Mon Spr W3 - Comparative Genomics (Lec3) Describe how comparative genomics has been used to analyse the genomes of prokaryotes such as E .coli Forward Genetic Analysis Commensal strain (K-12 MG1655) 200 600 1500 Uropathogenic strain (CFT073) 3000 500 200 1350 Enteropathogenic strain (O157:H7) A 'core' genome of 3000 genes Chemmanama innings nem nast Forward genetic analysis in E. Coli 1) Make random mutations & screen for interesting phenotypes (like a nutritional requirement) 2) Map the mutation, identify the gene that is disrupted and study the function of the gene The functions of 2000 E. coli genes were discovered and characterised in this way Problems: 1) The genome sequence of E.coli reveals ~4300 genes and the core genome is 3000 genes 2) Many mutant phenotypes are not accessible to forward genetics min Cons 1) Induce random mutations - check phenotypes 2) Map mutation to find changed gene -> study function of that gene - Gives underestimate of core no. E. coli genes - Due to conditions don't match E.coli's natural environment ... so not all phenotypes expressed + detected - May be due to other issues such as: incomplete mutagenesis screen? More extensive screen needed? Some mutations are lethal? Reverse genetic analysis Use plating robot to help make library of every mutation in every gene 1) Complete sequence of E.coli genome + predict where all genes are located 2) Make a library of strains - each with single gene deletion 3) Screen library of mutated strains for its phenotype + identify gene's function
Describe how comparative genomics provides evidence to support the endosymbiotic theory Comparative genomics provided proof of the endosymbiotic theory and revealed much about the origins of chloroplasts & mitochondria Plant cells contain at least three genomes (nuclear, mitochondrial & chloroplast) Organelles (mitochondrial & chloroplast) have retained fragments of their original genomes How many genes in the model plant genome such as Arabidopsis thaliana have been acquired and retained from prokaryotes? What experiments have been done that help answer this question? pre-chloroplast bacterium eukaryotic cell with a nucleus incorporation in host cell Endosymbiotic theory: botanist Konstantin Mereschkowski in 1910 microbiologist Lynn Margulis in 1967 loss of bacterial cell wall transfer of genes to the nucleus We can use c.g to prove to us the origins of genes in eukaryotes In doing so it also provided proof for endosymbiotic theory of chloroplast and mitoch Comparative genomics Size of genome Number of genes Genes of prokaryotic origin A. thaliana nuclear genome 130 Mb 25,678 genes ~4300 genes Photosynthetic prokaryote 5 Mb ~4000 genes prokaryotic ancestor of chloroplasts Chloroplast genome 154 Kb 87 genes 87 genes In the table: - Compare genes and see where they originate - Last column shows no. genes from prokaryote - Chloroplasts found in plant (A.thaliana) originated from photosynthetic prokaryote thus all 87 genes are from a prokaryote - Plant genome contains chloroplast genome thus ~4300 from 25,678 genes from prokaryotic origin 1700 (13400) From diagram: 900 (4600) Secretory Other - 87 genes present in chloroplast