Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae)

Ecology and Evolution - Tập 11 Số 7 - Trang 3286-3299 - 2021
Peng‐Cheng Fu1, Shan‐Shan Sun1, Alex D. Twyford2,3, Bei‐Bei Li1, Rui‐Qi Zhou1, Shi‐Long Chen4,5, Qingbo Gao4,5, Adrien Favre6
1School of Life Science, Luoyang Normal University, Luoyang, China
2Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
3Royal Botanic Garden Edinburgh, Edinburgh, UK
4Key laboratory of adaptation and evolution of plateau biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
5Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
6Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany

Tóm tắt

AbstractThe structure and sequence of plastid genomes is highly conserved across most land plants, except for a minority of lineages that show gene loss and genome degradation. Understanding the early stages of plastome degradation may provide crucial insights into the repeatability and predictability of genomic evolutionary trends. We investigated these trends in subtribe Gentianinae of the Gentianaceae, which encompasses ca. 450 species distributed around the world, particularly in alpine and subalpine environments. We sequenced, assembled, and annotated the plastomes of 41 species, representing all six genera in subtribe Gentianinae and all main sections of the species‐rich genus Gentiana L. We reconstructed the phylogeny, estimated divergence times, investigated the phylogenetic distribution of putative gene losses, and related these to substitution rate shifts and species’ habitats. We obtained a strongly supported topology consistent with earlier studies, with all six genera in Gentianinae recovered as monophyletic and all main sections of Gentiana having full support. While closely related species have very similar plastomes in terms of size and structure, independent gene losses, particularly of the ndh complex, have occurred in multiple clades across the phylogeny. Gene loss was usually associated with a shift in the boundaries of the small single‐copy and inverted repeat regions. Substitution rates were variable between clades, with evidence for both elevated and decelerated rate shifts. Independent lineage‐specific loss of ndh genes occurred at a wide range of times, from Eocene to Pliocene. Our study illustrates that diverse degradation patterns shape the evolution of the plastid in this species‐rich plant group.

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Ecology and Evolution

Tập 11 Số 7

3286-3299

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