Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp
AffiliationUniv Arizona, Sch Plant Sci
Univ Arizona, Sch Plant Sci, BIO5 Inst
MetadataShow full item record
PublisherOXFORD UNIV PRESS
CitationAndreina I Castillo, Andrew D L Nelson, Eric Lyons, Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp., Genome Biology and Evolution, Volume 11, Issue 2, February 2019, Pages 497–507, https://doi.org/10.1093/gbe/evz015
JournalGENOME BIOLOGY AND EVOLUTION
Rights© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/license/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at firstname.lastname@example.org.
AbstractPlasmodium parasites are valuable models to understand how nucleotide composition affects mutation, diversification, and adaptation. No other observed eukaryotes have undergone such large changes in genomic Guanine-Cytosine (GC) content as seen in the genus Plasmodium (approximate to 30% within 35-40 Myr). Although mutational biases are known to influence GC content in the human-infective Plasmodium vivax and Plasmodium falciparum; no study has addressed how different gene functional classes contribute to genus-wide compositional changes, or if Plasmodium GC content variation is driven by natural selection. Here, we tested the hypothesis that certain gene processes and functions drive variation in global GC content between Plasmodium species. We performed a large-scale comparative genomic analysis using the genomes and predicted genes of 17 Plasmodium species encompassing a wide genomic GC content range. Genic GC content was sorted and divided into ten equally sized quantiles that were then assessed for functional enrichment classes. In agreement that selection on gene classes may drive genomic GC content, trans-membrane proteins were enriched within extreme GC content quantiles (Q1 and Q10). Specifically, variant surface antigens, which primarily interact with vertebrate immune systems, showed skewed GC content distributions compared with other trans-membrane proteins. Although a definitive causation linking GC content, expression, and positive selection within variant surface antigens from Plasmodium vivax, Plasmodium berghei, and Plasmodium falciparum could not be established, we found that regardless of genomic nucleotide composition, genic GC content and expression were positively correlated during trophozoite stages. Overall, these data suggest that, alongside mutational biases, functional protein classes drive Plasmodium GC content change.
NoteOpen access journal
VersionFinal published version
SponsorsNational Science Foundation [NSF IOS-1339156, IOS-1444490]; CyVerse [NSF IOS-1339156, IOS-1444490, NSF DBI-0735191, DBI-1265383]
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