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Area of Science:

  • Plant evolutionary biology
  • Phylogenomics
  • Molecular evolution

Background:

  • Phylogenomic studies often use limited single-copy genes due to homology inference challenges.
  • Few studies extend beyond species relationship reconstruction in phylogenomics.
  • The Caryophyllales clade is hyperdiverse, offering a rich system for evolutionary studies.

Purpose of the Study:

  • To develop and apply a novel phylogenomic approach for analyzing homolog and ortholog groups in Caryophyllales.
  • To reconstruct the species phylogeny of Caryophyllales using a large nuclear gene dataset.
  • To investigate patterns of gene evolution, duplication, and genome-wide duplication events within Caryophyllales.

Main Methods:

  • Collected 69 transcriptomes from Caryophyllales and 27 outgroup genomes.
  • Employed a combined similarity- and phylogenetic tree-based method to identify 10,960 homolog groups and 17,273 ortholog groups.
  • Reconstructed species phylogeny using 1,122 genes with 92.1% gene occupancy and analyzed gene duplication events.

Main Results:

  • Herbaceous lineages exhibit synonymous and nonsynonymous substitution rates up to three times faster than woody relatives across thousands of nuclear genes.
  • Identified 13 putative genome duplication events, including three previously unrecognized whole-genome duplications within Caryophyllales.
  • Gene family expansions are enriched in signal transduction and oxidoreduction, notably a cytochrome P450 involved in betalain synthesis.

Conclusions:

  • The study presents a robust phylogenomic framework for non-model organisms, integrating homolog and ortholog group analyses.
  • Demonstrates accelerated molecular evolution in herbaceous Caryophyllales and reveals significant genome duplication history.
  • Provides insights into the evolution of key metabolic pathways, such as betalain synthesis, through gene family expansion.