DNA Composition,Structure And Evolution Of The Centromere In Sugarcane

Sugarcane is one of the most important sugar crops,accounting for about 80% of the world’s sugar production.SES208,Molokai6081 and LA Purple are important sugarcane breeding materials,and the features of their polyploid genome,a large number of chromosome and high-ratio of repeat sequences severely restrain the sugarcane genomics research.At present,the genome sequence of AP85-441,a haploid of SES208,has been published and the draft genome of Molokai6081 and LA Purple have been completely assembled.The centromere is physically primary constriction on the metaphase chromosome in the cell division and it is functionally very conserved,mediating the accurate separation of chromosomes during cell division.The centromeric DNA sequence is mainly composed of satellite repeats,retrotransposons and a few gene sequences,which evolve quickly and usually lack conserved structures.Therefore,the centromeric regions are often difficult to sequence,which seriously hinders the genome assembly.Based on the typical feature of the functional centromeric region containing the histone Cen H3,which is a mutant of histone H3,we conducted chromatin immunoprecipitation experiments in Molokai6081 and LA purple,and the bioinformatics analyses of the sequencing data were carried out.The research results are as follows:(1)Based on sequence similarity clustering analyses,the repeat sequences of Molokai6081 and LA Purple were obtained.The genome proportion of repeat sequences are as high as 82.2% and 82.8%,and the LTR retrotransposon sequences are 42.08% and 44.80%,respectively.The highly proportion of repeat sequences severely hampers the assembly of the sugarcane genome.(2)Candidate centromere-specific sequences of Molokai6081 and LA Purple were obtained based on enrichment analyses of repeat sequences.Five centromere-specific repeats were obtained by cytological verification,and these sequences have high similarity and are conservative between Molokai6081 and LA Purple.Sequence annotation revealed that centromeric sequences of Molokai6081 and LA Purple with classical centromeric sequence characteristics,consist of satellite sequence and Ty3/Gypsy-like retrotransposon.(3)Based on the results of sequence alignment analyses and cytology experiments,these five sequences were found to be more conserved among SES208,Molokai6081 and LA Purple.Further analysis revealed that two Ty3/Gypsy-like retrotransposons belong to the centromeric retrotransposon of maize(CRM).These results indicated that the CRM sequence is more conserved among the three sugarcane species,and it is speculated that these sequences are formed before the chromosome doubling event and are more completely preserved in the long-term evolution process.(4)Based on bioinformatic analyses,the centromeric positions of the genome of SES208,Molokai6081 and LA Purple were clarified,and the misassemble of centromeric regions on partial chromosomes was pointed out,which provided a reference for genome assembly.Based on transcriptome data analyses,it was found that there were transcriptionally active genes in the centromeric regions of the genome of SES208,Molokai6081 and LA Purple,and these genes were all present in the H3 region.These results provide a reference for the composition,structure and evolution of centromeric sequence in sugarcane,and provide suggestions for the assembly of genomic centromeric regions,and promote the research of sugarcane genomics.