ArticleGenetics2007
The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) Genome: a high frequency of deletions in tandem duplicates.
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 52 citations in OpenAlex.
- Development of genome-wide insertion/deletion markers and genetic diversity inFrontiers in genetics · 2025Article
- Genetic Diversity of MHC B-F/B-L Region in 21 Chicken Populations.Frontiers in genetics · 2021Article
- The Impact of Natural Selection on Short Insertion and Deletion Variation in the Great Tit Genome.Genome biology and evolution · 2019Article
- Two Proximally Close Priority Candidate Genes for diplopodia-1, an Autosomal Inherited Craniofacial-Limb Syndrome in the Chicken: MRE11 and GPR83.The Journal of heredity · 2019Article
- Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.BMC genomics · 2016Article
- Genomic variations and distinct evolutionary rate of rare alleles in Arabidopsis thaliana.BMC evolutionary biology · 2016Article
- Evolutionary Footprints of Short Tandem Repeats in Avian Promoters.Scientific reports · 2016Article
- Dynamics of Transcription Factor Binding Site Evolution.PLoS genetics · 2015Article
- Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes.BMC genomics · 2015Article
- Single nucleotide polymorphism analysis of Korean native chickens using next generation sequencing data.Molecular biology reports · 2015Article
- Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing.PloS one · 2015Article
- Genome-wide characterization of insertion and deletion variation in chicken using next generation sequencing.PloS one · 2014Article
- Artemisinin resistance in rodent malaria--mutation in the AP2 adaptor μ-chain suggests involvement of endocytosis and membrane protein trafficking.Malaria journal · 2013Article
- Insertions and deletions trigger adaptive walks in Drosophila proteins.Proceedings. Biological sciences · 2012Article
- Genetic diversity of myanmar and indonesia native chickens together with two jungle fowl species by using 102 indels polymorphisms.Asian-Australasian journal of animal sciences · 2012Article
- Evolutionary genomics of Colias Phosphoglucose Isomerase (PGI) introns.Journal of molecular evolution · 2012Article
- Ruler arrays reveal haploid genomic structural variation.PloS one · 2012Article
- Massive turnover of functional sequence in human and other mammalian genomes.Genome research · 2010Article
- Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon.BMC genomics · 2010Article
- Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method.Genome biology and evolution · 2010Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 (0.25x) 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 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 x 10(-4) indel events/bp, approximately 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.
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