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Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)
Daniel Spalink1, Kevin Stoffel2, Genevieve K Walden3
1Department of Biology, University of Utah, Salt Lake City, UT, USA.
Molecular Phylogenetics and Evolution
|April 28, 2018
Summary
Genomic and phylogenetic analysis of pepper relatives (Capsiceae) reveals significant gene tree discordance and identifies 787 positively selected genes, crucial for understanding economically important traits in peppers.
Area of Science:
- Evolutionary Biology
- Genomics
- Phylogenetics
Background:
- Gene tree discordance presents challenges in evolutionary inference.
- Understanding gene history, function, and evolution across lineages is crucial.
Purpose of the Study:
- To investigate gene tree discordance, evolutionary rates, and selection pressures in the Capsiceae tribe.
- To correlate gene characteristics with their genomic position and function.
Main Methods:
- Combined annotated Capsicum genomes with newly sequenced Lycianthes and Capsicum transcriptomes.
- Developed phylogenies for 6747 genes using concordance and phylogenetic network approaches.
- Quantified phylogenetic discordance, substitution rates, and tested for positive selection.
Main Results:
- Observed substantial gene tree discordance, with a bifurcating species tree supported over networks.
- Synonymous and nonsynonymous substitution rates varied significantly, being lower in pericentromeric regions.
- Identified 787 genes under positive selection during Capsiceae diversification.
Conclusions:
- Gene tree discordance is substantial and influenced by gene subset selection and genomic location.
- Positive selection has acted on specific genes throughout Capsiceae evolution.
- Identified genes offer targets for investigating economically important traits in peppers.
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