1. BME 130 – Genomes
Lecture 8
Genome Anatomies

2. (Black Death) genome sequenced
Genomics in the news
Yersinia pestis
(Black Death) genome sequenced
Johannes
Krause

4. Exon and Intron length distribution in the human genome

5. Nucleosomes:
beads on a string

6. More condensed:
30 nm fiber

11. Yeast centromere

12. Yeast kinetochore

14. Human kinetochore

15. Telomeric repeats

16. Gene Density on chr1 of Arabidopsis
Human chr1

18. This “region” in current human genome assembly (hg19)

20. Genome sizes

21. Table 7.2 Genomes 3 (© Garland Science 2007)

24. http://www.ncbi.nlm.nih.gov/homologene 26,887 17,959 22,165
Table 7.4 Genomes 3 (© Garland Science 2007)

25. Figure 7.16 Genomes 3 (© Garland Science 2007)

26. Figure 7.17 Genomes 3 (© Garland Science 2007)

27. Table 7.5 Genomes 3 (© Garland Science 2007)

28. Figure 7.18 Genomes 3 (© Garland Science 2007)

29. Gene families
Figure Genomes 3 (© Garland Science 2007)

30. Figure 7.20 Genomes 3 (© Garland Science 2007)

31. Figure 7.21 Genomes 3 (© Garland Science 2007)

32. Figure 7.22 Genomes 3 (© Garland Science 2007)

33. Figure 7.23 Genomes 3 (© Garland Science 2007)

34. Figure 7.24 Genomes 3 (© Garland Science 2007)

35. Prokaryotic Genome Anatomies
No nuclear envelope. Instead, a nucleoid

36. Genome can be naturally compacted by supercoiling it

37. Model for bacterial genome organization
HU protein – binds DNA

39. Plasmid and extra-chromosomal elements complicate the question of what is the genome

43. Prokaryotic genomes are gene-dense

45. Absence of repeat sequence simplifies assembly
From 384 assembled bacterial and archaeal genomes
Kingsford et al. BMC Bioinformatics :21   doi: /

46. Gene organization in prokaryotic genomes

49. An operon from Aquifex aeolicus
Glutamyl-tRNA aminotransferase C
Recombinase protein
Twitching mobility protein
Cytidylate kinase
Phosphotidylglycero-phosphate
synthase

50. Genome sizes are proportional to the number of genes, but vary greatly

51. Different modes of life require radically different gene catalogs

52. Horizontal gene transfer is rampant
So what is a species?

53. Eukaryotic organelle genomes

54. Human mitochondrial genome (mtDNA)

57. Green et al.,
Cell 134(3):

59. Yeast mitochondrial genome (mtDNA)

61. Bacteriophages

63. Overlapping ORFs

65. Lytic infection

66. Figure 9.4b part 1 of 2 Genomes 3 (© Garland Science 2007)

67. Figure 9.4b part 2 of 2 Genomes 3 (© Garland Science 2007)

68. Lysogenic
infection

69. Eukaryotic retrovirus structure

72. Retrovirus genome

82. Figure 9.16 Genomes 3 (© Garland Science 2007)

87. Drosophila phylogeny and P-elements