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Genomic screen for adaptive genes in fishes

English title Genomic screen for adaptive genes in fishes
Applicant Montoya-Burgos Juan-Ignacio
Number 122303
Funding scheme Project funding (Div. I-III)
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Genetics
Start/End 01.12.2008 - 31.05.2011
Approved amount 166'667.00
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All Disciplines (2)

Discipline
Genetics
Zoology

Keywords (11)

genomics; evolution; adaptive genes; phenotype; selection; subtractive hybridization; positive selection; transcripts; adaptive trait; macro-array; genome

Lay Summary (English)

Lead
Lay summary
Title:GENOMIC SCREEN FOR ADAPTIVE GENES IN FISHESPrincipal applicant:PhD, Juan I. Montoya-Burgos, Dept Zoology and Animal Biology, University of GenevaLead:The identification of genes governing adaptive traits is extremely challenging, even more for non-model organisms. We have developed and will perform a new method aimed at isolating candidate genes that evolve under positive selection, which is the typical sign of adaptive evolution. Summary:Are there specific genes or biological functions more likely to govern adaptive evolution of organisms? Identification of genes underlying adaptive traits is an extremely challenging task, even for model organisms for which extensive information is available. For non-model organisms, no genomic-scale methods have yet been developed aimed at identifying genes evolving via positive Darwinian selection. Here, we present and will perform a new genomic approach for isolating fast evolving transcripts that show typical signs of positive selection. It consists of two rounds of transcripts selection: 1) fast evolving transcripts are isolated via an interspecific subtractive hybridization; 2) using a macroarray approach, candidates are tested for signatures of positive selection. The classification of the genes according to their biological function and cellular location will highlight if particular biological processes are more likely to underlie adaptive evolution. We will also propose correlations between genotypes and phenotypes. This research will be performed on a highly diverse group of Neotropical catfishes, the Loricariina.Goals:Perform our new experimental method for isolating candidate genes that show typical signs of positive Drawinian selection. Classification of the isolated genes according to the biological processes they belong to. Analysis of the strength of the selective pressure acting on some selected genes to confirm the validity of the method.SignificationIdentifying genes and biological functions governing adaptation is central in evolutionary biology. This knowledge opens new avenues for our understanding on how evolution proceeds and how species adapt in varying environments. This knowledge is particularly crucial for conservation planning in the context of global climatic changes.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Name Institute
Surget-Groba Yann

Publications

Publication
Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
Montoya-Burgos Juan I. (2011), Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu, in PLoS ONE, 6(9), e24800-e24800.
Optimization of de novo transcriptome assembly from next-generation sequencing data
Surget-Groba Y., Montoya-Burgos J. I. (2010), Optimization of de novo transcriptome assembly from next-generation sequencing data, in Genome Research, 20(10), 1432-1440.
Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH)
Montoya-Burgos Juan I, Foulon Aurélia, Bahechar Ilham (2010), Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH), in BMC Genomics, 11(1), 126-126.

Associated projects

Number Title Start Funding scheme
141233 Adaptive evolution and key innovation in Neotropical fishes 01.11.2012 Project funding (Div. I-III)
141233 Adaptive evolution and key innovation in Neotropical fishes 01.11.2012 Project funding (Div. I-III)

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