sequencing a genome

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;

Genome size & complexity

Issues for consideration when sequencing:

DNA source Genome size Repeat content Duplications and inversions

Increasing complexity

Viruses Bacteria Protozoa Mammals Plants

Issues for consideration when annotating: Genome size Repeat content Splicing Genefinding resources Likely comparator species

Inverterbrates

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

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Sequencing a Genome

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.

Sequence coverage

The sequencing of the human genome

Animation of genome sequencing

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