Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp
Affiliation
Univ Arizona, Sch Plant SciUniv Arizona, Sch Plant Sci, BIO5 Inst
Issue Date
2019-02
Metadata
Show full item recordPublisher
OXFORD UNIV PRESSCitation
Andreina 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/evz015Journal
GENOME BIOLOGY AND EVOLUTIONRights
© 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/).Collection Information
This 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 repository@u.library.arizona.edu.Abstract
Plasmodium 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.Note
Open access journalISSN
1759-6653PubMed ID
30689842Version
Final published versionSponsors
National Science Foundation [NSF IOS-1339156, IOS-1444490]; CyVerse [NSF IOS-1339156, IOS-1444490, NSF DBI-0735191, DBI-1265383]ae974a485f413a2113503eed53cd6c53
10.1093/gbe/evz015
Scopus Count
Collections
Except where otherwise noted, this item's license is described as © 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/).
Related articles
- Plasmodium parasites of birds have the most AT-rich genes of eukaryotes.
- Authors: Videvall E
- Issue date: 2018 Feb
- The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium.
- Authors: Nikbakht H, Xia X, Hickey DA
- Issue date: 2014 Sep
- The Plasmodium gaboni genome illuminates allelic dimorphism of immunologically important surface antigens in P. falciparum.
- Authors: Roy SW
- Issue date: 2015 Dec
- Evidence of purifying selection on merozoite surface protein 8 (MSP8) and 10 (MSP10) in Plasmodium spp.
- Authors: Pacheco MA, Elango AP, Rahman AA, Fisher D, Collins WE, Barnwell JW, Escalante AA
- Issue date: 2012 Jul
- The origin and diversification of the merozoite surface protein 3 (msp3) multi-gene family in Plasmodium vivax and related parasites.
- Authors: Rice BL, Acosta MM, Pacheco MA, Carlton JM, Barnwell JW, Escalante AA
- Issue date: 2014 Sep