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Artemia Genome & sex locus

Artemia Genome & sex locus. ir. Stéphanie De Vos Promotors: Marnik Vuylsteke Gilbert Van Stappen Peter bossier. Overview. Artemia AFLP-based genetic map Sex markers Genome sequence. 1. Artemia. Use Live feed Research Model toxicity assay

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Artemia Genome & sex locus

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  1. Artemia Genome& sex locus ir. Stéphanie De Vos Promotors: Marnik Vuylsteke Gilbert Van Stappen Peter bossier

  2. Overview • Artemia • AFLP-based genetic map • Sex markers • Genome sequence Confidential

  3. 1. Artemia Use • Live feed • Research Model • toxicity assay • biodiversity • metabolism crustaceans • Interaction sexual & parthenogenetic populations • evolution Confidential

  4. 2. AFLP-based genetic map Confidential

  5. 2. AFLP-based genetic map • Genetic map = • Linkage map showing the relative positions of genetic markers along chromosomes • Purpose • efficiently develop Artemia breeds, more • Nutritious • Productive • Resistant to diseases & other types of stress • by marker assisted selection (MAS). Confidential

  6. 2. AFLP-based genetic map Female genetic map 22 Linkage groups Confidential

  7. 3. Sex markers Confidential

  8. 3. Sex markers Why sex locus? • Known in Artemia => Extrapolate to commercial Crustaceans => Genetic sex test => Patent • Genotypic sex determination Crustaceans => fenotypic sex change (cfr. Tilapia) => shrimp aquaculture • Paternity / Maternity assignments Crustaceans Confidential

  9. 3. Sex markers Male & female `sex chromosomes` Sequenced Confidential

  10. 4. Genome sequence Confidential

  11. 4. Genome sequence Strategy • 1. Sequence pools • 2. Assembly • 3. Evaluate assembly • 4. Find exact sex locus Confidential

  12. 4. Genome sequence 1. Sequencing • Paired-end libraries • 100 bp reads • Cleaned off 14 % 1 2 Confidential

  13. 4. Genome sequence 2. Assembly Challenges: Short reads, genome size, de novo, RAM, CPU Assemblers Confidential

  14. 4. Genome sequence 3. Evaluate assembly Reads/Scaffolds        99 % Average coverage  148 % Scaffolds 1Gb  Genome 1,5 - 3 Gb • Highly repetitive sequences • Genome size: 1.5 -> 3 Gb => flow cytometry Confidential

  15. 4. Genome sequence 3. Evaluate assembly • AlignArtemia Expressed  Artemia assembly EST 93 % • AlignArthropod protein  TranslatedArtemia assembly Confidential

  16. Genome sequence D. pulex D. melanogaster N.vitripennis Artemia franciscana T. urticae Confidential

  17. Future work Confidential

  18. Future work • Best assembly • Find sex locus on genome • Develop genotypic sex test • Sex genes in other shrimp • Artemia full genome & extra genes (salinity, T, Vibrio, …) Confidential

  19. Thank you Confidential

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