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23589520
Widespread selection across coding and noncoding DNA in the pea aphid genome.

G3 (Bethesda), 2013/6/21;3(6):993-1001.

Bickel RD[1], Dunham JP, Brisson JA

Affiliations

PMID: 23589520DOI: 10.1534/g3.113.005793

Impact factor: 3.542

Abstract
Genome-wide patterns of diversity and selection are critical measures for understanding how evolution has shaped the genome. Yet, these population genomic estimates are available for only a limited number of model organisms. Here we focus on the population genomics of the pea aphid (Acyrthosiphon pisum). The pea aphid is an emerging model system that exhibits a range of intriguing biological traits not present in classic model systems. We performed low-coverage genome resequencing of 21 clonal pea aphid lines collected from alfalfa host plants in North America to characterize genome-wide patterns of diversity and selection. We observed an excess of low-frequency polymorphisms throughout coding and noncoding DNA, which we suggest is the result of a founding event and subsequent population expansion in North America. Most gene regions showed lower levels of Tajima's D than synonymous sites, suggesting that the majority of the genome is not evolving neutrally but rather exhibits significant constraint. Furthermore, we used the pea aphid's unique manner of X-chromosome inheritance to assign genomic scaffolds to either autosomes or the X chromosome. Comparing autosomal vs. X-linked sequence variation, we discovered that autosomal genes show an excess of low frequency variants indicating that purifying selection acts more efficiently on the X chromosome. Overall, our results provide a critical first step in characterizing the genetic diversity and evolutionary pressures on an aphid genome.

Keywords: Acyrthosiphon; pea aphid; population genomics; selection; sex chromosome

MeSH terms
Animals; Aphids; California; Chromosomes, Insect; DNA; DNA, Intergenic; Female; Genes, Insect; Genes, X-Linked; Genome, Insect; Life Cycle Stages; Male; New England; Open Reading Frames; Pisum sativum; Polymorphism, Genetic; Polymorphism, Restriction Fragment Length; Selection, Genetic; X Chromosome
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