The angiosperm family Elaeagnaceae comprises three genera and ca.100 species distributed mainly in Eurasia and North America.Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted,limiting the application and preservation of natural genetic resources.Here,we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand interand intrageneric relationships,as well as the origin and biogeographical history of the family.For this purpose,we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and,along with current distributional data,infer historical biogeographical processes.Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera.Elaeagnus was resolved as sister to the well-supported clade of Hippophae and Shepherdia.The intrageneric relationships of Elaeagnus and Hippophae were also well resolved.High levels of nuclear gene tree conflict and cytonuclear discordance were detected within Elaeagnus,and our analyses suggest putative ancient and recent hybridization.We inferred that Elaeagnaceae originated at ca.90.48 Ma(95%CI?89.91e91.05 Ma),and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution.This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date,offers new insights into previously unresolved relationships in Elaeagnus,and provides a foundation for further studies on classification,evolution,biogeography,and conservation of Elaeagnaceae.
The genus Hippophae includes deciduous shrubs or small trees,which provide many ecological,economic,and social benefi ts.We assembled and annotated the chloroplast genomes of sympatric Hippophae gyantsensis(Rousi)Lian and Hippophae rhamnoides Linn subsp.yunnanensis Rousi and comparatively analyzed their sequences.The fulllength chloroplast genomes of H.gyantsensis and H.rhamnoides subsp.yunnanensis were 155,260 and 156,415 bp,respectively;both featured a quadripartite structure with two copies of a large inverted repeat(IR)separated by small(SSC)and large(LSC)single-copy regions.Each Hippophae chloroplast genome contained 131 genes,comprising 85 protein-coding,8 ribosomal RNA,and 38 transfer RNA genes.Of 1302 nucleotide substitutions found between these twogenomes,824(63.29%)occurred in the intergenic region or intron sequences,and 478(36.71%)were located in the coding sequences.The SSC region had the highest mutation rate,followed by the LSC region and IR regions.Among the protein-coding genes,three had a ratio of nonsynonymous to synonymous substitutions(Ka/Ks)>1 yet none were signifi-cant,and 66 had Ka/Ks<1,of which 46 were signifi cant.We found 20 and 16 optimal codons,most of which ended with A or U,for chloroplast protein-coding genes of H.gyantsensis and H.rhamnoides subsp.yunnanensis,respectively.Phylogenetic analysis of fi ve available whole chloroplast genome sequences in the family Elaeagnaceae—using one Ziziphus jujube sequence as the outgroup—revealed that all fi ve plant species formed a monophyletic clade with two subclades:one subclade consisted of three Hippophae species,while the other was formed by two Elaeagnus species,supported by 100%bootstrap values.Together,these results suggest the chloroplast genomes among Hippophae species are conserved,both in structure and gene composition,due to general purifying selection;like many other plants,a signifi cant AT preference was discerned for most proteincoding genes in the Hippophae chloroplast genome.This study provides a valuable reference tool
