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Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)

Comprising ca. 200 species, Saxifraga sect. Ciliatae is the most species‐rich section of Saxifraga s.str., whose center of diversity is in the Tibeto‐Himalayan region. The infra‐sectional classification of sect. Ciliatae is still in debate due to the high level of species richness, as well as remark...

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Autores principales: Yuan, Rui, Ma, Xiaolei, Zhang, Zhuoxin, Gornall, Richard J., Wang, Yongcui, Chen, Shilong, Gao, Qingbo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9817205/
https://www.ncbi.nlm.nih.gov/pubmed/36620410
http://dx.doi.org/10.1002/ece3.9694
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author Yuan, Rui
Ma, Xiaolei
Zhang, Zhuoxin
Gornall, Richard J.
Wang, Yongcui
Chen, Shilong
Gao, Qingbo
author_facet Yuan, Rui
Ma, Xiaolei
Zhang, Zhuoxin
Gornall, Richard J.
Wang, Yongcui
Chen, Shilong
Gao, Qingbo
author_sort Yuan, Rui
collection PubMed
description Comprising ca. 200 species, Saxifraga sect. Ciliatae is the most species‐rich section of Saxifraga s.str., whose center of diversity is in the Tibeto‐Himalayan region. The infra‐sectional classification of sect. Ciliatae is still in debate due to the high level of species richness, as well as remarkable variations of habitat, morphology, physiology and life cycles. Subdivisions of this section proposed in various taxonomic systems have not been adequately tested in previous phylogenetic studies, partly due to low taxonomic sampling density, but also to the use of few DNA markers. In order to achieve a more robust infra‐sectional classification of sect. Ciliatae, complete chloroplast genomes of 94 taxa from this section were analyzed, of which 93 were newly sequenced, assembled and annotated. The length of the 94 plastomes of sect. Ciliatae taxa range from 143,479 to 159,938 bp, encoding 75 to 79 unique protein‐coding genes (PCGs). Analyses of the 94 plastomes revealed high conservation in structural organization, gene arrangement, and gene content. Gene loss and changes of IR boundaries were detected but in extremely low frequency. The molecular phylogenetic tree from concatenated PCGs and complete chloroplast genome sequences exhibited high resolution and support values and confirms that sect. Ciliatae is monophyletic. Three well‐supported clades were revealed within the section that agree relatively well with the subsectional taxonomy of Gornall (1987), but some minor modifications should be made. Firstly, the monotypic subsection Cinerascentes should be abandoned and its constituent species, S. cinerascens, assigned to subsect. Gemmiparae. Secondly, subsections Rosulares and Serpyllifoliae should be merged and become subsect. Rosulares. Section Ciliatae thus comprises: subsect. Hirculoideae Engl. & Irmsch.; subsect. Rosulares Gornall; subsect. Gemmiparae Engl. & Irmsch.; subsect. Flagellares (C. B. Clarke) Engl. & Irmsch. and subsect. Hemisphaericae (Engl. & Irmsch.) Gornall.
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spelling pubmed-98172052023-01-06 Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae) Yuan, Rui Ma, Xiaolei Zhang, Zhuoxin Gornall, Richard J. Wang, Yongcui Chen, Shilong Gao, Qingbo Ecol Evol Research Articles Comprising ca. 200 species, Saxifraga sect. Ciliatae is the most species‐rich section of Saxifraga s.str., whose center of diversity is in the Tibeto‐Himalayan region. The infra‐sectional classification of sect. Ciliatae is still in debate due to the high level of species richness, as well as remarkable variations of habitat, morphology, physiology and life cycles. Subdivisions of this section proposed in various taxonomic systems have not been adequately tested in previous phylogenetic studies, partly due to low taxonomic sampling density, but also to the use of few DNA markers. In order to achieve a more robust infra‐sectional classification of sect. Ciliatae, complete chloroplast genomes of 94 taxa from this section were analyzed, of which 93 were newly sequenced, assembled and annotated. The length of the 94 plastomes of sect. Ciliatae taxa range from 143,479 to 159,938 bp, encoding 75 to 79 unique protein‐coding genes (PCGs). Analyses of the 94 plastomes revealed high conservation in structural organization, gene arrangement, and gene content. Gene loss and changes of IR boundaries were detected but in extremely low frequency. The molecular phylogenetic tree from concatenated PCGs and complete chloroplast genome sequences exhibited high resolution and support values and confirms that sect. Ciliatae is monophyletic. Three well‐supported clades were revealed within the section that agree relatively well with the subsectional taxonomy of Gornall (1987), but some minor modifications should be made. Firstly, the monotypic subsection Cinerascentes should be abandoned and its constituent species, S. cinerascens, assigned to subsect. Gemmiparae. Secondly, subsections Rosulares and Serpyllifoliae should be merged and become subsect. Rosulares. Section Ciliatae thus comprises: subsect. Hirculoideae Engl. & Irmsch.; subsect. Rosulares Gornall; subsect. Gemmiparae Engl. & Irmsch.; subsect. Flagellares (C. B. Clarke) Engl. & Irmsch. and subsect. Hemisphaericae (Engl. & Irmsch.) Gornall. John Wiley and Sons Inc. 2023-01-06 /pmc/articles/PMC9817205/ /pubmed/36620410 http://dx.doi.org/10.1002/ece3.9694 Text en © 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Yuan, Rui
Ma, Xiaolei
Zhang, Zhuoxin
Gornall, Richard J.
Wang, Yongcui
Chen, Shilong
Gao, Qingbo
Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)
title Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)
title_full Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)
title_fullStr Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)
title_full_unstemmed Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)
title_short Chloroplast phylogenomics and the taxonomy of Saxifraga section Ciliatae (Saxifragaceae)
title_sort chloroplast phylogenomics and the taxonomy of saxifraga section ciliatae (saxifragaceae)
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9817205/
https://www.ncbi.nlm.nih.gov/pubmed/36620410
http://dx.doi.org/10.1002/ece3.9694
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