Population Genetics And Selected Genes Bioinformatic Analysis Of Two Related Sympatric Walnuts (Juglans Regia And J.sigillata)

Juglans regia L.and J.sigillata Dode,which belong to Section Dioscaryon or Sect.Juglans,Juglans,Juglandaceae,Fagales,are considered a relict species of the Tertiary.Walnuts are widely distributed in the temperate regions of the northern hemisphere.As an economically important tree,because of its high nutritional and medicinal value and ecological value for its nuts and timber,so they reflect high economic value.Iron walnut is an endemic species in China.Since walnut and iron walnut show significant sympatric distribution in southwestern China,it is of great theoretical significance to study gene introgression of the two closed related species.In recent years,most studies only focus on population genetics of one species in this group,lacking a comprehensive comparison of two related species in Juglans,and failing to fully reveal the deep phylogenetic relationship and gene introgression between the two related species.In the present study,we analyzed population genetics,structure,and introgression between J.regia and J.sigillata populations,which are sympatric distribution of each other from southwestern China,using 25 EST-SSR screened from five species of Juglans.In addition,bioinformatics analysis was performed on 10 selected gene sequences filtered from the two related species based on transcriptome difference analysis.The main findings are as follows:?1?In this study,25 EST-SSR loci were used to analyze the comprehensive study between population genetics and interspecific gene introgression of 506 individuals from 28 populations of J.regia and J.sigillata?190 individuals in 15 J.regia populations;316 individuals in 13 J.sigillata populations?in southwestern China.Our genetic diversity results indicated that all J.regia populations possess slightly higher genetic diversity than J.sigillata populations?J.regia:H_O=0.291,H_E=0.306,PPL=0.328;J.sigillata:H_O=0.260,H_E=0.267,PPL=0.273?.The Geostatistical IDW technique?H_O,PPL,N_A and PrA?revealed that northern Yunnan and Guizhou provinces had high genetic diversity for J.regia while the northwestern Yunnan province had high genetic diversity for J.sigillata.The STRUCTURE analysis of four datasets shows a strong signal for K=2,this implies that the J.regia and J.sigillata populations revealed two genetic clusters in which gene introgression exists,therefore,the boundary of separation between these two walnut species is not apparent.Moreover,these results were validated by NJ and UPGMA analysis with additional conformation from the PCoA.We speculate that they are closely related to their systematic relationship.AMOVA analysis revealed that significant genetic variation was mainly distributed within population as 73%in J.regia and 76%in J.sigillata.The gene flow analysis produced?and M values greater than zero.The?-value and the size of the immigration rate?M?revealed a highly asymmetric historical gene flow across the two species.The Mantel test showed no significant correlation between genetic distance and geographical distance of J.regia?r=0.065,P=0.27>0.05?and J.sigillata?r=0.05,P=0.32>0.05?.Combined with the results of this study,it should provide some theoretical support for the follow-up study of J.regia and J.sigillata germplasm.?2?In this study,based on high-throughput sequencing technology,two related species of walnuts and iron walnuts were selected for elimination analysis,and combined with transcriptome sequencing and published reference genome annotation of walnuts,a total of 10differentially selected genes were screened for analysis,and analysised by bioinformatics analysis.Physicochemical properties showed that the range of gene encoded amino acids was varied from 204 to 945.The Theoretical pI ranged from 4.86 to 9.31.80%of the gene-coding proteins belong to instability proteins.Aliphatic index varied between 54.97 between 106.98.Hydrophilicity analysis showed that the average hydrophobicity of all genes was negative,it was predicted that the coding proteins of all genes were hydrophilic proteins.The prediction of transmembrane domain indicated that only WALNUT₀0006189 and WALNUT₀0025804genes had obvious transmembrane region,which belonged to transmembrane protein.The other genes did not have transmembrane structure and did not belong to transmembrane protein.All gene-encoded proteins don't have significant signal peptide characteristics,presumably not belonging to secreted proteins.Subcellular localization showed that 10 selected genes were located in eukaryotes.The main secondary and tertiary structures are?-helix and Random coil.Phylogenetic analysis showed that J.regia and Q.suber were clustered into one branch,showing high sequence homology.Functional domain prediction revealed that each gene has its own unique functional characteristics,and plays an important role in plant growth and development,stress,signal transduction and other aspects,which can provide theoretical basis for guiding agricultural production.