Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets

Liping Zeng, Ning Zhang, Qiang Zhang, Peter K. Endress, Jie Huang, Hong Ma

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

Explosive diversification is widespread in eukaryotes, making it difficult to resolve phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important for human livelihood and terrestrial ecosystems, and have probably experienced explosive diversifications. The eudicot phylogenetic relationships, especially among those of the Pentapetalae, remain unresolved. Here, we present a highly supported eudicot phylogeny and diversification rate shifts using 31 newly generated transcriptomes and 88 other datasets covering 70% of eudicot orders. A highly supported eudicot phylogeny divided Pentapetalae into two groups: one with rosids, Saxifragales, Vitales and Santalales; the other containing asterids, Caryophyllales and Dilleniaceae, with uncertainty for Berberidopsidales. Molecular clock analysis estimated that crown eudicots originated c. 146 Ma, considerably earlier than earliest tricolpate pollen fossils and most other molecular clock estimates, and Pentapetalae sequentially diverged into eight major lineages within c. 15 Myr. Two identified increases of diversification rate are located in the stems leading to Pentapetalae and asterids, and lagged behind the gamma hexaploidization. The nuclear genes from newly generated transcriptomes revealed a well-resolved eudicot phylogeny, sequential separation of major core eudicot lineages and temporal mode of diversifications, providing new insights into the evolutionary trend of morphologies and contributions to the diversification of eudicots.

Original languageEnglish (US)
Pages (from-to)1338-1354
Number of pages17
JournalNew Phytologist
Volume214
Issue number3
DOIs
StatePublished - May 1 2017

Fingerprint

Phylogeny
transcriptomics
genomics
Transcriptome
Dilleniaceae
phylogeny
Genes
Fossils
genes
transcriptome
Berberidopsidales
Pollen
Eukaryota
Crowns
Vitales
Santalales
Saxifragales
Uncertainty
Ecosystem
Caryophyllales

All Science Journal Classification (ASJC) codes

  • Physiology
  • Plant Science

Cite this

Zeng, Liping ; Zhang, Ning ; Zhang, Qiang ; Endress, Peter K. ; Huang, Jie ; Ma, Hong. / Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. In: New Phytologist. 2017 ; Vol. 214, No. 3. pp. 1338-1354.
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Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. / Zeng, Liping; Zhang, Ning; Zhang, Qiang; Endress, Peter K.; Huang, Jie; Ma, Hong.

In: New Phytologist, Vol. 214, No. 3, 01.05.2017, p. 1338-1354.

Research output: Contribution to journalArticle

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