The Genomic Landscape of Short Insertion and Deletion Polymorphisms in the Chicken (Gallus gallus) Genome: A High Frequency of Deletions in Tandem Duplicates
- 1 July 2007
- journal article
- Published by Oxford University Press (OUP) in Genetics
- Vol. 176 (3) , 1691-1701
- https://doi.org/10.1534/genetics.107.070805
Abstract
It is increasingly recognized that insertions and deletions (indels) are an important source of genetic as well as phenotypic divergence and diversity. We analyzed length polymorphisms identified through partial (0.25×) 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 of upstream sequence, 5′-UTR, and first introns than in intergenic DNA and in other introns. Indel density was highly correlated with single nucleotide polymorphism (SNP) density. The mean density of indels in pairwise sequence comparisons was 1.9 × 10−4 indel events/bp, ∼5% the density of 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 overrepresentation 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.Keywords
This publication has 71 references indexed in Scilit:
- An initial map of insertion and deletion (INDEL) variation in the human genomeGenome Research, 2006
- Synergy between sequence and size in Large-scale genomicsNature Reviews Genetics, 2005
- Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammalsNature, 2005
- Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionNature, 2004
- Microsatellites: simple sequences with complex evolutionNature Reviews Genetics, 2004
- Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human GenomesGenome Research, 2004
- MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence EvolutionGenome Research, 2004
- Initial sequencing and comparative analysis of the mouse genomeNature, 2002
- Segmental duplications and the evolution of the primate genomeNature Reviews Genetics, 2002
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997