Analysing Evolution And Genetic Variations Of Pyrus Genomes

Pyrus L.is an important genus in Rosaceae with more than 30 species.Among them,P.pyrifolia Nakai and P.communis L.have important economic value and are the mainly cultivated species in East Asia and European countries,respectively.P.ussuriensis Maxim.,P.×sinkiangensis Yu,P.pashia D.Don,P.betulifolia Bunge and P.calleryana Dcne are cultivated in some areas or used as rootstocks.Genome is an important foundation for genetic mapping,gene cloning and phylogenetic research while genetic variations are important resources for germplasm improvement.This study comprehensively utilized genomic sequencing data to analyze the evolutionary relationship and the genetic variations within Pyrus.The main research results are as follows:1.Eight high-quality pear genomes have been de novo assembled,involving P.pyrifolia,P.communis,P.ussuriensis and P.pashia.The Contig N50 of the eight pear genomes reached above 1 Mb,with BUSCO values greater than 95%.Pan-genome analysis was conducted based on 11 pear genomes and a total of 39,283 gene families(orthogroups)were identified.The number of core gene families is 14,447.Genes are further divided into core genes,shell genes and private genes.Among them,the core genes are relatively conservative in evolution and relatively active in expression.2.The evolutionary relationship within Pyrus was analyzed using genomic assemblies and re-sequencing data and it was found that hybridization between P.pyrifolia and wild P.ussuriensis occurred during the formation of cultivated P.ussuriensis.The structural variations of Pyrus was identified using high-quality genome assemblies.Focusing on structural variations that intersect with promoter regions or gene regions,it was found that a 3.98 Kb In Del which near the MYB10 promoter exhibited interspecific polymorphism.Systematic mining of SNPs,small In Dels(less than 50 bp)and large In Dels(larger than or equal to 50 bp)of P.pyrifolia was conducted using genome assemblies and re-sequencing data.SNPs,small In Dels and large In Dels were found at 52,484,749,1,215,776 and 175,983 loci,respectively.Among them,95,995 SNPs and 31,164 small In Dels are annotated as having a significant effect.3.The Dormancy-Associated MADS-box(DAM)genes was identified in the assembled pear genome and five DAM genes were obtained.There is one DAM locus on chromosome 8 and one DAM locus on chromosome 15 and both of them have strong collinearity with the peach EVG locus.The result of phylogenetic analysis showed that the replication of DAM genes occurred independently in Rosaceae species after their differentiation.Based on the re-sequencing data,it was found that there is a rare SNP in the DAM1 gene,which leads to the prematurely terminating of the protein translation of DAM1 and may affect the dormancy characteristics of pears.In the less-dormant pear variety ‘Hengshanli’,this SNP is homozygous and the degree of heterozygosity in its vicinity is relatively low.4.Genetic variations of pears that have red peel and originated from bud sports were explored.Two red pear cultivars(‘Max Red Bartlett’ and ‘Red D’Anjou’)were found to have single nucleotide variations in BBX24,resulting in the deletion of the nuclear localization signal and VP motif in the C-terminal of the proteins.Based on the allele data of BBX24,it was found that ‘Hongzaosu’ is a chimera.Due to the change of the chimeric state,the re-green phenomenon and the different coloring patterns in peel are caused in ‘Hongzaosu’.Phylogenetic analysis indicates that BBX24 may be related to anthocyanin biosynthesis.Genetic transformation and other molecular biology experiments confirmed that BBX24 could interact with HY5 and regulated pear anthocyanin accumulation.Using the obtained next-generation and third-generation sequencing data,the genome of ‘Hongzaosu’ was assembled.In summary,this study conducted pan-genome analysis,evolutionary analysis and genetic variation exploration in Pyrus based on genomic data,found genetic variations related to pear dormancy and coloration and finally provided valuable references for pear genomic research and breeding.