ArticleAnnals of botany2020
A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae).
Article in Annals of botany, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 66 citations in OpenAlex.
- Article
- High-Resolution Chromosome-Level Genome Assembly and Annotation of Triplophysa stewarti, an Endemic Plateau Loach from the Qinghai-Tibet Plateau.Scientific data · 2026Article
- New generic classification for Korean Peucedanum L. (Apiaceae) species based on deep phylogenomic study.BMC plant biology · 2026Article
- Evolutionary dynamics and phylogenetic analysis of the mitochondrial genome of the medicinal plant Peucedanum praeruptorum.BMC plant biology · 2026Article
- Climate adaptation and functional constraints drive pollen evolution in Apiales.The New phytologist · 2026Article
- Revisiting the phylogeny of Conioselinum (Apiaceae) by integrating nrDNA, plastomes and morphology evidence.BMC plant biology · 2026Article
- GeneMiner2: Accurate and Automated Recovery of Genes From Genome Skimming Data.Molecular ecology resources · 2026Article
- Gene loss and positively selected genes in chloroplast genomes reveal adaptive evolution in Styracaceae.BMC plant biology · 2026Article
- Development of molecular markers for marker-assisted breeding and quality evaluation of Aconitum carmichaelii cultivars.BMC plant biology · 2025Article
- Catalytic mechanism underlying the regiospecificity of coumarin-substrate transmembrane prenyltransferases in Apiaceae.Plant & cell physiology · 2025Article
- Widely targeted metabolomics analysis reveals differences in volatile metabolites among four Angelica species.Natural products and bioprospecting · 2025Article
- A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum.Scientific reports · 2025Article
- Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes.BMC plant biology · 2024Article
- Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis.Plant methods · 2024Article
- The gradual establishment of complex coumarin biosynthetic pathway in Apiaceae.Nature communications · 2024Article
- Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae.Archives of virology · 2024Article
- Phylogeny and Taxonomic Revision of the GenusPlants (Basel, Switzerland) · 2024Article
- The complete plastomes of thirteen Libanotis (Apiaceae, Apioideae) plants: comparative and phylogenetic analyses provide insights into the plastome evolution and taxonomy of Libanotis.BMC plant biology · 2024Article
- Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses.BMC plant biology · 2024Article
- Genome skimming provides evidence to accept two new genera (Apiaceae) separated from theFrontiers in plant science · 2024Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
aimsA long-standing controversy in the subfamily Apioideae concerns relationships among the major lineages, which has prevented a comprehensive study of their fruits and evolutionary history. Here we use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae.
methodsIn total, 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Fruit morphology and anatomy were studied in combination with the species tree. Eleven SCGs were screened out for dating analysis with two fossils selected for calibration. KEY
resultsA well-supported species tree was generated with a topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] that differed from previous trees. Daucinae and Torilidinae were not in the tribe Scandiceae and existed as sister groups to the Acronema Clade. Five branches (I-V) of the species tree showed low quartet support but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Mya (95 % highest posterior density interval, 45.18-73.53 Mya).
conclusionsThis study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimation methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of Apioideae might have evolved in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggests that Daucinae and Torilidinae should be restored to the tribe level. Our results provide new insights into the morphological evolution of this subfamily, which may contribute to a better understanding of species diversification in Apioideae. Molecular dating analysis suggests that uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes probably drove rapid speciation and diversification of Apioideae in the QTP region.
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