Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp

Andreina I. Castillo, Andrew D.L. Nelson, Eric H Lyons

Research output: Contribution to journalArticle

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 (∼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.

Original languageEnglish (US)
Pages (from-to)497-507
Number of pages11
JournalGenome biology and evolution
Volume11
Issue number2
DOIs
StatePublished - Feb 1 2019

Fingerprint

Plasmodium
cytosine
guanine
Base Composition
Tail
genomics
tail
genome
Genome
gene
Genes
antigen
genes
protein
membrane
Plasmodium vivax
immune system
eukaryote
transmembrane proteins
natural selection

Keywords

  • CoGe
  • comparative genomics
  • GC bias
  • GC content
  • gene function
  • genome evolution
  • Plasmodium

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp. / Castillo, Andreina I.; Nelson, Andrew D.L.; Lyons, Eric H.

In: Genome biology and evolution, Vol. 11, No. 2, 01.02.2019, p. 497-507.

Research output: Contribution to journalArticle

Castillo, Andreina I. ; Nelson, Andrew D.L. ; Lyons, Eric H. / Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp. In: Genome biology and evolution. 2019 ; Vol. 11, No. 2. pp. 497-507.
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