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Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)

Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial...

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Autores principales: Zhao, Jing, Zhou, Xinmao, Fang, Shaoli, Zhu, Zhangming, Li, Yuxin, Yu, Hong, He, Zhaorong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10301251/
https://www.ncbi.nlm.nih.gov/pubmed/37375862
http://dx.doi.org/10.3390/plants12122237
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author Zhao, Jing
Zhou, Xinmao
Fang, Shaoli
Zhu, Zhangming
Li, Yuxin
Yu, Hong
He, Zhaorong
author_facet Zhao, Jing
Zhou, Xinmao
Fang, Shaoli
Zhu, Zhangming
Li, Yuxin
Yu, Hong
He, Zhaorong
author_sort Zhao, Jing
collection PubMed
description Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, a dataset of 26 transcriptomes (including 11 newly generated) were used to assess single-copy nuclear genes and to obtain the organelle gene sequences. Through phylotranscriptomic analysis, the phylogeny and hybridization events of Marattiaceae were explored and a robust phylogenomic framework for the evolution of Marattiaceae was provided. Using both concatenation- and coalescent-based phylogenies, the gene-tree discordance, incomplete lineage sorting (ILS) simulations, and network inference were examined. Except the low support with mitochondrial genes of Marattiaceae, nuclear genes and chloroplast genes strongly supported a sister relationship between Marattiaceae and leptosporangiate ferns. At the genus level, all phylogenetic analysis based on nuclear genes datasets recovered five genera in Marattiaceae as monophyletic with strong support. Danaea and Ptisana were the first two diverged clades in turn. Christensenia was a sister clade to the clade Marattia + Angiopteris s.l. In Angiopteris s.l., three clades (Angiopteris s.s., the Archangiopteris group, and An. sparsisora) were well identified with maximum support. The Archangiopteris group was derived from Angiopteris s.s. at ca. 18 Ma. The putative hybrid species An. sparsisora between Angiopteris s.s. and the Archangiopteris group was verified by the species network analyses and the maternal plastid genes. This study will improve our understanding for using the phylotranscriptomic method to explore phylogeny and investigate hybridization events for difficult taxa in ferns.
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spelling pubmed-103012512023-06-29 Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae) Zhao, Jing Zhou, Xinmao Fang, Shaoli Zhu, Zhangming Li, Yuxin Yu, Hong He, Zhaorong Plants (Basel) Article Marattiaceae is a phylogenetically isolated family of tropical eusporangiate ferns including six genera with more than one-hundred species. In Marattiaceae, monophyly of genera has been well-supported phylogenetically. However, the phylogenetic relationships among them were elusive and controversial. Here, a dataset of 26 transcriptomes (including 11 newly generated) were used to assess single-copy nuclear genes and to obtain the organelle gene sequences. Through phylotranscriptomic analysis, the phylogeny and hybridization events of Marattiaceae were explored and a robust phylogenomic framework for the evolution of Marattiaceae was provided. Using both concatenation- and coalescent-based phylogenies, the gene-tree discordance, incomplete lineage sorting (ILS) simulations, and network inference were examined. Except the low support with mitochondrial genes of Marattiaceae, nuclear genes and chloroplast genes strongly supported a sister relationship between Marattiaceae and leptosporangiate ferns. At the genus level, all phylogenetic analysis based on nuclear genes datasets recovered five genera in Marattiaceae as monophyletic with strong support. Danaea and Ptisana were the first two diverged clades in turn. Christensenia was a sister clade to the clade Marattia + Angiopteris s.l. In Angiopteris s.l., three clades (Angiopteris s.s., the Archangiopteris group, and An. sparsisora) were well identified with maximum support. The Archangiopteris group was derived from Angiopteris s.s. at ca. 18 Ma. The putative hybrid species An. sparsisora between Angiopteris s.s. and the Archangiopteris group was verified by the species network analyses and the maternal plastid genes. This study will improve our understanding for using the phylotranscriptomic method to explore phylogeny and investigate hybridization events for difficult taxa in ferns. MDPI 2023-06-07 /pmc/articles/PMC10301251/ /pubmed/37375862 http://dx.doi.org/10.3390/plants12122237 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhao, Jing
Zhou, Xinmao
Fang, Shaoli
Zhu, Zhangming
Li, Yuxin
Yu, Hong
He, Zhaorong
Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)
title Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)
title_full Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)
title_fullStr Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)
title_full_unstemmed Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)
title_short Transcriptome-Based Study on the Phylogeny and Hybridization of Marattialean Ferns (Marattiaceae)
title_sort transcriptome-based study on the phylogeny and hybridization of marattialean ferns (marattiaceae)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10301251/
https://www.ncbi.nlm.nih.gov/pubmed/37375862
http://dx.doi.org/10.3390/plants12122237
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