1 Gene Geography Dan Graur Department of Biology and Biochemistry 3c.
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Transcript of 1 Gene Geography Dan Graur Department of Biology and Biochemistry 3c.
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Gene GeographyGene Geography
Dan GraurDan GraurDepartment of Biology and BiochemistryDepartment of Biology and Biochemistry
3c
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Gene density (genes/Kb)Mycoplasma genitalium 0.8 Escherichia coli 0.6 Saccharomyces cerevisiae 0.5 Caenorhabditis elegans 0.2 Arabidopsis thaliana 0.2 Homo sapiens 0.03 Alu in Homo sapiens 1.1
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Genes are distributed evenly among the 16 chromosomes of Saccharomyces cerevisiae.
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Periodicity in gene density along chromosome XI of Saccharomyces cerevisiae.
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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 of gene-empty regions (deserts).
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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).
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Genetic material
ChromosomesExtrachromosomal
material
Plasmids Episomes
Cryptic(linear)
Giant(circular)
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Chromosomes Chromosomes contain genes contain genes that are that are unconditionallunconditionallyy essentialessential. .
Extrachromosomal elementsExtrachromosomal elements contain genetic information contain genetic information that is that is not necessarnot necessaryy under all under all conditionsconditions. .
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plasmidplasmid
episomeepisome
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BrucellaBrucella
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22 11
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==
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Even in BacteriaEven in Bacteriachromosome number chromosome number does notdoes not correlate correlate with DNA content.with DNA content.
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Classification of eukaryotic chromosomes by centromere position.
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Gene lossGene loss
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Gene additionGene addition
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Gene rearrangementGene rearrangement
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Exchanges of genetic information between two nonhomologous chromosomes.
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Mouse-human synteny.Mouse-human synteny. Human chromosomes Human chromosomes can be cut into a relatively small number pieces, can be cut into a relatively small number pieces, then shuffled into a reasonable approximation of then shuffled into a reasonable approximation of the mouse genome. the mouse genome.
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Regions of conserved synteny between human chromosome 22 and the mouse genome.
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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
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Muntiacus reevesi
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2N = 44 + (XX or XY)
2N = 6 + (XX or XY1Y2
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Inferring the number of Inferring the number of gene-order-rearrangement gene-order-rearrangement
events events
1 2 3 4 5
3 2 5 4 5
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The alignment-reduction methodby
David Sankoff
deletion distance (D) = the minimal number of deletions or insertions necessary to turn genome contentgenome content A into genome content B.
rearrangement distance (R) = the minimal number of inversions and transpositions necessary to convert gene ordergene order of A into the gene order of B.
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evolutionary edit distance (E):
E = D + R
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To estimate E, we employ three geometrical procedures: deletion, bundling, and inversion
D = 2bundle is w/o price
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1 2 3 4 5
3 2 5 4 5
R = 3
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Tsuzumi graph Tsuzumi drum
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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 chain.
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OTUsa Hs Gg Sp Ap Po Dy As
Hs 1 18 16 19 13 25
Gg 0 19 17 17 12 26
Sp 0 0 2 1 26 27
Ap 4 4 4 1 22 25
Po 1 1 1 5 23 24
Dy 0 0 0 4 1 28
As 1 1 1 5 2 1
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).
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Sorting by reversals
Nicotiana
Lobelia
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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.
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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.
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Assumption:Assumption:
A uniform distribution of genes over the genome
Estimate:Estimate:
Number of genomic disruptions required to explain the differences between two genomes.
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Conclusions:
(1) gene-order rearrangements occur at high rates.
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Conclusions:
(2) rates of synteny disruption vary widely among mammalian lineages.The mouse lineage has a rate of The mouse lineage has a rate of synteny disruptions that is 25 times synteny disruptions that is 25 times higher than that of the cat lineage.higher than that of the cat lineage.
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Conclusions:
(3) interinterchromosomal rearrangements occur approximately four times more frequently than intraintrachromosomal ones.