Syntenic Analysis of the Dog Genome

1
Syntenic Analysis of the Dog
Genome Michael Kamal, Bob Handsaker, Kerstin
Lindblad-Toh, Michael C. Zody, Jill P. Mesirov,
Eric S. Lander The Broad Institute at
MIT and Harvard, 320 Charles St., Cambridge, MA
02141 USA

• Synteny between dog chromosomes and the chicken,
  human, mouse, and rat genomes
• Pairwise synteny maps are based on full genomic
  alignments of masked sequence
• Well-behaved runs of non-crossing alignments
  (syntenic anchors) are clustered into segments
  of a minimum size of 500Kb.
• Segments have directionality and represent either
  intra- or interchromosomal rearrangements.
• Contiguous segments are merged to define syntenic
  blocks disregarding directionality. Blocks only
  capture interchromosomal events.
• Plots below show syntenic anchors for a 300Kb
  region in human, 256Kb region in dog and 247Kb
  region in mouse.

Dog has less power than mouse for identifying
human regions under selection because more
neutral sequence aligns.
Histograms show conservation score for each 50bp
window beyond the neutral conservation rate in
the 1Mb neighborhood z-score for p.i.d where
mean is neutral rate and standard deviation
based on a binomial model.
Excess of genome distribution over neutral
identifies human windows under selection