基于全基因组重测序的菠萝蜜裂皮病病菌胡萝卜果胶杆菌遗传多样性分析OA

The study was aimed to clarify the population genetic structure and genetic variation characteristics of Pec-tobacterium carotovorum(the pathogen causing split skin disease)in the main jackfruit-producing areas of Hainan Province,and to provide a theoretical basis for the precise prevention and control of jackfruit split skin disease and the research on its pathogenic mechanism.Eight pathogenic strains of P.carotovorum were isolated from the split skin samples collected from six main jackfruit-producing areas in Hainan,namely Qionghai,Wenchang,Danzhou,Dongfang,Changjiang and Baisha.Whole-genome resequencing was used to analyze the characteristics of single nucleotide poly-morphism(SNP)and insertion-deletion(INDEL)variations of the strains.Combined with collinearity analysis,gene family analysis,and phylogenetic analysis,the genetic diversity and geographical differentiation of the strains were investigated.The genome sequencing depth of the 8 strains reached 50×,with coverage≥68%for all.A total of 74 089 663 SNP loci and 238 283 INDEL loci were identified.Among SNPs,the number of transitions was significantly higher than that of transversions;among INDELs,the number of deletions exceeded that of insertions,and the vast majority of variant loci were homozygous.SNP annotation revealed that variations were mainly distributed in synonymous mutation regions of coding sequences.Strain S9 exhibited significant differences in the number of SNP and INDEL loci as well as mutation regions compared with other strains.Collinearity analysis showed close genomic collinearity between S4 and S5,S7 and S8,and S10 and S15.Gene family analysis identified 4162 orthologous gene groups,including 3106 core conserved gene groups and 42 species-specific orthologous groups,with strains S9 and S14 harboring unique gene clusters.Phylogenetic analysis displayed obvious regional clustering of the strains.Strains from eastern production ar-eas(Qionghai,Wenchang),Danzhou(western),and Baisha-Changjiang(southwestern)formed separate clades respec-tively.Strain S9 from the Dongfang production area showed significant genetic differentiation from other strains.The P.carotovorum strains associated with jackfruit split skin disease in Hainan exhibit high genetic diversity and a distinct geographical differentiation pattern.Genome-wide SNP and INDEL variations would lay a molecular foundation for dissecting the pathogenic mechanism and evolutionary dynamics of this pathogen.