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Citation for Study 22028

About Citation title: "A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families".
About Study name: "A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families".
About 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

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  • Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S22028
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