Gene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome‐scale phylogeny and identify large‐scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai–Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae.
Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.
Distributional shifts driven by Quaternary climatic oscillations have been suggested to cause interspecific hybridization and introgression. In this study, we aimed to test this hypothesis by using population transcriptomes and coalescent modeling of two alpine none-sister gentians. Previous studies suggested that historical hybridizations occurred between Gentiana siphonantha and G. straminea in the high-altitude Qinghai-Tibet Plateau although both species are not sister to each other with the most recent divergence. In the present study, we sequenced transcriptomes of 33 individuals from multiple populations of G. siphonantha and G. straminea. The two species are well delimited by nuclear genomic SNPs while phylogenetic analyses of plastomes clustered one G. straminea individual into the G. siphonantha group. Further population structure analyses of the nuclear SNPs suggested that two populations of G. siphonantha were admixed with around 15% ancestry from G. straminea. These analyses suggested genetic introgressions from G. straminea to G. siphonantha. In addition, our coalescent-based modeling results revealed that gene flow occurred between the two species since Last Glacier Maximum after their initial divergence, which might have leaded to the observed introgressions. Our results underscore the significance of transcriptome population data in determining timescale of interspecific gene flow and direction of the resulting introgression.
Many species of the subfamily Polygonoideae are economically important. However, phylogenetic relationships and taxonomic treatments of these species remain disputed. In this study, we used highly orthologous nuclear genes and plastome sequence variation extracted from transcriptomes from 98 species of 26 genera of Polygonaceae mainly from the subfamily Polygonoideae to construct a robust phylogeny. We discerned six successively diverged and well-defined clades and both nuclear and plastome phylogenies are highly consistent with each other in this subfamily. Phylogenetic relationships between all clades and subclades were well resolved within Polygonoideae. Our analyses revealed that the shrub tribe Atraphaxideae and the herbal genera Polygonum, Persicaria, and Fallopia are polyphyletic. The sampled species of Polygonoideae started to diversify around the Cretaceous/Tertiary boundary (70 Ma) when the global climate exhibited large oscillations. Further origins of more herbal and woody species were found to have clearly increased during later climatic oscillations. We found that woody habits, especially shrubs, originated multiple times from ancestral herbs in this subfamily.Local dry climates may have favored such habit shifts from ancestral herbs. Our results deepen our understanding of evolutionary diversification of Polygonoideae.
The complete chloroplast genome sequence of Saussurea integrifolia, a flowering plant occurring in Hengduan Mountains with high altitudes, is determined in this study. The plastome is 152,584 bp in length, with one large single-copy region of 83,497 bp, one small single-copy region of 18,646 bp, and two inverted repeat (IR) regions of 25,221 bp. It contains 123 genes, including 86 protein-coding genes, 8 ribosomal RNA, and 36 transfer RNA. Phylogenetic tree shows that this species is a sister to Arctium lappa. The published plastome within Saussurea provides significant insight for elucidating the phylogenetic relationship of taxa within tribe Compositae.
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