genome maps - linkage maps showing relative location of genes 

• 1st map made in 1911 when 5 genes of Drosophila mapped
• distances measured in centimorgans (cM)
• genetic maps - distances between genes found by recombination frequencies
• physical maps - diagrams showing relative landmarks within sequences
  • landmark - specific DNA sequences, where restriction enzymes cut DNA
  • contig - contiguous segment of genome made from pieces cut by restriction enzymes
• sequenced-tagged sites (STS) - 100-500 base-pair sequence of a clone
  • physical map can be made by overlapping STSs
  • useful when 2 different groups working on certain nonsequenced DNA

sequencing - automated sequencing required for the very large genomes 

• automated sequencers - provides accurate sequences for up to 500 base-pairs
  • errors still possible, 5-10 copies used
  • DNA prepared w/ fluorescent nucleotides, unlabeled nucleotides
  • fluorescent nucleotides lack hydroxyl groups, halt replication
  • DNA separated by size (1st base in sequence found in shortest band, last base in sequence found in longest band)
• artificial chromosome - used to clone larger DNA pieces
  • contained replication origin (to replicate independently of genome) and centromere sequences (for stability)
  • bacterial artificial chromosomes (BAC) - used for large-scale sequencing, accepts DNA inserts 100-200kb long
• clone-by-clone sequencing - physical mapping followed by sequencing
  • cuts DNA fragments which are each cloned into smaller fragments
• shotgun sequencing - sequencing all the clone fragments all at once, uses computer to put together overlaps
  • assembles consensus sequence from multiple copies of sequenced regions
  • doesn’t use extra info about genome

human genome project - 3.2 gigabase nucleotide sequence in humans 

• number of genes doesn’t indicate complexity of organism (rice has more genes than humans)
• physical map finished on June 26, 2000