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Abstract Detail



Comparative Genomics/Transcriptomics

Spalink, Daniel [1], Stoffel, Kevin [2], Genevieve, Walden [3], Amanda, Hulse-Kemp [4], Theresa, Hill [2], Allen, Van Deynze [2], Bohs, Lynn Allison [5].

Comparative Transcriptomics and Genomic Patterns of Discordance in Capsiceae.

The integration of genomics and phylogenetics allows new insight into the structure of gene discordance, the relationships among gene position, gene history, and rate of evolution, and the correspondence across lineages of gene function, positive selection, and gene ontology enrichment. 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 6,747 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, and a bifurcating species tree placing Capsicum within a paraphyletic Lycianthes was supported over all phylogenetic networks. Rates of synonymous and nonsynonymous substitution varied 41-fold and 130-fold among genes, respectively, and were significantly lower in pericentromeric regions. We found that results of concordance tree analyses vary depending on the subset of genes used, and that genes within the pericentromeric regions only capture a portion of the observed discordance. We identified 787 genes that have been positively selected throughout the diversification of Capsiceae.


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1 - University Of Utah, Department Of Biology, 257 South 1400 East, Salt Lake City, UT, 84112, United States
2 - University of California-Davis
3 - California Department of Food and Agriculture
4 - USDA-ARS
5 - University Of Utah, Department Of Biology, 257 South 1400 East, 201 South Biology, Salt Lake City, UT, 84112, United States

Keywords:
Capsiceae
genealogical discordance
pungency
positive selection.

Presentation Type: Oral Paper
Session: 21, Comparative Genomics and Transcriptomics I
Location: 102/Mayo Civic Center
Date: Tuesday, July 24th, 2018
Time: 8:00 AM
Number: 21001
Abstract ID:531
Candidate for Awards:None


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