centromere is highly conserved among different species,the centromeric DNA sequences varied much and showed a rapid evolution model.Sugarcane plays the essential role in sugar crop,which accounting for～75%of global world production.At present,the whole genome sequencing of sugarcane(Saccharum spontaneum)has been launched.However,since the high-level of repetitive sequences existing,especially in the centromeric regions,the structure and composition of the sugarcane genome are so complex,which has severely hindered the process of the whole genome assembly.Here,we conducted a genome-wide survey of the repetitive DNAs in S.spontaneum following a similarity-based sequence clustering strategy.These results will provide insights into the composition of sugarcane genome and will be helpful for the S.spontaneum genome assembly.In this study,the centromeric repetitive DNA sequences specific for S.spontaneum SES208 were isolated through combining the chromatin immunoprecipitation sequencing(ChIP-seq)with bioinformatics methods.And meanwhile,the molecular cytogenetic techniques were used to identify the putative sequences.Finally,we obtained five centromeric DNA sequences and revealed the DNA composition of the centromere region in S.spontaneum SES208.We also revealed the distribution and evolution of centromeric repetitive DNA sequences in different sugarcane species.The results showed that there were mainly SCEN-like satellite repeats(Ssl)and Ty3/Gypsy retrotransposons(Ss51,Ss68,Ss166 and Ss262)in the centromeric regions of SES208.Ssl dominated in the centromeric regions as tandem distribution and spanned up to 500kb.However,Ss51 Ss68,Ss166 and Ss262 either clustered spanning over a short range,or dispersed in the centromere regions.These results improved our understanding of the composition and structure of sugarcane centromeric DNA sequence.Interestingly,Ss1 exhibited a chromosome-specific enrichment in S.spontaneum SES208 and S.robustum Molokai6081,but not in S.officinarum LA purple and modern sugarcane cultivars ROC22 and Funong38,suggesting the evolution of sugarcane centromere.Furthermore,5S rDNA and Ssl enrichment signals were on different chromosomes,which revealed the autopolyploid genome of S.spontaneum SES208 and suggested that there was a high level of homology among its eight sub-genomes.