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Genetics Presentation: Sea Squirts

Genetics Presentation: Sea Squirts. Catherine Dong 9/6/12 Bio303 H Dr. Ely. The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis.

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Genetics Presentation: Sea Squirts

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  1. Genetics Presentation: Sea Squirts Catherine Dong 9/6/12 Bio303 H Dr. Ely

  2. The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Cionaintestinalis Georgia Tsagkogeorga1,2,*, Vincent Cahais1, and Nicolas Galtier1 1Universite ́ Montpellier 2, CNRS UMR 5554, Institut des Sciences de l’Evolution de Montpellier, Montpellier, France 2School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom Accepted: June 20, 2012

  3. Tunicate Cionaintestinalis • Goal: What are the causes of high amino acid substitution rates in tunicates? • A urochordata (sea squirt) • Closet invertebrate relative to humans • Phylogenomicsis the intersection of the fields of evolution and genomics • Fast evolving animal phyla • Amino acid substitution rate, across proteins are higher than other lineages.

  4. amino acid substitution • Where the similarity between sequences depends on their divergence time (time at which two lineages separated from each other) and the substitution rates are recorded

  5. Tunicates (and nematodes and platyhelminthes) evolve much faster than cnidarians and vertebrates in regards to protein sequences • Problem: why do some proteins evolve faster in some groups and slow in others? • Many evolutionary forces affect aa sub rate • Answer: Obvious one is mutation • High rate due to strong adaptive processes • Or, protein evolution could be accelerated due to less efficient natural selection • Expected more in small pop. Size

  6. Method • Gathered polymorphism sequence data sets • occurs when two or more clearly different phenotypes exist in the same population of a species • Validate max-likelihood framework for single-nucleotide polymorphism and genotype calling • Used high-throughput short-read typing • complementary DNA (cDNA) is made from mRNA catalyzed by enzymes. • Made cDNA library from 5 micrograms of RNA extracted from each sample • >1,500 cDNAsequences and >30,000 SNPs

  7. Next Generation Sequencing (NGS) • Next-generation sequencing of whole transcriptomes gives the opportunity for such a comparative approach across animals, at a reasonable cost. • Sequenced 8 tunicates in the wild Single-nucleotide polymorphism (SNP) DNA sequence variation in a single nucleotide pair Genotype calling Determines the genotype for each individual at each site.

  8. Conclusion • Proteome has high within-species diversity, efficient purifying selection, substantial percentage of adaptive amino acid sub • Increased rate of aa seq. evolution in tunicates (compared to vertebrates) is consequence of 2-6 times higher per-year mutation rate and adaptive evolution, not due to relaxing of natural selection.

  9. Significance • Tunicates offer promising comparative perspectives with respect to their slow-evolving sister group, vertebrates

  10. Questions? http://gbe.oxfordjournals.org/content/4/8/740.full.pdf

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