@ARTICLE{TreeBASE2Ref27964,
author = {Xinping Qi and Li-Yaung Kuo 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 Chien-Hsun Huang and Hong Ma},
title = {A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families},
year = {2018},
keywords = {fern phylogeny, nuclear genes, transcriptomes, divergence time estimation, transcription factors},
doi = {10.1016/j.ympev.2018.06.043},
url = {http://},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {},
number = {},
pages = {},
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.}
}
Citation for Study 22028
Citation title:
"A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families".
Study name:
"A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families".
This study is part of submission 22028
(Status: Published).
Citation
Qi X., Kuo L., Guo C., Li H., Li Z., Qi J., Wang L., Hu Y., Xiang J., Zhang C., Guo J., Huang C., & Ma H. 2018. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. Molecular Phylogenetics and Evolution, .
Authors
-
Qi X.
-
Kuo L.
-
Guo C.
-
Li H.
-
Li Z.
-
Qi J.
-
Wang L.
-
Hu Y.
-
Xiang J.
-
Zhang C.
-
Guo J.
-
Huang C.
(submitter)
-
Ma H.
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.
Keywords
fern phylogeny, nuclear genes, transcriptomes, divergence time estimation, transcription factors
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S22028
- Other versions:
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- Show BibTeX reference
@ARTICLE{TreeBASE2Ref27964,
author = {Xinping Qi and Li-Yaung Kuo 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 Chien-Hsun Huang and Hong Ma},
title = {A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families},
year = {2018},
keywords = {fern phylogeny, nuclear genes, transcriptomes, divergence time estimation, transcription factors},
doi = {10.1016/j.ympev.2018.06.043},
url = {http://},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {},
number = {},
pages = {},
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.}
}
- Show RIS reference
TY - JOUR
ID - 27964
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
T1 - A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families
PY - 2018
KW - fern phylogeny
KW - nuclear genes
KW - transcriptomes
KW - divergence time estimation
KW - transcription factors
UR - http://dx.doi.org/10.1016/j.ympev.2018.06.043
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.
L3 - 10.1016/j.ympev.2018.06.043
JF - Molecular Phylogenetics and Evolution
VL -
IS -
ER -