Genetic Diversity,population Structure And Species Distribution Modeling Of Ailanthus Altissima In China

Despite sufficient evidence that habitat loss of tree species has consistently negative effects on biodiversity,a limited number of studies have attempted to quantify the consequences of habitat loss of tree species on genetic diversity and structure.In addition,habitat loss through anthropogenic activities,global climatic oscillations and associated landscape changes likely impact the current distribution of biodiversity through range expansion or reduction and isolation across large geographical areas.Understanding how anthropogenic disturbance affects the genetics of tree species is essential.However,how the tree populations in the wild can tolerate this anthropogenic activity remains unexplored.The tree of Heaven（Ailanthus altissima）,the genus Ailanthus placed within the family Simaroubaceae,is a deciduous tree species occurring naturally（native）in Eastern Asia.Considering the ongoing and intensifying anthropogenic disturbances,we used A.altissima to gain new insight into the effects of these pressures on genetic variability in natural and disturbed forests.A.altissima has a great potential in decorative,bioenergy,and industrial applications in many countries.To date,despite its comprehensive importance,the genomic and genetic resources available for this species are still insufficient.In this study,we first characterized complete chloroplast genome and transcriptome sequences of A.altissima,then developed ten polymorphic chloroplast microsatellite（cp SSR）markers and thirteen EST-SSRs based on Illumina paired-end RNA sequencing（RNA-seq）.Based on developed markers,we further conducted the level of genetic diversity and population structure of A.altissima in China,and explored if A.altissima range expanded/contracted in the past despite occupying unglaciated areas,and if so,were there refugial area/s.Our results showed that the tree of the heaven chloroplast genome is a circular molecule of160,815 base pairs（bp）in size and possesses a quadripartite structure.The A.altissima chloroplast genome contains 113 unique genes,of which 79 and 30 are protein coding and transfer RNA（t RNA）genes,respectively.Microsatellite marker detection identified A/T mononucleotides as the majority SSRs in all the seven analyzed genomes.Repeat analyses of seven Sapindales revealed a total of 49 repeats in A.altissima,Rhus chinensis,Dodonaea viscosa,Leitneria floridana,while Azadirachta indica,Boswellia sacra,and Citrus aurantiifolia had a total of 48repeats.The phylogenetic analysis using protein coding genes revealed that A.altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to the Rutaceae family.The transcriptome data produced 87,797 unigenes,of which 64,891（73.91%）unigenes were successfully annotated in at least one protein database.Among the 20 cp SSR primers designed in the A.altissima genome,ten primers were polymorphic.The number of alleles（N_a）per marker varied from 1.429 to 2.857,and the unbiased haploid diversity indices（uh）varied from 0.111 to0.485,and haploid diversity indices（h）ranged from 0.101 to 0.444 with an average unbiased haploid diversity index（uh）of 0.274.Overall,the polymorphism information content（PIC）for each cp SSR ranged from 0.281 to 0.723,averaging to 0.483.Of the eighteen EST-SSR loci,thirteen displayed polymorphism with the number of alleles varying from 2.143（Ail 22）to 9.357（Ail 09）,with a mean of 5.599.However,seven EST-SSR loci yielded monomorphic products.The allele number per locus for EST-SSRs varied from 2.143 to 9.357 and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826,respectively.The developed molecular markers will facilitate future genetic diversity,population structure,long distance-gene transfer and pollen-based gene flow analyses of A.altissima populations from its known distribution ranges in China,focusing on disturbed and undisturbed forest stands.The genetic diversity and population structure of A.altissima were analyzed by EST and chloroplast microsatellite markers.The genetic diversity across the 34 study populations based on EST-SSR was moderate to high（H_E=0.569-0.751）with a mean unbiased H_E of 0.681.Bayesian clustering,principal coordinate analysis（PCOA）,and discriminant analysis of principal component（DAPC）congruently divided the populations into three distinct groups based on EST-SSR.Allelic combinations of 92 different chloroplast size variants from 10 cp SSR loci resulted in a total of 292 chloroplast haplotypes.The mean haplotypic diversity was relatively high（H_E=0.941）,and the mean haplotypic richness was 2.690,averaged across the 34 populations of A.altissima.Values of F_ST in A.altissima from chloroplast and nuclear markers were 0.751 and 0.130,respectively.The reproduction system of A.altissima,habitat disturbance and wide distribution area might have facilitated pollen movement,resulting in high genetic variation or maintenance of genetic diversity of remnant populations.Modeling results showed evidence for population range contraction during the Last Glacial Maximum with subsequent population expansion in the Holocene and Future.The knowledge of how plant species response to past climatic changes may help refine projections of how species together with biotic communities will respond to future climatic changes.While disturbed and undisturbed sites did not significantly differ in genetic variation,overall,slight trends were indicating increased amounts of genetic diversity and population bottlenecks in disturbed forests.Thus,disturbed habitats can exhibit unexpected genetic patterns that are difficult to predict and should not be underestimated.To further understand habitat loss effects of this species,more factors such as disturbances onset and genetic outcomes time-lags,number of genetic molecular markers should be considered to ensure a more effective assessment of its genetic diversity characteristics.This research provides a framework for investigating the evolutionary history of A.altissima a step towards understanding the genetic diversity in its altered native range.