Genomes & The Tree of LifeChloroplast DNA in Green PlantsSlide 3Slide 4What about genetic complexity?Slide 6Mycoplasma : How many genes essential for growth (under lab conditions)?Genomic and species differences contributing to the wide range of nuclear genome sizesGenetic RedundancySlide 10Impact of Horizontal Transfer on GenomesWhat can you do with whole genomes & sequences?Slide 13Slide 14Slide 15What can you do with whole genome sequences?Genomes & The Tree of Life•Archaea - small circular genome •Prokarya - small to very small (e.g., Mycobacterium) circular genomes•Eukarya - 3 genomes–Mitochondrial – small to micro-sized, linear and circular, prokaryotic origin–Chloroplast – small, circular, prokaryotic origin –Nucleus – large, linear chromosomes; evidence of archaea, prokaryotic and “protoeukaryotic” originsChloroplast DNA in Green Plants1. Circular, multi-copy (20-100/organelle)2. ~160,000 bp; ~125 genes3. Most genes of two types:•Photosynthesis•Genetic functions (mostly translation)From Kloppstech, Westhof et al.Tobacco (Nicotiana tabacum) chloroplast genomePlant nuclear genome sizes are large and widely varied.x 1000 to get bpLilium longiflorum (Easter lily) = 90,000 MbFritillaria assyriaca (butterfly) = 124,900 MbProtopterus aethiopicus (lungfish) = 139,000 MbWhat about genetic complexity?How many genes do organisms have?Mycoplasma prokaryote517E. coli prokaryote4300Archaeoglobus archaeon2500Cyanidioschyzon rhodophyte 4700Saccharomyces yeast 6000Drosophila insect 13,600Chlamydomonas chlorophyte (unicell)15,500Arabidopsis angiosperm, dicot 25,000Homo sapiens primate 32,000Oryza (rice) angiosperm, monocot32-39,000Organism Taxon # GenesTexas wild riceMycoplasma : How many genes essential for growth (under lab conditions)?•Using transposon mutagenesis, ~150 of the 517 genes could be knocked out; ~ 300 genes deemed essential (under lab conditions), which included:–~100 of unknown function–Genes for glycolysis & ATP synthesis–ABC transporters–Genes for DNA replication, transcription and translationScience 286, 2165 (1999)Genomic and species differences contributing to the wide range of nuclear genome sizesThere can be great variation in the:1. Fraction of highly repeated DNA 2. Abundance of "Selfish DNA“ (transposons, etc.)3. Frequency and sizes of introns–Humans have many & larger introns4. Genetic redundancyGenetic Redundancy•The sizes of many gene families has increased in some organisms more than others•Accounts at least partially for the relatively high genetic complexity of plants.yeast Drosophila ArabidopsisNo. of genes6200 13,600 25,000No. of gene families4380 8065 11,000No. of genes from duplication1820 5535 14,000Genetic Redundancy or DuplicationImpact of Horizontal Transfer on Genomes•~ 20% of the E. coli genome was obtained by lateral transfer.•Viral and bacterial pathogens can transfer DNA from host to host. •Some nuclear genes came from organellar genomes (some relatively recently).•Selfish DNAs such as mobile introns and transposons occasionally transfer horizontally.What can you do with whole genomes & sequences?1. Predict much about the functions of a poorly studied or difficult organism- only ~1-5% of bacteria in theenvironment are culturableTransport and metabolic pathways of the Lyme disease spirochaete, Borreliapredicted from the genome sequence.Nature 390, 583What can you do with whole genomes & sequences?1. Predict much about the functions of a poorly studied or difficult organism.2. Can examine genome-wide expression patterns with microarrays (e.g., cancer versus normal cells).Can immobilize 1,000-5,000 DNAs (genes) on one microarray glass slide.1. Hybridize slide to cDNAs that were obtained by reverse transcription from total mRNAs with a fluorescent nucleotide. 2. Scan slide with a laser and process fluorescent image.Can simultaneously compare 2 different mRNA preparations by using different colored fluorescent nucleotides.Red- induced mRNAGreen- decreased mRNAYellow – unchanged mRNAWhat can you do with whole genome sequences?1. Predict much about the functions of a poorly studied or difficult organism.2. Can examine genome-wide expression patterns with microarrays (e.g., cancer v. normal cells).3. Identify new drug targets.4. More rapidly identify genes linked to a trait. 5. Rapidly identify a gene for an identified protein by mass spectrometry – compare mass spectrum of the protein with the predicted patterns from all of the genes of a sequenced genome
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