gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the plasmodium genusgene-specific签名的升高在疟原虫属非同义替换率相关不佳.pdfVIP

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gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the plasmodium genusgene-specific签名的升高在疟原虫属非同义替换率相关不佳.pdf

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gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the plasmodium genusgene-specific签名的升高在疟原虫属非同义替换率相关不佳

Gene-Specific Signatures of Elevated Non-Synonymous Substitution Rates Correlate Poorly across the Plasmodium Genus 1 1 1,2 Gareth D. Weedall *, Spencer D. Polley , David J. Conway 1 Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom, 2 Medical Research Council Laboratories, Fajara, Banjul, The Gambia Abstract Background: Comparative genome analyses of parasites allow large scale investigation of selective pressures shaping their evolution. An acute limitation to such analysis of Plasmodium falciparum is that there is only very partial low-coverage genome sequence of the most closely related species, the chimpanzee parasite P. reichenowi. However, if orthologous genes have been under similar selective pressures throughout the Plasmodium genus then positive selection on the P. falciparum lineage might be predicted to some extent by analysis of other lineages. Principal Findings: Here, three independent pairs of closely related species in different sub-generic clades (P. falciparum and P. reichenowi; P. vivax and P. knowlesi; P. yoelii and P. berghei) were compared for a set of 43 candidate ligand genes considered likely to be under positive directional selection and a set of 102 control genes for which there was no selective hypothesis. The ratios of non-synonymous to synonymous substitutions (dN/dS) were significantly elevated in the candidate ligand genes compared to control genes in each of the three clades. However, the rank order correlation of dN/dS ratios for individual candidate genes was very low, less than the correlation for the control genes. Significance: The inability to predict positive selection on a gene in one lineage by identifying elevated dN/dS ratios in the