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Gene Geography

This study explores the gene density and chromosomal rearrangements in various organisms, including Mycoplasma genitalium, Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Arabidopsis thaliana, and Homo sapiens. The findings reveal the distribution of genes among chromosomes, the periodicity in gene density, and the impact of gene rearrangements on genome evolution. Additionally, the study examines the correlation between chromosomal numbers and DNA content in bacteria. The results provide valuable insights into genetic organization and evolution across different species.

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Gene Geography

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  1. 3c Gene Geography Dan Graur Department of Biology and Biochemistry

  2. Gene density (genes/Kb) Mycoplasma genitalium 0.8 Escherichia coli 0.6 Saccharomyces cerevisiae 0.5 Caenorhabditiselegans 0.2 Arabidopsis thaliana 0.2 Homo sapiens 0.03 AluinHomo sapiens 1.1

  3. Genes are distributed evenly among the 16 chromosomes of Saccharomyces cerevisiae.

  4. Periodicity in gene density along chromosome XI of Saccharomyces cerevisiae.

  5. In large plant genomes, most protein-coding genes are clustered in long DNA segments (gene space, urban aggregations) that represent a small fraction (12-24%) of the nuclear genome, and which are separated from one another by vast expanses ofgene-empty regions(deserts).

  6. Only ~1/3 genes in eukaryotes are essential for viability. The proportion does not vary much between organisms (25-35%). • Organisms with a large number of genes (e.g., humans, fish). • Organisms with an intermediate number of genes (nematodes, Drosophila). • Organisms with a low gene number (e.g., yeast).

  7. Cryptic (linear) Giant (circular) Genetic material Chromosomes Extrachromosomal material Plasmids Episomes

  8. Chromosomes contain genes that are unconditionally essential. Extrachromosomal elements contain genetic information that is not necessary under all conditions.

  9. plasmid episome

  10. Brucella 2 1 = 2 1

  11. Even in Bacteria chromosome number does not correlate with DNA content.

  12. Classification of eukaryotic chromosomes by centromere position.

  13. Gene loss

  14. Gene addition

  15. Gene rearrangement

  16. Exchanges of genetic information between two nonhomologous chromosomes.

  17. Mouse-human synteny. Human chromosomes can be cut into a relatively small number pieces, then shuffled into a reasonable approximation of the mouse genome.

  18. Regions of conserved synteny between human chromosome 22 and the mouse genome.

  19. Chromosome-number reduction Chinese water deer (Hydropotes inermis) n = 70 Brown-brocket deer (Mazama gouazoubira) n = 70 Chinese muntjac (Munitacus reevesi) n = 46 Black muntjac (M. muntiacus crinifrons) n = 8 Indian muntjac (M. muntiacus vaginalis) n = 6

  20. Muntiacus reevesi

  21. 2N = 44 + (XX or XY) 2N = 6 + (XX or XY1Y2

  22. 1 2 3 4 5 3 2 5 4 5 Inferring the number of gene-order-rearrangement events

  23. The alignment-reduction method by David Sankoff deletion distance (D) = the minimal number of deletions or insertions necessary to turn genome content A into genome content B. rearrangement distance (R) = the minimal number of inversions and transpositions necessary to convert gene order of A into the gene order of B.

  24. evolutionary edit distance (E): E = D + R

  25. To estimate E, we employ three geometrical procedures: deletion, bundling, and inversion D = 2 bundle is w/o price

  26. 1 2 3 4 5 3 2 5 4 5 R = 3

  27. Tsuzumi drum Tsuzumi graph

  28. The conserved S10 region. The three arrows represent operons in E. coli. A dot (·) indicates the existence of a gene at a site; a minus sign (–) indicates that the gene has been translocated elsewhere in the genome; indicates that the gene was not found in the genome. L and S = large and small ribosomal-proteins; prlA = preprotein-translocation secY subunit; adk = adenylate kinase; map = methionine aminopeptidase; infA = initiation-factor 1; rpoA = DNA-directed RNA-polymerase a chain.

  29. Evolutionary-edit distance between pairs of animal mitochondria. Rearrangement distances and deletion distances are above and below the diagonal, respectively. aHs = Homo sapiens; Gg = Gallus gallus; Sp = Strongylocentrotus purpuratus (sea urchin); Ap = Asterina pectinifera (starfish); Po = Pisaster ochraceus (starfish); Dy = Drosophila yakuba; As = Ascaris suum (pig roundworm).

  30. Sorting by reversals Nicotiana Lobelia

  31. Synteny =occurrence of two or more genes on the same chromosome. Conserved synteny = synteny of two or more homologous genes in two species. Conserved linkage = conservation of both synteny and gene order of homologous genes between species. Disrupted synteny = a pair of genes are syntenic in one species but their orthologs are located on different chromosomes in the second species. Disrupted linkage = a difference in gene order between the species.

  32. Empirical variables: (1) number of conserved syntenies (2) distribution of number of genes among conserved syntenies (3) number of conserved linkages (4) distribution of number of genes among conserved linkages.

  33. Assumption: A uniform distribution of genes over the genome Estimate: Number of genomic disruptions required to explain the differences between two genomes.

  34. Conclusions: (1) gene-order rearrangements occur at high rates.

  35. Conclusions: (2) rates of synteny disruption vary widely among mammalian lineages. The mouse lineage has a rate of synteny disruptions that is 25 times higher than that of the cat lineage.

  36. Conclusions: (3) interchromosomal rearrangements occur approximately four times more frequently than intrachromosomal ones.

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