10.4 Sequencing Genomes

genome

complete set of genes or genetic material present in a cell or organism

whole genome shotgun sequencing

random overlapping genomic DNA fragments are sequenced and the sequences are assembled by a computer until the entire genome sequence is complete

contigs

continuous base pair sequences

transposable elements

existence of repetitive sequences in the genome 

step 1 of whole genome shotgun

make a collection of overlapping fragments in plasmid vectors

step 2 of whole genome shotgun

sequence the DNA inserts

step 3 of whole genome shotgun

look for overlaps between the sequence reads

step 4 of whole genome shotgun 

computer assembles them into contigs 

reconstruction of the genome in computer’s memory 

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when does sequencing stop (how many contigs for human genome?)

transposable elements

existence of repetitive sequence in the genome

paired end sequencing

both ends of single BAC (vector) clones being sequenced 

knowing the two sequence reads are connected on a single BAC insert allows genome assembly despite repeated elements 

bacterial artificial chromosome 

BAC