A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families

Xinping Qi, Li Yaung Kuo, Chunce Guo, Hao Li, Zhongyang Li, Ji Qi, Linbo Wang, Yi Hu, Jianying Xiang, Caifei Zhang, Jing Guo, Chien Hsun Huang, Hong Ma

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.

Original languageEnglish (US)
Pages (from-to)961-977
Number of pages17
JournalMolecular Phylogenetics and Evolution
Volume127
DOIs
StatePublished - Oct 1 2018

Fingerprint

Ferns
Phylogeny
fern
ferns and fern allies
phylogeny
Transcription Factors
transcription factors
Spermatophytina
history
Seeds
seed
tree ferns
Mya
phylogenetics
Gleicheniales
Hymenophyllales
gene
vascular plants
Dipteridaceae
vascular plant

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Qi, Xinping ; Kuo, Li Yaung ; Guo, Chunce ; Li, Hao ; Li, Zhongyang ; Qi, Ji ; Wang, Linbo ; Hu, Yi ; Xiang, Jianying ; Zhang, Caifei ; Guo, Jing ; Huang, Chien Hsun ; Ma, Hong. / A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. In: Molecular Phylogenetics and Evolution. 2018 ; Vol. 127. pp. 961-977.
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abstract = "Ferns account for 80{\%} of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85{\%} of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.",
author = "Xinping Qi and Kuo, {Li Yaung} and Chunce Guo and Hao Li and Zhongyang Li and Ji Qi and Linbo Wang and Yi Hu and Jianying Xiang and Caifei Zhang and Jing Guo and Huang, {Chien Hsun} and Hong Ma",
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Qi, X, Kuo, LY, Guo, C, Li, H, Li, Z, Qi, J, Wang, L, Hu, Y, Xiang, J, Zhang, C, Guo, J, Huang, CH & Ma, H 2018, 'A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families', Molecular Phylogenetics and Evolution, vol. 127, pp. 961-977. https://doi.org/10.1016/j.ympev.2018.06.043

A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. / Qi, Xinping; Kuo, Li Yaung; Guo, Chunce; Li, Hao; Li, Zhongyang; Qi, Ji; Wang, Linbo; Hu, Yi; Xiang, Jianying; Zhang, Caifei; Guo, Jing; Huang, Chien Hsun; Ma, Hong.

In: Molecular Phylogenetics and Evolution, Vol. 127, 01.10.2018, p. 961-977.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families

AU - Qi, Xinping

AU - Kuo, Li Yaung

AU - Guo, Chunce

AU - Li, Hao

AU - Li, Zhongyang

AU - Qi, Ji

AU - Wang, Linbo

AU - Hu, Yi

AU - Xiang, Jianying

AU - Zhang, Caifei

AU - Guo, Jing

AU - Huang, Chien Hsun

AU - Ma, Hong

PY - 2018/10/1

Y1 - 2018/10/1

N2 - Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.

AB - Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.

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