The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: a high frequency of deletions in tandem duplicates
Mikael Brandstrom 1 and Hans Ellegren 1*
1 Uppsala University
* To whom correspondence should be addressed. E-mail: hans.ellegren{at}ebc.uu.se.
Submitted on January 11, 2007
Revised on May 9, 2007
Accepted on 13 May 2007
 |
Abstract |
|---|
It is increasingly recognised that insertions and deletions (indels) are an important source to genetic as well as phenotypic divergence and diversity. We analysed length polymorphisms identified through partial (0.25X) shotgun sequencing of three breeds of domestic chicken made by the International Chicken Polymorphism Map Consortium. A data set of 140,484 short indel polymorphisms in unique DNA was identified after filtering for microsatellite structures. There was a significant excess of tandem duplicates at indel sites, with deletions of a duplicate motif outnumbering the generation of duplicates through insertion. Indel density was lower in microchromosomes than in macrochromosomes, in the Z chromosome than in autosomes, and in 100 bp upstream sequence, 5' UTR and first introns than in intergenic DNA and in other introns. Indel density was highly correlated with SNP density. The mean density of indels in pairwise sequence comparisons was 1.9 x 10-4 indel events per bp, roughly 5% the density of single nucleotide polymorphisms (SNPs) segregating in the chicken genome. The great majority of indels involved a limited number of nucleotides (median 1 bp), with A-rich motifs being overrepresented at indel sites. The over-representation of deletions at tandem duplicates indicates that replication slippage in duplicate sequences is a common mechanism behind indel mutation. The correlation between indel and SNP density indicates common effects of mutation and/or selection on the occurrence of indels and point mutations.
Key Words:
SNP, chicken, genome size, indel, length polymorphism
