Gene Introgression And Genetic Differentiation Among Sympatric/Parapatric Quercus Species

Habitat heterogeneity caused by geological changes and climate fluctuations is considered to be the main driving force for spatial distribution of species diversity and genetic divergence.Quercus L.possesses high species diversity and is considered as the important economic and ecological tree species in the forest ecosystem of northern hemisphere.However,the mechanisms of genetic introgression and genetic differentiation in the sympatric/parapatric distribution of Quercus are rarely reported.In this study,seven Quercus species were selected as the research objects,which distributed in Qinling Mountains of central China with the same slope direction.Morphological analyses and population genetics at genome level(including chloroplast genome and transcriptome data)were used to infer the genetic introgression and differentiation of these oak species.Meanwhile,comparative transcriptome of female flowers and male inflorescence of Q.aliena var.acuteserrata and Q.liaotungensis were conducted to explore the genetic differences and evolution mechanism of sex-determining genes in the related Quercus species.The major results are summarized as follows:1.The morphological characteristics of 297 mature leaves(including leaf length,leaf width,petiole length,number of veins on the right side of leaf,ratio of leaf length to width,angle between main vein and base)of seven Quercus species(Q.aliena,Q.aliena var.acuteserrata,Q.dentata,Q.liaotungensis,Q.variabilis,Q.spinosa,Q.baronii)in the north slope of Qinling Mountains were measured.UPGMA and principal component analysis(PCA)results showed that all individuals were divided into three groups,including Group Quercus(Q.aliena,Q.aliena var.acuteserrata,Q.dentata,Q.liaotungensis),Group Cerris(Q.variabilis),Group Ilex(Q.spinosa and Q.baronii).Except for Group Quercus,other individuals were clustered by species.These results supported that large morphological differentiations were presented among the Quercus groups,while the morphological variations of the related species in Group Quercus was relatively small.2.Phylogenetic relationships and haplotypes network inferred based on maternal chloroplast genome datasets supported that Quercus species were divided into the Group Quercus,Cerris and Ilex.Within the Group Quercus,the chloroplast haplotype network showed the existence of central haplotypes sharing phenomenon of three closely species(Q.aliena,Q.aliena var.acuteserrata and Q.dentata),which might be due to incomplete lineage sorting caused by recent species differentiation.Meanwhile,the selection pressure analyses indicated that mat K,ycf1 and rpo A genes were undergone positive selection,suggesting that these loci might play an important role in the adaptive evolution process of Quercus species.3.A total of 32,863 high quality single nucleotide polymorphisms(SNP)were identified based on RNA sequencing(RNA-Seq).The phylogenetic analysis indicated that all individuals belong to Group Quercus were divided into four monophyletic clades according to species,and seven Quercus species in China were clustered into three Quercus groups.PCA showed that all Group Quercus individuals were clustered in the same group,and others were clustered based on species levels.This result was consistent with relationships inferred from NJ phylogenetic tree.ADMIXTURE analysis indicated that Group Quercus individuals were divided into four clusters by species,but a few individuals showed mosaic pattern.Further analysis of genetic structure of Group Quercus showed that Q.liaotungensis have mixed genetic components came from the other three species.TREEMIX indicated a strong gene flow between Q.aliena var.acuteserrata and Q.liaotungensis;D statistics analysis suggested that there was incomplete lineage sorting among the species of Q.liaotungensis,Q.aliena var.acuteserrata and Q.dentata,and significant gene introgression were detected among species of Q.liaotungensis,Q.aliena var.acuteserrata and Q.dentata;MIGRATE-N revealed that there was a symmetrical gene flow between Q.liaotungensis and Q.aliena var.acuteserrata,while asymmetric gene flows were detected between other paired species.These results indicated that there were complex evolutionary relationships among Group Quercus species.These genes(e.g.Qrob_T0300210.2,Qrob_T0652500.2,Qrob_T0652510.2)related to drought resistance and low temperature identified by selective sweep analysis might contribute to the genetic differentiation of Quercus related species.4.Comparative transcriptome of female flowers and male inflorescences showed that 8126 genes were differentially expressed of Q.aliena var.acuteserrata,of which 3921 genes(48.25%)were up-regulated in male inflorescence.4367 genes were identified as differentially expressed genes between female and male inflorescence of Q.liaotungensis,of which 2123 genes(48.61%)were up-regulated.The Kyoto Encyclopedia of Genes and Genomes(KEGG)enriched analysis indicated that some differentially expressed genes were enriched in nutrient metabolism(Carbon metabolism and Biosynthesis of amino acids)and some important hormone pathway(tryptopedia metabolism,phenylpropanoid biosynthesis pathways,Phenylalanine metabolism),suggesting that genes might be closely related to sex-determining of floral organs in Quercus.