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Polymorphic segmental duplications in the nematode Caenorhabditis elegans

Polymorphic segmental duplications in the nematode Caenorhabditis elegans. Ismael Vergara Chen Lab Thursday February 12 th , 2009. Simon Fraser University Department of Molecular Biology and Biochemistry Vancouver Bioinformatics Users Group (VanBUG). Introduction.

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Polymorphic segmental duplications in the nematode Caenorhabditis elegans

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  1. Polymorphic segmental duplications in the nematode Caenorhabditis elegans Ismael Vergara Chen Lab Thursday February 12th, 2009 Simon Fraser University Department of Molecular Biology and Biochemistry Vancouver Bioinformatics Users Group (VanBUG)

  2. Introduction Different types of genomic structural variations have been found in most eukaryotic genomes. Duplications at the gene, segment and genome level have been detected. Duplications are a driving force for the generation of new genes.

  3. OrthoCluster: a tool for detecting segmental duplications Genome Paralogous relations g1 g4 g2 g5 . . gi gj . . … G1 … g1 g2 g3 g4 g5 … gM …

  4. OrthoCluster: a tool for detecting segmental duplications Genome Paralogous relations g1 g4 g2 g5 . . gi gj . . … G1 … g1 g2 g3 g4 g5 … gM … G1 … g1 g2 g3 g4 g5 … gM …

  5. C. elegans: a model organism

  6. C. elegans: a model organism Sydney Brenner Established C. elegans as a model organism. Nobel Prize in Physiology or Medicine (2002)

  7. C. elegans: a model organism Sydney Brenner Established C. elegans as a model organism. Nobel Prize in Physiology or Medicine (2002) The C. elegans Sequencing Consortium, 1998

  8. (1)Distribution of perfect segmental duplications in C. elegans

  9. 3,484 duplicons generated by 1,980 segmental duplications Frequency Duplicon Size (number of genes)

  10. Frequency Duplicon Size (number of genes)

  11. Frequency Duplicon Size (number of genes) V

  12. (2)Molecular characterization of the largest segmental duplication

  13. 99.7% similarity

  14. 99.7% similarity

  15. (3)Experimental characterization of the largest segmental duplication

  16. Jim Huang, Dr. Allan Mah, Dr. David Baillie

  17. Jim Huang, Dr. Allan Mah, Dr. David Baillie

  18. 38% of strains tested have this large tandem duplication Jim Huang, Dr. Allan Mah, Dr. David Baillie

  19. Has large duplication Does not have large duplication CGC: Caenorhabditis Genetics Center

  20. Other nearly-identical tandem duplications in C. elegans F: forward (head-to-tail) R: reversed (tail-to-tail)

  21. Next Steps • Extend this analysis to all nearly-identical tandem duplications. • Inspect further the correlation between different types of segmental duplications and Transposable Elements. • Analyze the function of F56A4.3 and its potential role in stabilizing the segmental duplication.

  22. Conclusions • We have developed a computer program, OrthoCluster, for the genome-wide detection of segmental duplications. • We have identified 1,980 perfect segmental duplications in C. elegans. • The largest segmental duplication is polymorphic in Wild Type C. elegans strains. • This large duplication may represent only one of many cases of polymorphic regions within C. elegans strains.

  23. OrthoClusterDB http://genome.sfu.ca/orthoclusterdb

  24. Acknowledgements Dr. Jack Chen Dr. Maja Tarailo • Dr. David Baillie (MBB) • Dr. Allan Mah • Dr. Bob Johnsen • Jim Huang • Dr. Jian Pei (CS) • Dr. Ke Wang • Xinghuo Zeng • The C. elegans community • Supported by Weyerhaeuser Molecular Biology and Biochemistry Fellowship, NSERC, and MSFHR.

  25. OrthoCluster: a tool for the detection of synteny blocks Genomes G1 … g11 g12 g13 g14 g15 … g1M … G2 … g21 g22 g23 g24 g25 … g2M … G3 … g31 g32 g33 g34 g35 … g3M … . . . GN … gN1 gN2 gN3 gN4 gN5 … gNM …

  26. OrthoCluster: a tool for the detection of synteny blocks Genomes Correspondence File … g11 g21 g31 … gN1 g12 g22 g32 … gN2 g13 g23 g33 … gN3 g14 g24 g34 … gN4 . . . . . . . . . g1M g2M g3M … gNM … G1 … g11 g12 g13 g14 g15 … g1M … G2 … g21 g22 g23 g24 g25 … g2M … G3 … g31 g32 g33 g34 g35 … g3M … . . . GN … gN1 gN2 gN3 gN4 gN5 … gNM …

  27. OrthoCluster: a tool for the detection of synteny blocks Genomes Correspondence File … g11 g21 g31 … gN1 g12 g22 g32 … gN2 g13 g23 g33 … gN3 g14 g24 g34 … gN4 . . . . . . . . . g1M g2M g3M … gNM … G1 … g11 g12 g13 g14 g15 … g1M … G2 … g21 g22 g23 g24 g25 … g2M … G3 … g31 g32 g33 g34 g35 … g3M … . . . GN … gN1 gN2 gN3 gN4 gN5 … gNM … G1 … g11 g12 g13 g14 g15 … g1M … G2 … g21 g22 g23 g24 g25 … g2M … G3 … g31 g32 g33 g34 g35 … g3M … . . . GN … gN1 gN2 gN3 gN4 gN5 … gNM …

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