Genomics_miRNA

Genomics_miRNA - Advances for genomics Genome projects...

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1 Genome projects Require understanding of genetics as well as molecular biology Biochemical advances of 1970’s and 80’s, followed by bioinformatics advances of the 1990’s made genome analysis possible Still have limited knowledge about most genomes Advances for genomics Frederic Sanger's invention of dideoxy sequencing late 1980’s technique involves the separation of flourescent labeled DNA fragments according length on polyacrylamide gels (PAGE) Base at end of each fragment is visualized and identified by the dye with which it reacts Time and labor intensive - gel preparation, running; amounts and purity of sample required increase time and costs of genomic sequencing Gilbert also invented a sequencing technique Not as amenable to automation Milestones in genomic sequencing φ X174 was first genome sequenced in 1977 – done by an ordered approach involving restriction fragments viral genome of 5,368 bp – fairly small 1983: Sanger first used "shotgun" sequencing to complete bacteriophage λ sequence 48,502 bp Also a viral genome, but 10X size of φ X174 1995: first complete non-viral genomes: the bacteria Haemophilus influenzae (1.8 Mb) and Mycoplasma genitalium (0.6 Mb) 1997: E. coli genome completed Milestones in genomic sequencing 1997: first complete eukaryotic genome: Saccharomyces cerevisiae (12 Mb) 1998: first complete metazoan genome: Caenorhabditis elegans (98 Mb) 2000: first complete plant genome: Arabidopsis thaliana (125 Mb) 2001: Homo sapiens genome report (draft sequence) (~3,000 Mb). Comparative genome sizes Organism Estimated size Estimated gene # Ave gene density Chrom. number Homo sapiens 2900 Mb ~30,000 1 per 100,000 bp 46 R. norvegicus (rat) 2,750 Mb ~30,000 1 per 100,000 bp 42 M. musculus (mouse) 2500 Mb ~30,000 1 per 100,000 bp 40 Drosophila 180 Mb 13,600 1 per 9,000 bp 8 Arabidopsis thaliana 125 Mb 25,500 1 per 4000 bp 5 C. elegans 97 Mb 19,100 1 per 5000 bases 6 S. cerevisiae 12 Mb 6300 1 per 2000 bases 16 E. coli 4.7 Mb 3200 1 per 1400 bases 1 H. influenzae 1.8 Mb 1700 1 per 1000 bases 1 Also done or nearly done: ~1,400 viral genomes ~200 eubacteria, inc. Streptomyces coelicolor (more genes than yeast!) ~20 archaea Schizosaccharomyces pombe (~18 single celled fungi) Aspergillus nidulans (~10 mycelial fungi) Plasmodium falciparum (and ~10 other protists) Caenorhabditis briggsae (3 nematodes) Drosophila melanogaster (~15 insects) Danio rerio (~4 fish)
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2 Also done or nearly done: Gallus gallus (chicken) Mus musculus (mouse), Pan troglodytes (chimp) (~9 mammals) Arabidopsis thaliana (~4 plants) First diatom What constitutes “done”? Human genome has been announced as “finished” three
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Genomics_miRNA - Advances for genomics Genome projects...

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