Population Genetic Analysis Of Opisthopappus Shih

Opisthopappus Shih,as a unique perennial herb,mainly distributed in Shanxi,Henan and Hebei provinces of China,has important economic,medicinal and ornamental values.This genus has been listed as Second-class protection plants in China due to its restricting habitats,lower breeding rate and serious artificial picking.In this paper,dd-RDA seq（Double digest restriction site associated DNAs sequencing）technology was used to obtain the partial genome of Opisthopappus and analyze its population genetic characteristics.1.After sequencing,the high quality data（HQ datas）with high Q30 and Q20values（over 90%）and low GC content were obtained,accounting for 98.25%of the original data.When taking the Chrysanthemum genome dates as a reference,the double-terminal alignment rate of HQ data performed a very high coverage ranged from 89.84%to 98.60%.A large number of tags（818,625-1,631,437）were obtained from all samples,and the sequencing depth was 6.45X-23.02X.A total of 149,495effective SNPs were identified from the tags.The number of SNP loci was in direct proportion to the length of chromosome.The C:G>T:A was the main mutation type of SNP.And the preferred base of mutation site is A/T.The SNP locus was multilocated in the intergenic region,followed by the intron and exon regions.2.In population genetics analysis,the Opisthopappus showed high genetic diversity（H_o=0.2710～0.3157;H_e=0.1680～0.1925;Pi/π=0.1772～0.2027;H_d=0.1892）.Compared with Opisthopappus taihangensis（π=0.1907,H_d=0.1907）,Opisthopappus longilobus had higher diversity（π=0.1878,H_d=0.1879）.All of the estimated inbreeding coefficients(F_IS)were less than 0,indicating that there were many heterozygotes in Opisthopappus.The F_ST values between O.longilobus and O.taihangensis were more than 0.25,indicating that a relatively high genetic differentiation occurred between the two species.However,the slow decay rate of LD and the F_ST value lower than 0.15 reflected the low degree of genetic differentiation among populations within species.3.The phylogenetic tree showed that all populations were divided into two branches corresponding to the specific populations in each species.Principal component analysis and structure analysis were consistent with the results of phylogenetic analysis.The gene flow occurred mainly among populations within species rather than among species.Slight hybridization was also detected between structure groups,which indicated that two-way gene exchange existed between species and some populations within species.4.In evolutionary process,species generally contained more specific genes involved in adaptability for environmental changes.No matter in OL&OT,OLa&OTd or OLb&OTc group,the specific SNPs of Opisthopappus longilobus were more than that of Opisthopappus taihangensis,suggesting that the former species has more adaptive potential.Moreover,the specific SNPs of the edge populations were higher than that of the middle populations,and the habitat of the edge populations might be more severe.5.In the selective sweeping analysis,GO annotation showed that the enrichment results of the two species were similar,but the selected genes of Opisthopappus longilobus also participated in the transport process.KEGG Pathway functional annotation showed that there were significant differences in metabolic pathways between the two species.Opisthopappus longilobus was mainly enriched in metabolic related pathways,while Opisthopappus taihangensis was mainly enriched in genetic information processing pathway.There were differences in the response of the two species to the environment,and thesedifferences might just be reflected by the adaptation to the environment.