Population Genomics And Phylogeny Of Walnut (Juglans)

The genus Juglans L.(walnut)belong to the family of Fagaceae.It is long-lived deciduous important hardwood trees distributed and cultivated worldwide for its edible,timber,medicinal,ecological and artistic value.According to morphological and geographical distribution characteristics,the phylogenetic relationships of Juglans were generally accepted as four sections,including section Dioscaryon,section Cardiocaryon,section Trachycaryon and section Rhysocaryon.Previous studies based on multiple datasets indicated that the evolutionary history of walnut species relatively clear.However,However,all analysis based on parental inheritance data indicated that the divergence of phylogenetic relationship of J.cinerea might be due to hybridization and chloroplast capture of related species of Juglans.In this study,Juglans were analyzed for phylogeny and evolution based on complete chloroplast genome,mitochondrial fragments and single nucleotide polymorphism(SNP)datasets by using resequencing technology,molecular biology,bioinformatics,population genetics and genealogical geography.The main content and results are as follows:Bioinformatics analysis showed that the chloroplast genome of Juglans was highly conserved,and exhibited a typical quadripartite structure(LSC/SSC/IRa/IRb).The average length of the Juglans complete cp genomes was ～160 kb.The cp genome of all Juglans species encoded 130-137 genes,of which we identified 83-87 protein-coding genes,37-40 t RNA genes,8 r RNA genes and 2 pseudogenes(ycf15 and inf A).The GC content of all Juglans was 36.1-36.2%.The mitochondrial fragments of 46 individuals ranged from78,489 bp to 152252 bp.Statistics on the variation rate of the coding and non-coding regions of the chloroplast genome showed that the non-coding and SC(LSC/SSC)regions exhibited higher divergence levels than those of coding and IR regions,respectively.10 mutation hotspots regions were identified and could be used as potential markers to reconstruct phylogenetic relationships or identify plants of this genus.In Juglans,there are certain differences in the number of the four categories of repeats(forward(F),palindrome(P),reverse(R)and tandem(T)).The number of reverse repeats in J.regia and J.nigra was significantly higher than that of other species in the genus Juglans.In addition,the average number of SSRs for all individuals ranged from 75 to 91.The majority of SSRs were mononucleotides consisted of A or T.According to the selection pressure analysis of 79 common protein-coding genes,a total of 15 genes were identified with positive selection sites.At the same time,the molecular divergence dating of Juglans based on 79 common protein-coding genes showed that the divergence time between Juglans and outgroups(C.paliurus and C.illinoensis)was 55.89 Mya and 85.57 Mya(95%(HPD),53.97–57.78 Mya;83.58–87.47 Mya).Gene flow analysis based on chloroplast genome,mitochondrial fragments and nuclear SNPs indicated that there was significant and unbalanced historical gene flow among species of Juglans;population genetic analysis and phylogenetic analysis indicated that Juglans species could be classified into three sections(section Dioscaryon,section Cardiocaryon,and section Rhysocaryon).J.cinerea was merged within section Rhysocaryon when analysis was conducted using both chloroplast genome and mitochondrial fragments,while it belonged to sect.Cardiocaryon when analysis was conducted using SNPs data.We further proposed a hypothetical scenario for chloroplast capture events to explain incongruous phylogenetic position of J.cinerea in genus Juglans.The results of this research will help reveal deeper divergent phylogenetic relationships and provide new insights into the complex evolutionary patterns of Juglans species.