ArticleAnnals of botany2020
Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences.
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 53 papers.
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53 citing papers in PubMed, 123 citations in OpenAlex.
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- The origin and diversification of Amaryllidaceae: A phylogenetic and biogeographic analysis.American journal of botany · 2025Article
- Phylogenomics of East Asian lineage within subgenus Anguinum (Allium, Amaryllidaceae): insights into its taxonomic puzzles and phylogenetic conflicts.BMC plant biology · 2025Article
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- Characterization of the complete plastid genome ofMitochondrial DNA. Part B, Resources · 2025Article
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- Comparative Chloroplast Genome Study ofGenes · 2024Article
- New insights on the phylogeny, evolutionary history, and ecological adaptation mechanism in cycle-cup oaks based on chloroplast genomes.Ecology and evolution · 2024Article
- Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle.BMC plant biology · 2024Article
- Comparative Analysis of Plastome Sequences of SevenInternational journal of molecular sciences · 2024Article
- Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Comparative Analysis of Chloroplast Genome ofInternational journal of molecular sciences · 2024Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
aimsThe genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study.
methodsIn this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families.
resultsOur phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species.
conclusionsOur results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
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