Final Report Summary - PICOPOP (Inferring adaptation, population size and lifecycle, from population genomics in a marine picoplanktonic species : Ostreococcus tauri (Chlorophyta))
Photosynthesis is usually associated with terrestrial plants. However, they only account for half of all photosynthetic activity, the other half is contributed by aquatic organisms, principally marine phytoplankton [1]. These enigmatic microscopic organisms are present in all of the world’s oceans in vast numbers. They are, however, very poorly characterized due to difficulty in maintaining most in culture. In fact the diversity of these organisms has only become apparent due to environmental genomics – the random sequencing of DNA extracted from environments such as sea water - which has revealed a dazzling diversity of eukaryotic planktonic life [2]. Besides their important role in the marine carbon cycle they have biotechnological potential as possible sources of Biofuels and omega3 food supplements (Patent No.’s WO/2005/012316 and WO/2006/069710).
Unfortunately we know relatively little about the genetics, ecology and evolutionary biology of marine phytoplankton due to the difficulty of growing them in the laboratory. There are therefore many unanswered questions about their biology. In this project we set out to address several major questions using Ostreococuus tauri, a model marine phytoplankton that can be grown in the laboratory. Ostreococcus spp. are very small (~1m) unicellular autotrophic cells, with a very small nuclear genome (~13MB) [3,4], containing a single chloroplast and mitochondrion. They have a worldwide distribution and although they account for a modest fraction of the oceanic biomass, they contribute significantly to primary production in many oceanic waters [5,6]. We sort to answer the following questions:
1. What is the frequency of sexual reproduction and recombination?
2. What is the nature of adaptive evolution in this organism?
3. What is the genomic rate of deleterious mutation?
4. What is pattern and nature of natural selection on new mutations in O. tauri?
To address these questions we have used a population genomic dataset of 12 strains of O.tauri that have been sequenced by Joint Genome Institute at more 100-fold coverage. We first used these to improve the reference genome of O. tauri. The initial assembly contained ~1600 gaps [3], which we have now been able to reduce to 600 using the new data. This will help greatly in subsequent analyses.
Unfortunately we know relatively little about the genetics, ecology and evolutionary biology of marine phytoplankton due to the difficulty of growing them in the laboratory. There are therefore many unanswered questions about their biology. In this project we set out to address several major questions using Ostreococuus tauri, a model marine phytoplankton that can be grown in the laboratory. Ostreococcus spp. are very small (~1m) unicellular autotrophic cells, with a very small nuclear genome (~13MB) [3,4], containing a single chloroplast and mitochondrion. They have a worldwide distribution and although they account for a modest fraction of the oceanic biomass, they contribute significantly to primary production in many oceanic waters [5,6]. We sort to answer the following questions:
1. What is the frequency of sexual reproduction and recombination?
2. What is the nature of adaptive evolution in this organism?
3. What is the genomic rate of deleterious mutation?
4. What is pattern and nature of natural selection on new mutations in O. tauri?
To address these questions we have used a population genomic dataset of 12 strains of O.tauri that have been sequenced by Joint Genome Institute at more 100-fold coverage. We first used these to improve the reference genome of O. tauri. The initial assembly contained ~1600 gaps [3], which we have now been able to reduce to 600 using the new data. This will help greatly in subsequent analyses.