BACKGROUND AND AIMS: The 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. METHODS: In 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. RESULTS: Our 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. CONCLUSIONS: Our 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.
BACKGROUND AND AIMS: The 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. METHODS: In 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. RESULTS: Our 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. CONCLUSIONS: Our 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.
Authors: A B Nicotra; O K Atkin; S P Bonser; A M Davidson; E J Finnegan; U Mathesius; P Poot; M D Purugganan; C L Richards; F Valladares; M van Kleunen Journal: Trends Plant Sci Date: 2010-10-21 Impact factor: 18.313
Authors: Michael J Bayly; Philippe Rigault; Antanas Spokevicius; Pauline Y Ladiges; Peter K Ades; Charlotte Anderson; Gerd Bossinger; Andrew Merchant; Frank Udovicic; Ian E Woodrow; Josquin Tibbits Journal: Mol Phylogenet Evol Date: 2013-07-19 Impact factor: 4.286
Authors: Angela M Hancock; Benjamin Brachi; Nathalie Faure; Matthew W Horton; Lucien B Jarymowycz; F Gianluca Sperone; Chris Toomajian; Fabrice Roux; Joy Bergelson Journal: Science Date: 2011-10-07 Impact factor: 47.728
Authors: Robert K Jansen; Zhengqiu Cai; Linda A Raubeson; Henry Daniell; Claude W Depamphilis; James Leebens-Mack; Kai F Müller; Mary Guisinger-Bellian; Rosemarie C Haberle; Anne K Hansen; Timothy W Chumley; Seung-Bum Lee; Rhiannon Peery; Joel R McNeal; Jennifer V Kuehl; Jeffrey L Boore Journal: Proc Natl Acad Sci U S A Date: 2007-11-28 Impact factor: 11.205
Authors: Kelly A Frazer; Lior Pachter; Alexander Poliakov; Edward M Rubin; Inna Dubchak Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971
Authors: Victoria A Scobeyeva; Ilya V Artyushin; Anastasiya A Krinitsina; Pavel A Nikitin; Maxim I Antipin; Sergei V Kuptsov; Maxim S Belenikin; Denis O Omelchenko; Maria D Logacheva; Evgenii A Konorov; Andrey E Samoilov; Anna S Speranskaya Journal: Front Genet Date: 2021-07-08 Impact factor: 4.599