A Tale of Two Worms: Comparing the Genomes of C. elegans & C . briggsae

1. A Tale of Two Worms:Comparing the Genomes ofC. elegans & C. briggsae Lincoln Stein Cold Spring Harbor Laboratory

2. My Lab

3. International HapMap Project • Find common regions of genetic variation in human population to reduce cost of genetic association studies. • Reduce cost of genetic association studies. • 600,000 SNPs x 270 individuals

4. Comparative genomics among monocots Rice as model system Rice genome, maps, proteins, mutants, QTLs, phenotypes Map alignments to maize, wheat, oats, barley &c. Gramene

5. Genome KnowledgeBase • Biological pathways in human • Curated by experts in the field • Designed for • Education • Data mining & discovery • Open data/Open software

6. WormBase • Community database for C. elegans • C. elegans genome • C. briggsae genome • Genetic maps • Developmental anatomy • RNAi screens • Microarray screens • Evolutionary biology

7. Generic Model Organism Db • Reusable software for building model organism databases • Used by WormBase, FlyBase, Gramene, RatDB, SGD, MGD… • Genome browsers, genetic maps, curation tools…

10. 200 µm 200 µm hermaphrodite male (lateral) male (ventral) 10 µm 10 µm

11. Sequencing C. briggsae • Isolate DNA, make libraries (2 mo) • Map libraries (4 mo) • Shotgun sequence genome (1 wk) • Assemble genome (6 mo) • Analyze genome (9 mo)

12. The Draft BAC Map Sequence Contigs Supercontigs Scaffolds Jim Mullikin, Sanger Center; LaDeana Hillier, WUSTL

13. Calling C. briggsae Genes

14. briggsae genes: “hybrid” strategy Elegans predictions Briggsae predictions Avril Coghlan, University of Dublin

15. How accurate is it? • C. elegans gold standard • 2,257 genes entirely confirmed by mRNA data • Results on C. elegans set • 92% of time, hybrid method picked the “gold standard gene” correctly • 32 genes incorrectly split into 2 or more predictions (1.4%) • 49 genes incorrectly merged into 1 prediction (1%)

16. Gene Sets Very Similar

17. (Todd Harris, CSHL) best similarity match Use colinearity to resolve ambiguities best similarity match Identifying Orthologs ortholog pair Cb Ce ortholog vs paralog?

18. Comparing Orthologs • 12,155 orthologs • 807 C. briggsae “orphans” • 1,061 C. elegans “orphans” • Divergence date: 80-110 Mya • All genes under various degrees of purifying selection (Todd Harris, Jason Stajich)

19. Orthologs Similar but Differ in Detail Briggsae has 1 new intron every 5th gene.

20. Comparing Gene Families:TRIBE-MCL

21. Comparing Gene Families:TRIBE-MCL

22. Comparing Gene Families:TRIBE-MCL

23. Comparing Gene Families:TRIBE-MCL

24. Comparing Gene Families:TRIBE-MCL Cluster 3 Cluster 2 Cluster 1 Cluster 4 Cluster 5

25. Cb/Ce protein clusters 2169 clusters of >= 2 members 24% of elegans single-copy genes 28% of briggsae single-copy genes (Jason Stajich, rotation student)

26. Protein Family Clusters >200 clusters unbalanced by more than 2-fold

27. A Rapidly Evolving Family:Olfactory Receptors PFAM Class C. elegansC. briggsae 7tm_4 269 222 7tm_5 322 163 sra 37 18 srb 16 12 sre 55 51 srg 32 30 Total 718 476

28. Sra Olfactory Receptor Family Putative ortholog pair elegans exclusive subtree

29. Synteny: Aligning C.b. to C.e. Type Intergen Upstr Downst CDS Intron 5' UTR 3'UTR Repeat Total Strong 61,615 27,512 30,192 49,358 114,323 2,783 7,239 28,313 321,335 Coding 41,817 11,600 15,571 152,086 49,135 855 1,557 12,095 284,716 Weak 115,200 53,189 59,542 188,601 250,603 5,885 11,823 49,624 734,467 TOTAL 218,632 92,301 105,305 390,045 414,061 9,523 20,619 90,032 1,340,518 (Todd Harris & Jason Stajich)

30. Synteny Reconstruction raw aligned segments (WABA) Merge overlaps Merge adjacent merged segments Reconstruct interrupted segments reconstructed segments (Yours truly)

31. Reconstructing briggsae • 4,837 reconstructed segments • ~85% of genome • 0.5-0.7 bkpts/Mb/My)

32. Rearrangement is Local Junctions of elegans chromosomes on briggsae contigs

33. Rearrangement is Local Junctions of elegans chromosome arms on briggsae contigs

34. big map Syntenic blocks Genes & meiotic map Orthologs Orphans Essential genes Repetitive elements KA/KS KS

35. Improving elegans: new gene?

36. Improving elegans: bad exon?

37. Corrections to C. elegans

38. Recent Work:Chemosensory Receptors • Third largest C. elegans protein family. • Subclass of GPCR 7TM receptors. PFAM Class C. elegans C. briggsae 7tm_4 269 222 7tm_5 322 163 sra 37 18 srb 16 12 sre 55 51 srg 32 30

39. Questions • Are these differences real? • Mechanism of the differences? • Amplification vs gene loss • Why are some subfamilies unbalanced and not others? • Phenotypic consequences of the differences?

40. Sra Olfactory Receptor Family Putative ortholog pair elegans exclusive subtree

41. sra sra sra sra sra sra sra sra sra sra sra sra similarity searching elegans genome briggsae genome new new new new new new Are the Differences Real? • Intensive search for missing sra family members. C. elegans C. briggsae (Jack Chen, Postdoc; Shraddha Pai, URP)

42. Results • Family size differences real (still roughly twice as manyelegans sra as briggsae sra) • Differences due to species-specific tandem duplications, not due to conversion into pseudogenes. • But…

43. Hitting non-sra elegans genes? 18 non-sra C. elegans genes 17 non-sra C. briggsae genes

44. A New Nematode Chemosensory (Sub)family? sra family sra-like genes

45. C36C5.7 7TM Domain Structure • Most candidates showed 7 transmembrane domain signatures characteristic of GPCR membrane receptors.

46. …Usually

47. missed exon Repairing Incomplete Genes

48. Before & After Before repairing: 6 TMs After repairing: 7 TMs

49. After Repair

50. Expression Patterns Co-Cluster with sra Family Genes sra-like genes sra genes Kim et alScience, 293: 2087-2092. 2001