Transcript 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 genomewide comparisons between individuals and between
species;
Genome size & complexity
Increasing
complexity
Viruses
Bacteria
Protozoa
Inverterbrates
Issues for consideration when sequencing:
Mammals
Plants
Issues for consideration when annotating:
 DNA source
 Genome size
 Genome size
 Repeat content
 Repeat content
 Splicing
 Duplications and inversions
 Genefinding resources
 Likely comparator species
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
Sequencing a Genome
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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.
The sequencing of the human
genome
Animation of genome
sequencing
Some current and potential
applications of genome research
include
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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