Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)

Publication date: September 2018Source: Molecular Phylogenetics and Evolution, Volume 126Author(s): Daniel Spalink, Kevin Stoffel, Genevieve K. Walden, Amanda M. Hulse-Kemp, Theresa A. Hill, Allen Van Deynze, Lynn BohsAbstractThe integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lycianthes and Capsicum (peppers). In combining the annotated genomes of Capsicum with newly sequenced transcriptomes of four species of Lycianthes and Capsicum, we develop phylogenies for 6747 genes, and construct a backbone species tree using both concordance and explicit phylogenetic network approaches. We quantify phylogenetic discordance among individual gene trees, measure their rates of synonymous and nonsynonymous substitution, and test whether they were positively selected along any branch of the phylogeny. We then map these genes onto the annotated Capsicum genome and test whether rates of evolution, gene history, and gene ontology vary significantly with gene position. We observed substantial discordance among gene trees. A bifurcating species tree placing Capsicum within a paraphyletic Lycianthes was supported over all phylogenetic networks. Rates of sy...

Source: Molecular Phylogenetics and Evolution - July 10, 2018 Category: Molecular Biology Source Type: research