Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster

1. Comparative Genome andProteome Analysis of Anophelesgambiae and Drosophilamelanogaster Evgeny M. Zdobnov, Christian von Mering, Ivica Letunic, David Torrents, Mikita Suyama, Richard R. Copley, George K. Christophides, Dana Thomasova, Robert A. Holt, G. Mani Subramanian, Hans-Michael Mueller, George Dimopoulos, John H. Law, Michael A. Wells, Ewan Birney, Rosane Charlab, Aaron L. Halpern, Elena Kokoza, Cheryl L. Kraft, Zhongwu Lai, Suzanna Lewis, Christos Louis, Carolina Barillas-Mury, Deborah Nusskern, Gerald M. Rubin, Steven L. Salzberg, Granger G. Sutton, Pantelis Topalis, Ron Wides, Patrick Wincker, Mark Yandell, Frank H. Collins, Jose Ribeiro, William M. Gelbart, Fotis C. Kafatos, Peer Bork Presented by Leon G Xing SCIENCE VOL 298 4 OCTOBER 2002

2. Why Anopheles gambiae? • It is the principal vector of malaria • It carries many other infectious diseases • Malaria afflicts more than 500 million people • Morethan 1 million people die each year from malaria

3. The Culprit

4. Why Drosophila melanogaster • One of the most intensively studied organisms in biology • Serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes • Modest genome size ~ 180 MB • Its genome has been sequenced in 2000

5. Mosquito vs. Fruit Fly • They diverged about 250 million years ago • (Human and pufferfish diverged about 450 million years ago) • Share considerable similarities • Half of the genes in both genomes are interpreted as orthologs • Average sequence identity about 56%,

6. Mosquito vs. Fruit Fly • Anopheles genome is twice the size of Drosophila • Female Anopheles feeds on blood (Hematophagy), which is essential for egg development and propagation • Viruses and parasites use Anopheles as a vehicle for transmission

7. Orthologs • Genes in different species that evolved from a common ancestral gene by speciation • Typically retain the same function in the course of evolution

8. Paralogs • Genes related by duplication within an organism and have evolved a related but different function

9. Predict the function of a new protein • A powerful approach is to use bioinformatics and domain database searches to find its characterized orthologs • We know a lot about Drosophila but don’t know much about Anopheles • Compare their genomes may deduce a lot of information

10. Drosophila melanogaster Genome • The assembled and annotated genome sequence of 5 Drosophila melanogaster chromosomes is in GenBank • It’s the collaboration between Celera and the Berkeley Drosophila Genome Project • Published in the March 24, 2000 issue of Science.

11. Drosophila Genome

12. Anopheles vs DrosophilaGene Comparison at Protein Level • The proteins are classified into 4 categories based on: • 12,981 deduced Anopheles proteins out of 15,189 annotated transcripts • Omit transposon-derived bacterial like sequences, and alternative transcripts

13. Classification of Anopheles proteins • 1:1 orthologs: • Anopheles proteins with one clearly identifiable counterpart in Drosophila and vice versa • 47% of the Anopheles • 44% of the Drosophila proteins

14. Classification of Anopheles proteins • “Many-to-many” orthologs. • Gene duplication has occurred in one or both species after divergence • Includes 1779 Anopheles proteins

15. Classification of Anopheles proteins • The third category: • Have homologs in Drosophila and/or other species but without easily discernable orthologous relationships • 3590 Anopheles predicted proteins

16. Classification of Anopheles proteins • The fourth category • Has little or no homology in Drosophila but instead have best matches to other species. • 1283 proteins

17. Classification of Anopheles proteins • Remaining proteins: • No detectable homologs in any other species with a fully sequenced genome; • 1437 in Anopheles • 2570 in Drosophila • Might be new or quickly evolving genes.

18. Classification of proteins

19. Some Notes • The numbers and derived estimates are approximations. • Annotation of genomes is an ongoing effort • Some Anopheles genes have not been sequenced yet • Highly polymorphic regions or in highly repetitive contexts prone to errors • > 70% accuracy

20. The core of conserved proteins • The 1:1 orthologs (6089 pairs) can be considered the conserved core • The average sequence identity is 56% • Humans and pufferfish share 61% • Indicates that insect proteins diverge at a higher rate

21. Properties of 1:1 orthologs.

22. Orthologous proteins constitute a core of conserved functions • Early embryogenesis are conserved between Drosophila and Anopheles • 315 early developmental genes in Drosophila vs 251 genes showed a clear single ortholog in Anopheles

23. Orthologous proteins • 85% of the developmental genes havesingle orthologs • 47% for the genome as a whole

24. Protein family expansions and reductions • Due to adaptations to environment and life strategies • Leads to changes in cellular and phenotypic features • Implies duplicationsafter speciation

25. Protein family expansions and reductions example • Epsilon subunit of the adenosine triphosphate-synthase complex • Encoded by two genes in both Anopheles and Drosophila • They might share a single-copy ancestral gene • After speciation they were duplicated independently later

26. Expansions of proteins with FBN-like domains in Anopheles. • Fibrinogen (FBN) are found originally in human blood coagulationproteins • A large expansion of mosquitoproteins contains a domain resembling the COOH-terminus of thebeta and gamma chains of FBN

27. Expansions of proteins with FBN-like domains in Anopheles. • Phylogenetictree of 58 Anopheles and 13 Drosophila FBN genes • They largely belong to two distinct species-specificclades • Identified only two1:1 orthologous relationships

28. The significant implication of FBN gene expansion • The massive expansion of the Anopheles gene FBN familymight be associated with particular aspects of the mosquito's biology • That is, hematophagy and exposure to Plasmodium • Blood meal is a challenge associated with microbial flora in the gut and blood coagulation

29. The implication of FBN gene expansion • The bacteria-bindingproperties of FBNs might be important in controllingor aggregating bacteria in the midgut • These proteins might be used as competitive inhibitors i.e. anticoagulants • Some mosquito FBN proteins are up-regulated by invading malariaparasites

30. Expansion of FBN-like proteins in Anopheles

31. Gene losses in insects • Some genes are absent in both Anopheles and Drosophila but are present in other eukaryotes • Criteria: genes must be present in at least one animal but also in fungi or plants

32. Gene losses in insects.

33. Gene genesis and gene loss • 1437 predicted genes in Anopheles haveno detectable homology with genes of other species • 522 of thesehave putative paralogs only within Anopheles • At least 26of such genes expressed in the adult female salivary glands

34. Strategy for identifying gene losses • Search for genes that are present in only one of the two insects but thatdo have orthologs in other species

35. Gene Losses • Widespread orthologs missingfrom both Anopheles and Drosophila are putativeinsect-specific gene losses • Example: • Insects are known to unable to synthesize sterols • Absence of severalenzymes involved in sterol metabolism

36. Gene Losses example • Absence of the DNA repair enzyme uracil-DNA glycosylase in insects • DNA methylation can lead to spontaneousdeamination of cytosine to uracil • Drosophila has long been known to have no or only very littleDNA methylation

37. Cladogram based on Orthologs

38. Intron gain and loss • Drosophila are known to have a reduction of noncoding regions • 11,007 outof 20,161 Anopheles introns in 1:1 orthologs have equivalent positionsin Drosophila • Almost 10,000 introns have either beenlost or gained

39. The DrosophilaDscam gene • Able to encode up to 38,000 proteinsthrough extensive alternative splicing • Three different cassettes of duplicatedexons that can generate exponential combinations of splice variants • The numbers of exons within the cassettes are at least similarin Anopheles

41. Microsynteny • Through evolution genome structure may vary greatly, but smallregions of conserved gene will be retained • Microsynteny studies the localized region of sequences with high similarity

42. Microsynteny blocks

43. Mapping of orthologs and microsyntenyblocks to chromosomal arms in Anophelesand Drosophila.

44. Chromosome mapping • Both Anopheles and Drosophila have five major chromosomal arms(X, 2L, 2R, 3L, and 3R, and a small chromosome 4 in Drosophilamelanogaster). • In Drosophila, reassortment of recognizablechromosomal arms occurs by fission and fusion at the centromeres

45. Chromosome mapping • The most conserved pair of chromosomal arms is Dm2L and Ag3R • 76% of the orthologs and 95% of microsynteny blocks inDm2L mapping to Ag3R

46. Chromosome mapping.

47. Chromosome mapping surprise • Significant portions of the Anopheles X chromosome appear to have been derived from what are presently autosomal Drosophilachromosome segments • 11% of Dm3R and33% of Dm4

48. Homology of chromosomal arms

49. Thank you!