Comparative Genomics and the Evolution of Animal Diversity

1. Comparative Genomicsandthe Evolution of Animal Diversity 03生科一班第二组 曾莹莹 200331060121

2. Outline 1.Most animals have essentially the same genes. 2.Three ways gene expression is charged during evolution. 3.Experimental manipulations that alter animal morphology. 4.Genome evolution and human origins.

3. Our world is full Of diversity. Annelids: simple repeating body Segments. Mollusks: twisted or coiled. But there is one striking feature: Most animals have essentially the same genes!!!

4. Topic 1: Most Animals Have Essentially the Same Genes

5. Comparison of pufferfish, mouse and human In spite of millions of years of evolutionary divergence, pufferfish, mouse and humans each contain about 30,000 genes. Every human gene has a clear counterpart in the mouse genome; and three quarters of human and bufferfish genes can be unambiguously aligned.

7. Comparison of sea squirt and vertebrates • Sea squirt, a chordate, contains half the number of genes present in vertebrates. • sea squirt genome contains 6 different FGF (fibroblast growth factor ), while mouse and human genomes at least 22 FGF—each gene in the sea squirt duplicated into average of four copies in vertebrates.

8. From the two comparison, we can conclude: • The genetic conservation is universal. • Increase in gene number is primarily due to the duplication of genes already present rather than the invention of entire new genes.

9. How does gene duplication give rise to biological diversity? There are two ways in which gene duplication can result in morphological diversity: 1.Conventional view: the duplicated new genes undergo mutation, this mutation creates genes encoding related proteins with slightly different activities. 2.Resent view: the duplicated genes doesn’t necessarily take on new functions, but instead acquire new regulatory DNA sequence, which allows different copies of the gene to be expressed in different patterns within the developing organism. (a general mechanism we focus attention on)

10. Topic 2: Three Ways Gene Expression Is Charged During Evolution

11. Three ways gene expression is changed during evolution 1.A pattern determining gene can be expressed in a new pattern, causing target genes to acquire new patterns of expression. 2.The regulatory protein encoded by a pattern determining gene can acquire new functions. (a transcriptional activation domain →repressiondomain) 3.Target genes of a pattern determining gene can acquire new regulatory DNA sequences, thus come under the control of a different regulatory gene. Pattern determining genes: changes in the activities and expression patterns of these genes cause significant changes in animal morphology.

12. Altering the function of the regulatory protein↓ ↑Altering the expression of the pattern determining gene Altering the target of the pattern determining gene→

13. Topic 3 Experimental Manipulations That Alter Animal Morphology

14. Abnormal morphologies are obtained through each of the three mechanisms described above: A.Altering the expression♀ B.Altering the function♀ C.Altering the targets of pattern determining genes♀

15. Topic 4 Genome evolution and human origins

16. Human contains surprisingly few genes • Human genome contains only 25,000-30,000 protein coding genes. (before the human genome was sequenced, there were popular estimates for 100,000 protein coding genes) • Higher vertebrates contain sophisticated mechanisms for gene regulation in order to produce many patterns of gene expression

17. The nematode worm: nearly 20,000 genes Fruit fly: less than 14,000 genes Nonetheless, fruit flies exhibit a far more Sophisticated range of range of morphologies and behaviors than those in worms ↓

18. Organismal complexity is not correlated with gene number, But instead depends on the number of gene expression patterns.

19. The human genome is very similar to that of the mouse and virtually identical to the chimp Mice and humans: 1.About 28,000 genes 2.80﹪of these genes possess a clear and unique one-to-one sequence alignment with one another between the two species 3.The protein encoded by these genes are highly conserved and share an average of 80﹪ amino acid sequence identity 4.Most of the remaining 20﹪ differ by virtue of lineage-specific gene duplication events

20. Chimp and human: the genomes vary by an average of just 2﹪ sequence divergence ↓ Regulatory DNA evolve more rapidly than proteins

21. The evolutionary origin of human speech Speech is one of the defining features of being human. How did our distinctive form of language arise in human evolution?

22. Speech depends on the precise coordination of the small muscles in our larynx and mouth. Reduced level of a regulatory protein called FOXP2 cause severe defects in speech. • The FOXP2 gene was isolated in a variety of mammals, including mice, chimps, and orangutans. • The human form of protein is slightly different. There are two amino acid residues that are unique: thr to asn (T to N) at position 303 and asn to ser (N to S) at position 325.

24. How FOXP2 fosters speech in humans • Changes in the FOXP2 expression pattern ♂ • Changes in its amino acid sequence ♂ • Changes in FOXP2 target genes ♂

25. The future of comparative genome analysis Now, there is a glaring limitation in our ability to infer the function of regulatory DNA from simple sequence inspection. Fewer than 100 regulatory DNAs have been carefully characterized in all animals combined. ↓

26. In the future, It might be possible to infer both the timing and sites of gene expression by simply scanning the DNA sequences associated with any given gene. It might also be possible to identify changes in the expression profiles of homologous genes. The continuing development of new computational methods and the availability of new genome assemblies offer exciting prospects for the use of comparative methods to reveal the mechanism of evolutionary diversity!

27. The End

28. Experiment Ⅰ Changes in Pax6 expression create ectopic eyes

29. Pax6: a pattern determining gene which controls eye development in most animals. • When Pax6 is misexpressed in the wrong tissues , it causes the development of extra eyes in those tissues, particularly in the wings and legs of adult flies. • Changes in the Pax6 expression pattern during evolution probably account for differences in the positioning of eyes in different animals.

31. Pax6 genes from other animals also produce ectopic eyes when misexpressed in Drosophila Fruit flies were engineered to misexpress the squid Pax6 gene, which results in extra eyes in the wings and legs.

32. Experiment Ⅱ Changes in Antp expression transform antennae into legs

33. Antp:a pattern determining gene that controls the development of the mesothorax • Antp encodes a homeodomain regulatory protein that is normally expressed in the mesothorax of developing embryo • a dominant Antp mutation brings the Antp protein ceding sequence under the control of a “foreign” regulatory protein DNA that mediates gene expression in head tissues

34. When misexpressed in the head, Antp causes a striking change in morphology ↓ leg development instead of antennae

35. Experiment of Ubx expression 1. Misexpression of Ubx changes the morphology of the fruit fly 2. Changes in Ubx expression explain modifications in limbs among the crustaceans

36. Ubx: a pattern determining gene that encodes a homeodomain regulatory protein that controls the development of the third thoracic segment, the metathorax. It specifically represses the expression of genes that are required for the second thoracic segment, mesothorax, eg Antp.

37. A. Mutants that lack the Ubx repressor exhibit an abnormal pattern of Antp expression ↓ Antp is not only expressed within the developing mesothorax, but it is also misexpressed in the developing metathorax ↓ metathorax→duplicated mesothorax

38. Ubx mutation → Antp misexpression → transformation of halteres into wings → four fully developed wings Mesothorax: contains a pair of legs and wings Metathorax: contains a pair of legs and halteres

39. B． A mutation called Cbx disrupt Ubx regulatory DNA without changing the Ubx protein coding region ↓ causes Ubx to be misexpressed in the mesothorax in addition to its normal site of expression in the metathorax↓mesothorax→duplicated metathorax

40. Cbx mutation → Ubx misexpression in the mesothorax → the wings are transformed into halteres → flies look like wingless ants

41. During the divergence of branchiopods and isopods, the Ubx regulatory sequences changed in isopods. As a result of this change, Ubx expression was eliminated in the first thoracic segment.↓ Branchiopods: contain swimming limbs on the T1 through T8 segments. (T: thoracic) Isopods: contain swimming limbs on the T2 through T8 segments, but the limbs on T1 has been modified. (which are called maxillipeds)

42. The Ubx regulatory DNA of isopods acquired mutation ↓ Loss of the Ubx repressor ↓ The Scr gene is expressed in T1 segment in isopods ↓ Maxillipeds develop in place of normal swimming limbs

43. Back

44. Experiment Ⅰ Importance of protein function: interconversion of ftz and Antp

45. There are two related pattern determining genes in Drosophila, the segmentation gene ftz and the homeotic gene Antp. These genes arose from an ancient duplication event. • The Antp and ftz proteins recognize distinct DNA-binding sites because they form heterodimers with different “partner” proteins.

46. Ftz:contains a pentapeptide sequence, LRALL, which mediates interaction with FtzF1 Antp: contains a tetrapeptide sequence YPWM, which mediates interaction withExd

47. Ftz-FtzF1 and Antp-Exd recognize distinct DNA sequences →Antp and Ftz regulate different target genes • In more primitive insects, the Ftz protein contains both the YPWM and LRALL motif, thus it can function as both a segmentation gene and homeotic gene.

48. Experiment of Ubx function 1.Changes in Ubx function modify the morphology of fruit fly embryos 2. Functional changes in the Ubx regulatory protein in insects and crustaceans

49. The conversion of Ubx into a transcriptional activator causes it to function like Antp and promote the development of the mesothorax • The Ubx protein contains specific peptide sequences that recruit repression complexes, which is composed of a stretch of alanine residues called alanine-rich domains.

50. Normally functions as a repressor, the Ubx can be converted into an activator by fusing the Ubx DNA-bindingdomain from the viral VP16 protein. ↓ In this way, it causes all of the segments to develop as mesothoracic segments.