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Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae)
The 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 ge...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019047/ https://www.ncbi.nlm.nih.gov/pubmed/33841784 http://dx.doi.org/10.1002/ece3.7281 |
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author | Fu, Peng‐Cheng Sun, Shan‐Shan Twyford, Alex D. Li, Bei‐Bei Zhou, Rui‐Qi Chen, Shi‐Long Gao, Qing‐Bo Favre, Adrien |
author_facet | Fu, Peng‐Cheng Sun, Shan‐Shan Twyford, Alex D. Li, Bei‐Bei Zhou, Rui‐Qi Chen, Shi‐Long Gao, Qing‐Bo Favre, Adrien |
author_sort | Fu, Peng‐Cheng |
collection | PubMed |
description | The 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. |
format | Online Article Text |
id | pubmed-8019047 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-80190472021-04-08 Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae) Fu, Peng‐Cheng Sun, Shan‐Shan Twyford, Alex D. Li, Bei‐Bei Zhou, Rui‐Qi Chen, Shi‐Long Gao, Qing‐Bo Favre, Adrien Ecol Evol Original Research The 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. John Wiley and Sons Inc. 2021-02-22 /pmc/articles/PMC8019047/ /pubmed/33841784 http://dx.doi.org/10.1002/ece3.7281 Text en © 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Research Fu, Peng‐Cheng Sun, Shan‐Shan Twyford, Alex D. Li, Bei‐Bei Zhou, Rui‐Qi Chen, Shi‐Long Gao, Qing‐Bo Favre, Adrien Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae) |
title | Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae) |
title_full | Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae) |
title_fullStr | Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae) |
title_full_unstemmed | Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae) |
title_short | Lineage‐specific plastid degradation in subtribe Gentianinae (Gentianaceae) |
title_sort | lineage‐specific plastid degradation in subtribe gentianinae (gentianaceae) |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019047/ https://www.ncbi.nlm.nih.gov/pubmed/33841784 http://dx.doi.org/10.1002/ece3.7281 |
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