Sequencing a genome

1. Sequencing a genome (a) outline the steps involved in sequencing the genome of an organism; (b) outline how gene sequencing allows for genome-wide comparisons between individuals and between species;

2. Genome size & complexity Increasing complexity Viruses Bacteria Protozoa Inverterbrates Mammals Plants Issues for consideration when sequencing: • DNA source • Genome size • Repeat content • Duplications and inversions Issues for consideration when annotating: • Genome size • Repeat content • Splicing • Genefinding resources • Likely comparator species

3. Genome sequencing Sequencing involves: • DNA fragmenting into small pieces • Sequence determination • Assembly into large contiguous sequences Problems occur: • Cloning steps • Bacterial transformation and amplification • Sequencing chemistry • Assembly of repetitive regions

4. 1 2 3 4 5 6 7 8 9 10 11 12 13 Sequencing a Genome

5. Sequence coverage Most genome sequences are not complete (not finished). Whole Genome Shotguns are referred to as having an X-fold coverage. Low coverage (2x) is sufficient for gene discovery and some regulatory element identification. High coverage (6x) is good for gene annotation. There will still be some missing genes. Finished sequence has no gaps and is presumed to contain all genes.

6. The sequencing of the human genome Animation of genome sequencing

7. Some current and potential applications of genome research include • Molecular medicine • Energy sources and environmental applications • Risk assessment • Bioarchaeology, anthropology, evolution, and human migration • DNA forensics (identification) • Agriculture, livestock breeding, and bioprocessing Detail of each bullet point