Dataset Information

Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses.

ABSTRACT: Dolomiaea is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomiaea species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plastome evolutionary history of Dolomiaea. Eight highly divergent regions (rps16-trnQ, trnC-petN, trnE-rpoB, trnT-trnL-trnF, psbE-petL, ndhF-rpl32-trnL, rps15-ycf1, and ycf1), along with a total of 51-61 simple sequence repeats (SSRs) were identified as valuable molecular markers for further species delimitation and population genetic studies. Phylogenetic analyses confirmed the evolutionary position of Dolomiaea as a clade within the subtribe Saussureinae, while revealing the discordance between the molecular phylogeny and morphological treatment. Our analysis also revealed that the plastid genes, rpoC2 and ycf1, which are rarely used in Asteraceae phylogenetic inference, exhibit great phylogenetic informativeness and promise in further phylogenetic studies of tribe Cardueae. Analysis for signatures of selection identified four genes that contain sites undergoing positive selection (atpA, ndhF, rbcL, and ycf4). These genes may play important roles in the adaptation of Dolomiaea to alpine environments. Our study constitutes the first investigation on the sequence and structural variation, phylogenetic utility and positive selection of plastomes of Dolomiaea, which will facilitate further studies of its taxonomy, evolution and conservation.

SUBMITTER: Shen J

PROVIDER: S-EPMC7174903 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses.

Shen Jun J Zhang Xu X Landis Jacob B JB Zhang Huajie H Deng Tao T Sun Hang H Wang Hengchang H

Frontiers in plant science 20200415

Dolomiaea is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomiaea species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plasto ...[more]

PMID: 32351518

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Project description:Lobelia species, as rich source of the alkaloid lobeline which has been shown to have important biological activity, have been used in folk medicine throughout East Asia to treat various diseases. However, Lobelia is a complex and varied genus in East Asia and is thus difficult to identify. Genomic resources would aid identification, however the availability of such information is poor, preventing a clear understanding of their evolutionary history from being established. To close this gap in the available genomic data, in this study, 17 plastomes of East Asian lobelias were newly sequenced and assembled. Although the plastomes of Lobelia sect. Hypsela, L. sect. Speirema, and L. sect. Rhynchopetalum shared the gene structure, the inverted repeat (IR)/large single copy (LSC) boundaries, genome size, and the number of repeats were variable, indicating the non-conservative nature of plastome evolution within these sections. However, the genomes of the Lobelia sect. Delostemon and L. sect. Stenotium showed rearrangements, revealing that these two sections might have undergone different evolutionary histories. We assessed nine hotspot genes and 27-51 simple sequence repeat motifs, which will also serve as valuable DNA barcode regions in future population genetics studies and for the delineation of plant species. Our phylogenetic analysis resolved the evolutionary positions of the five sections in agreement with previous evolutionary trees based on morphological features. Although phylogenetic reconstruction of Lobelioideae based on the rpoC2 gene has rarely been performed, our results indicated that it contains a considerable amount of phylogenetic information and offers great promise for further phylogenetic analysis of Lobelioideae. Our site-specific model identified 173 sites under highly positive selections. The branch-site model exhibited 11 positive selection sites involving four genes in the East Asian branches. These four genes may play critical roles in the adaptation of East Asian taxa to diverse environments. Our study is the first to detect plastome organization, phylogenetic utility, and signatures of positive selection in the plastomes of East Asian lobelias, which will help to further advance taxonomic and evolutionary studies and the utilization of medicinal plant resources.

Project description:BackgroundConsidered a biodiversity hotspot, the Canary Islands have been the key subjects of numerous evolutionary studies concerning a large variety of organisms. The genus Cheirolophus (Asteraceae) represents one of the largest plant radiations in the Canarian archipelago. In contrast, only a few species occur in the Mediterranean region, the putative ancestral area of the genus. Here, our main aim was to reconstruct the phylogenetic and biogeographic history of Cheirolophus with special focus on explaining the origin of the large Canarian radiation.ResultsWe found significant incongruence in phylogenetic relationships between nuclear and plastid markers. Each dataset provided resolution at different levels in Cheirolophus: the nuclear markers resolved the backbone of the phylogeny while the plastid data provided better resolution within the Canarian clade. The origin of Cheirolophus was dated in the Mid-Late Miocene, followed by rapid diversification into the three main Mediterranean lineages and the Macaronesian clade. A decrease in diversification rates was inferred at the end of the Miocene, with a new increase in the Late Pliocene concurrent with the onset of the Mediterranean climate. Diversification within the Macaronesian clade started in the Early-Mid Pleistocene, with unusually high speciation rates giving rise to the extant insular diversity.ConclusionsClimate-driven diversification likely explains the early evolutionary history of Cheirolophus in the Mediterranean region. It appears that the exceptionally high diversification rate in the Canarian clade was mainly driven by allopatric speciation (including intra- and interisland diversification). Several intrinsic (e.g. breeding system, polyploid origin, seed dispersal syndrome) and extrinsic (e.g. fragmented landscape, isolated habitats, climatic and geological changes) factors probably contributed to the progressive differentiation of populations resulting in numerous microendemisms. Finally, hybridization events and emerging ecological adaptation may have also reinforced the diversification process.

Dataset Information

Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses.

Publications

Plastome Evolution in <i>Dolomiaea</i> (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses.

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