Comparative Genomics of the Eukaryotes

1. Ishay Ben-Zion Comparative Genomicsof the Eukaryotes A paper by : Rubin, Yandell, Wortman,…

2. Motivation • Evolution – Charles Darwin (1838) Similarity between different species Model organisms • A human shares 50% of his genes with a banana. How ? • Humans and bananas are multi-cellular • Other Similarities Humans share 23% of their genes with Yeast • Could banana be a good model organism ?

3. Important requirements: Size Generation Time (for genetic research) Manipulation (genetic and not) Little “Junk DNA” (easy for sequencing) Money Model Organisms Heavily Studied – used as examples for other species Once it is studied enough – It is a good candidate

4. This paper describes: A comparison between the genomes of 3 Eukaryotes: Eukaryote – Cell has inner structures with membranes (nucleus) 1) A fruit fly - Drosophila melanogaster 2) A worm – C. elegans 3) Yeast – S. cerevisiae Other model organisms (E. coli, mouse, Zebrafish, Arabidopsis)

5. Taxonomic classification Cellular life Bacteria Archaea Eukaryota Domain: Kingdom: Animalia Protista Plantae Fungi H. influenzae Fly worm yeast Species:

6. Drosophila melanogaster • Popular model organism (for developmental biology) • A trial for the human genome (sequenced at 2000) • Easily induce mutations

7. Caenorhabditis elegans • Transparent, 1-mm long • Simple – 959 cells (300 neurons) • Eat, sleep & have sex (or self-fertilize) • Hermaphrodites – 99.95%, Males – 0.05%

8. Caenorhabditis elegans Good as a model organism for: • Genetics: First multi-cellular sequenced genome • Developmental biology: cell fate mapping • Neurobiology: neurons connectivity map

9. Saccharomyces cerevisiae • Also called Baker’s yeast • Single-celled • Diameter: 5-10 μ • Popular model organism • Simplest Eukaryote • First Eukaryotic sequenced genome

10. The 1st comparison • Instead of counting genes - count gene families • What are gene families ? Paralogs = highly similar proteins in the same genome Similar functionality – but not always • Remark: proteins = genes Sets of paralogs

11. Findings • Size of a family: one or more • No. of families – not a good measure for complexity

12. The 2nd comparison • Pool genes of large families of 3 species: • For each protein – search for orthologs • Orthologs = Similar proteins in other species • Among families found in flies and worms (but not yeast): Responsible for multi-cellular development • Among families found only in flies: Responsible for immune response and fly specific

13. A C G C T C G C A A C T A C G C T T G C Methods – BLAST algorithm • Basic Local Alignment Search Tool • For comparing biological sequences (to find Homology) Example: Proteins, DNA sequences Query Library of sequences (In the library – sequences of different lengths) • In the paper: Paralogy, Orthology - kinds of Homology

14. BLAST – Step 1 • Separate query to k-letter words Example: Proteins – Letters are Amino acids (L=Leucine) Query sequence: RPPQGLF (k=3) 3-letter words: RPP PPQ PQG QGL GLF

15. BLAST – Step 2 • Take one k-letter word – PQG • Search library for similar words – LGMCPQA, DPPEGVV • Define similarity: High score for 2 words Have common ancestor PQG – PQA : 12 PQG – PEG : 15 • Save similar words above a threshold T (save positions) • Repeat for all k-letter words in query Use scoring matrix for two k-letter words

16. BLAST – Step 3 • Align at saved positions: - - - R P P Q G L F - - - - - - D P P E G V V - - - Scores: -2 7 7 2 6 1 -1 • Extend match right and left for positive score • New pairs are called High-scoring Segment Pairs (HSP) • Save significant HSPs (above a threshold S) Total: 15 + 7 + 1 = 23

17. BLAST – Step 4 • Align saved HSPs (with gaps) Example: 2 Sequences with 2 HSPs Insert gap • Compute total score (involves gap penalties) • Report all matches above a threshold E

18. BLAST – Whole process Separate query to k-letter words Search library for similar k-letter words and save Extend to HSPs and save Align whole sequences and compute total score Return sequences with score above E These are homologous to query

19. The 3rd comparison • Compare all genes of three species with length limitation (80% of length) • 20% of the fly appear in worm and yeast They perform functions common to all eukaryotic cells

20. The 4th comparison • Compare all genes of three species to mammalian sequences (without length limitation) • 50% of the fly proteins appear in mammals • 36% of the worm proteinsappear in mammals Fly is closer to mammals • Most of mammalian sequences used here were short The similarities reflect conserved domains

21. What are conserved domains ? • Domains – independent parts that construct proteins • Appear in different combinations in different proteins • Similarity to short sequences Conserved domains Closeness in evolution ABC ADEG

22. To conclude Significant similarity between genomes of ”distant” species (Man – Yeast 23%) Similarity increases for taxonomically close species ( ) No. of genes or gene families – bad measure for complexity Why ? More information that is not encoded in the genome (Protein interactions – e.g. physical proximity of genes) How to define complexity ?