Microbial Genome Organization PDF

Microbial Genome Organization  Prokaryotic Do not have structures surrounded by membranes Few internal structures One-celled organisms, such as Bacteria, Cyanobacteria http://library.thinkquest.org/C004535/prokaryotic_cells.html ...

Microbial Genome Organization  Prokaryotic Do not have structures surrounded by membranes Few internal structures One-celled organisms, such as Bacteria, Cyanobacteria http://library.thinkquest.org/C004535/prokaryotic_cells.html  Eukaryotic Contain organelles surrounded by membranes Most living organisms Plant Animal http://library.thinkquest.org/C004535/eukaryotic_cells.html Differences between Prokaryotic and Eukaryotic cells Feature Prokaryote Eukaryote Small, about 0.5 Size Up to 40 micrometers micrometers Genetic DNA in form of linear chromosomes Circular DNA (in cytoplasm) material ( in nucleus) Many organelles: Double membranes e.g.: nucleus, Few present, no Organelles mitochondria & chloroplasts membrane bound Single membrane e.g.: GA, ER & lysosomes Fungi: rigid, formed from Rigid formed from polysaccharide, chitin. Cell walls glycoproteins Plant: rigid, formed from (mainly murein) polysaccharides. e.g.: cellulose. Animals no cell wall 70s 80s Ribosomes *Bacterial cells also contain flagellum, plasmid and capsule.  Genetics vs. Genomics What is a genome? Genomics and DNA sequencing: sequencing reveals not only genes but also how organism functions and its evolutionary history Compare genomes of organelles: mtDNA & cpDNA Are they symbionts? Genome Size & Complexity of Living Things Genome Ranges across Organisms Genome Size and Prokaryotes In prokaryotes (Archaea and Bacteria): linear relationship between genome size and the number of genes In what examples do you expect to find the smallest genome sizes? Is there a relationship between genome size and number of genes? Organism Scientific Name Genome Size (Mb) Number of Genes Archaea Crenarchaeota Aeropyrumpernix 1.55 1,522 Euryarchaeota Methanococcusjannaschii 1.66 1,715 Euryarchaeota Archaeoglobus 2.18 2,420 Bacteria Proteobacteria Buchnera sp. CCE 0.45 Gram positive Mycoplamagenitalium 0.58 479 Proteobacteria Buchnera sp. APS 0.64 564 Gram negative Haemophilusinfluenzae 1.8 1,727 Cyanobacteria Synechocystis sp. 3.6 3,168 Gram positive Bacillus subtilis 4.2 4,100 Proteobacteria Escherichia coli 4.6 4,288 Generalization in Prokaryotes genomes have a larger number of genes and are also more complex, i.e., the number of genes reflects the lifestyle. smaller bacteria are specialists, such as obligate parasites and endosymbionts, and larger bacteria are generalists, and may even have a certain degree of development, such as sporulation in Bacillus. Genome Size and Eukaryotes defined as the C-value or amount of DNA per haploid genome, such as that which exists in the nucleus of a spermatozoon. called C, for constant or characteristic, to indicate the fact that size is practically constant within a species. Organism Scientific Name Genome Size (Mb) Number of Genes Eukaryotes Baker’s yeast Saccharomyces cerevisiae 12 6,241 Nematode Caenorhabditiselegans 97 18,424 Cruciferous Arabidopsis thaliana 125 25,498 Fruit fly Drosophila melanogaster 180 13,601 Pufferfish Fugurubripes 400 35,000 Rice Oryza sativa 450 Sea urchin Strongylocentrotuspurpuratus 900 27,350 Maize Zea mays 2,400 Human Homo sapiens 3,400 35,000 Onion Allium cep 18,000 Amoeba Amoeba dubia 686,000 Comparison of Genome Size in Eukaryotes with Prokaryotes eukaryotes have larger genomes than prokaryotes, except for some endosymbiont or parasitic green algae, which have very small genomes. the smallest eukaryotic genome ever sequenced is that of Guillardia theta, a symbiont red algae, of only 0.55 Mb. there is a wide range of sizes, much greater than that of prokaryotes, more than 80,000-fold larger, from organisms such as yeast (1.2 Mb) to the amoeba (686,000 Mb). Genome size in some living beings. The height of the drawings is proportional to the size of their genome. The specimes are amoebae, onions, grasshoppers, toads, humans, hens, Drosophila and Caenorhabditis, a nematode worm. Latorre and Silva, 2013 Is there a relationship between genome size and complexity of the eukaryotic organism? large variation in genome sizes between eukaryotic species does not seem to have a relationship with either the complexity of the organism or the number of genes they contain., e.g., amoebae, which have the largest genomes, have 200 times more DNA than humans (3,400 Mb). compared with humans, fish, amphibians or plants, have much larger genomes. there are also wide differences in their C-values. How do you explain the mismatch between the C-values and the presumed amount of genetic information contained within the genomes of eukaryotes? Is it possible to produce a minimal genome? “minimal gene concept” Design → Build → Test reductive evolution