Genomic Insights Into Mutation, Recombination and Phytoplankton Fitness

Informations

Funding country

France

Acronym

PHYTNESS

URL

-

Start date

2/1/2014

End date

-

Budget

224,999 EUR

Fundings

Abstract

This project investigates two fundamental mechanisms involved in genome dynamics in eukaryotes; mutation and recombination, by combining experimental and population genomics approaches in the Mamiellophyceaen clade (phylum Chlorophyta). This clade included the three ecologically important marine genera Ostreococcus, Micromonas and Bathycoccus, that together encompass a large evolutionary divergence time reflected in phenotypic, gene content and genome architecture diversity. Mutation is the ultimate source of variation whereas recombination permits allele shuffling between individuals. The estimation of these two processes has broad importance for genetics, evolution and biodiversity studies. High Throughput Sequencing approaches revolutionized research on spontaneous mutation rates by allowing the direct observation of mutations accumulating during successive cell divisions in eukaryotes. Few direct spontaneous mutation rates have been estimated so far, and additional data is crucial to address the relative importance of the cost of deleterious mutations, genetic drift and genome size on the mutation rate. Mamiellophyceae green algae provide an ideal framework to investigate this issue by mutation accumulation experiments on four strains for which a complete genome has been fully sequenced: O. tauri RCC745, O. mediterraneus BCC102 and B. prasinos RCC1105 and M. pusilla RCC299. Recombination rates along chromosomes directly affect the efficiency of selection on mutations. Another consequence of crossing-overs is the possibility of biased gene conversion, the biased mismatch repair of paired homologous sequences during meiosis. Several lines of evidence suggest that GC biased gene conversion leaves a significant imprint on nucleotidic landscapes in animal and plant genomes. Knowledge about recombination rates is lacking in these organisms while it is critical to understand both the origin of genome architecture and the evolution of the mutation rate. We will take advantage of the availability of population genomics data to provide the first estimates of genome wide recombination rates from sequence polymorphism in two Ostreococcus species. While these are only two of the four studied species, the analysis of the correlation between the recombination map, the genetic diversity and the base composition will enable to draw significant advances to be made on the mechanisms involved in the genome architecture of this clade. Linking genetic diversity to phenotypes is the last objective of our project. To that end we will investigate whether we find genome wide associations between some haplotypes and discrete phenotypes, like the spectrum of viral resistance or continuous phenotypes like growth rates. We will use comparative genomics and population genomics data to assess the proportion of neutral, deleterious and advantageous mutations in coding regions. Genetic variation obtained from population genomic datasets and associated fitness effects will be integrated within a web-based resource to browse whole genomes and perform analysis on gene families across multiple species. The approaches developed through this project will provide important insights into the processes underlying genome evolution and diversification in a class including widely diverged genomes and serve as baseline for understanding the diversification of marine algae, that represent an as yet under-exploited reservoir of biodiversity.