1. 1/29 Comparative Genomics

2. 2/29 Overview of the Talk Comparing Genomes Homologies & Families Sequence Alignments

3. 3/29 Evolution at the DNA Level …ACTGACATGTACCA… …AC----CATGCACCA… Mutation Sequence edits Rearrangements Deletion Inversion Translocation Duplication

4. 4/29 We can better understand evolution/ speciation We can find important, functional regions of the sequence (codons, promoters, regulatory regions) It can help us locate genes in other species that are missing or not well-defined (also through comparison and alignments). Why Compare Genomes?

5. 5/29  Mammals have roughly 3 billion base pairs in their genomes  Over 98% human genes are shared with primates, wth more than 95-98% similarity between genes.  Even the fruit fly shares 60% of its genes with humans! (March 2000)  Differences: gene structure, sequence Remember… one nucleotide change can cause disease such as sickle cell anemia and cancer. Comparing Genomes

6. 6/29 Uses all the species Uses a representative protein (the longest) for every gene Builds a gene tree EnsemblCompara GeneTrees: Analysis of complete, duplication aware phylogenetic trees in vertebrates. Vilella AJ, Severin J, Ureta-Vidal A, Durbin R, Heng L, Birney E. Genome Res. 2008 Nov 24. How Does Ensembl Predict Homology?

7. 7/29 Load longest protein for every gene from all species WU Blastp + SmithWaterman longest translation of every gene against every other (Blast Reciprocal Hit/ Blast Score Ratio) Protein clustering, build multiple alignments (MCoffee) From each alignment, build a gene tree Reconcile each gene tree with the species tree to determine internal nodes (TreeBest) Orthologues, paralogues… Steps in Homology Prediction..MEDPATA…

8. 8/29 Viewing Trees in Ensembl

9. 9/29 Types of Homologues Orthologues : any gene pairwise relation where the ancestor node is a speciation event Paralogues : any gene pairwise relation where the ancestor node is a duplication event

10. 10/29 The Gene Tree for INS (insulin precursor) A red square is a duplication event (Paralogues) A blue square is a speciation event (Orthologues)

11. Reconciliation M R H M R H species tree unrooted gene tree Duplication node Speciation node MRHMRH MHRMHR gene loss R’ H’ M’

12. 12/29 Orthologue Types What is ‘1 to 1’? What is ‘1 to many’?

13. 13/29 Protein Families How: Cluster proteins for every isoform in every species + UniProt proteins. BLASTP comparison of: –all Ensembl ENSP… –all metazoan (animal) proteins in UniProt

14. 14/29 1.Find the human MYL6 gene: go to its gene summary. 2.How many paralogues does it have? Find them in the gene tree. 3.Which paralogue is closest to the human MYL6 gene? In what taxon is the common ancestor? Homologues Exercise

15. 15/29 Pan-Compara (Ensembl Genomes) Bacillus subtilis Escherichia coli K12 Mycobacterium tuberculosis H37Rv Neisseria meningitidis A 4A Pyrococcus horikoshii Staphylococcus aureus N315 Streptococcus pneumoniae TIGR4 Streptococcus pyogenes M1 SF370 Plasmodium falciparum Plasmodium vivax Anolis carolinensis Ciona savignyi Danio rerio Equus caballus Gallus gallus Homo sapiens Macaca mulatta Anopheles gambiae Caenorhabditis elegans Drosophila melanogaster Arabidopsis thaliana Oryza sativa japonica Vitis vinifera Saccharomyces cerevisiae Schizosaccharomyces pombe Monodelphis domestica Mus musculus Ornithorhynchus anatinus Pan troglodytes Pongo pygmaeus Xenopus tropicalis x8 x3 x2 x13

16. 16/29 www.ensemblgenomes.org

17. 17/29 Families

18. 18/29 Ensembl Proteins in the Family

19. 19/29 Overview of the Talk Comparing Genomes Homologies and Families Sequence Alignments

20. 20/29 Large stretches of non-coding regions in vertebrates Regulatory regions of: Developmental genes Transcription factors miRNA Non-Coding Regions Kikuta et. al, Genome Research, May 2007

21. 21/29 Comparative Genomics today

22. 22/29 To identify homologous regions To spot trouble gene predictions Conserved regions could be functional To define syntenic regions (long regions of DNA sequences where order and orientation is highly conserved) Aligning Whole Genomes- Why?

23. 23/29 Aligning large genomic sequences Difficulties: Requires a significant computer resource Scalability, as more and more genomes are sequenced Time constraint As the «true» alignment is not known, then difficult to measure the alignment accuracy and apply the right method

24. 24/29 Whole Genome Alignments BLASTZ-net (nucleotide level) closer species e.g. human – mouse Translated BLAT (amino acid level) more distant species, e.g. human – zebrafish EPO/PECAN multispecies alignments ORTHEUS used to determine ancestral alleles

25. 25/29 1.Find the Ensembl MYH2 gene for human and go to Region in Detail. 2.Turn on the BLASTZ alignment against cow. What part of the cow genome aligns to this region in human? 3.Jump to the region in cow. Alignments Exercise

26. 26/29 Go back to the human page. Use the Alignments (text) and Multi-species view links to explore the alignments. AlignmentsExercise Alignments Exercise

27. 27/29 Go back to region in detail Turn on the conservation score for 31 species, and the constrained elements tracks. Where are the regions of high conservation? 1.Click on the regulatory feature that corresponds to a highly conserved block of sequence. What is it? Conserved Regions Exercise

28. 28/29 Ancestral Alleles Go to the variation tab for rs34161789, and take the Phylogenetic Context link. What is the allele in the four primates? Hint… either go to the gene tab and click on the SNP ID from the variation table, or do a new search using rs34161789.

29. 29/29 Compara Team at EBI Javier Herrero Kathryn Beal Stephen Fitzgerald Albert Vilella

30. 30/29 End of Course Survey Exercises on page 43. Answers are on page 44.