Evolutionary Dynamics in the Aphid Genome: Search for Genes Under Positive Selection and Detection of Gene Family Expans
Aphids have a high adaptative potential and their capacity to adapt to various environments could be linked with specific expansions in gene repertoires. A large scale acquisition of genomic data has been recently undertaken with the genome of Acyrthosiph
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Evolutionary Dynamics in the Aphid Genome: Search for Genes Under Positive Selection and Detection of Gene Family Expansions Morgane Ollivier and Claude Rispe
Abstract Aphids have a high adaptative potential and their capacity to adapt to various environments could be linked with specific expansions in gene repertoires. A large scale acquisition of genomic data has been recently undertaken with the genome of Acyrthosiphon pisum (reference gene set) and EST data from three other species: Myzus persicae, Aphis gossypii and Toxoptera citricida. We identified paralogs through an intra-genomic Reciprocical Best Hit search in A. pisum and highlighted a high and steady level of duplications in A. pisum. We assembled, ESTs, predicted coding sequences and identified pairs of orthologs with A. pisum. We identified a fraction of fast-evolving sequences (high ratio of non-synonymous to synonymous rates) including genes shared by aphids but not identified in nonaphid species. Phylogenetic study of fast-evolving genes (Apo, C002, Spaetzel) shows that rate accelerations and duplication events are linked and could favour the emergence of specific biological functions.
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Introduction
Studies of the adaptation of species to their environment have historically been focused on analyses of phenotypic variation. The enormous increase in sequence data now allows to directly detect at the gene level processes which contribute to adaptation. In a given population, genes are under drift and selection effects. Selection can act against deleterious mutation or in favour of advantageous mutations. It is possible to detect traces of selection on genomes by comparing
M. Ollivier and C. Rispe INRA, UMR 1099 BiO3P, Domaine de la Motte, F-35653, Le Rheu, France e-mail: [email protected]
P. Pontarotti (ed.), Evolutionary Biology – Concepts, Molecular and Morphological Evolution, DOI 10.1007/978-3-642-12340-5_8, # Springer-Verlag Berlin Heidelberg 2010
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homologous sequences from different organisms and by computing maximum likelihood (ML) synonymous (dS) and non-synonymous (dN) evolutionary rates. The ratio omega (dN/dS) is indeed used as an indicator of variable evolutionary pressures among protein-coding genes: low ratios are typical of highly constrained sequences (under purifying selection), while values close to unity would reflect relaxed selection and values above unity would result from positive selection. Another interesting point to consider are gene duplications. Whereas the majority of duplicated sequences are removed from a genome, duplications can provide new evolutionary opportunities as duplicated genes are often under particular selective pressures (either relaxation or positive selection). Aphids (Insecta: Hemiptera) are small insects that feed on plant sap. Some species are crop-feeding and considered as pests in agriculture. Their effects on crops are enhanced by host–plant specialisation (Hawthorne and Via 2001; Hufbauer and Via 1999) and their rapid demographic increases due
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