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The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: A high frequency of deletions in tandem duplicates
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. (Molecular evolution)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. (Molecular evolution)
2007 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 176, no 3, 1691-1701 p.Article in journal (Refereed) Published
Abstract [en]

It is increasingly recognized that insertions and deletions(indels) are an important source of genetic as well as phenotypicdivergence and diversity. We analyzed length polymorphisms identifiedthrough partial (0.25x) shotgun sequencing of three breeds ofdomestic chicken made by the International Chicken PolymorphismMap Consortium. A data set of 140,484 short indel polymorphismsin unique DNA was identified after filtering for microsatellitestructures. There was a significant excess of tandem duplicatesat indel sites, with deletions of a duplicate motif outnumberingthe generation of duplicates through insertion. Indel densitywas lower in microchromosomes than in macrochromosomes, in theZ chromosome than in autosomes, and in 100 bp of upstream sequence,5'-UTR, and first introns than in intergenic DNA and in otherintrons. Indel density was highly correlated with single nucleotidepolymorphism (SNP) density. The mean density of indels in pairwisesequence comparisons was 1.9 x 10–4 indel events/bp, 5%the density of SNPs segregating in the chicken genome. The greatmajority of indels involved a limited number of nucleotides(median 1 bp), with A-rich motifs being overrepresented at indelsites. The overrepresentation of deletions at tandem duplicatesindicates that replication slippage in duplicate sequences isa common mechanism behind indel mutation. The correlation betweenindel and SNP density indicates common effects of mutation and/orselection on the occurrence of indels and point mutations.

Place, publisher, year, edition, pages
2007. Vol. 176, no 3, 1691-1701 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-96268DOI: 10.1534/genetics.107.070805ISI: 000248416300026PubMedID: 17507681OAI: oai:DiVA.org:uu-96268DiVA: diva2:170786
Available from: 2007-10-08 Created: 2007-10-08 Last updated: 2016-04-25Bibliographically approved
In thesis
1. Bioinformatic Analysis of Mutation and Selection in the Vertebrate Non-coding Genome
Open this publication in new window or tab >>Bioinformatic Analysis of Mutation and Selection in the Vertebrate Non-coding Genome
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The majority of the vertebrate genome sequence is not coding for proteins. In recent years, the evolution of this noncoding fraction of the genome has gained interest. These studies have been greatly facilitated by the availability of full genome sequences. The aim of this thesis is to study evolution of the noncoding vertebrate genome through bioinformatic analysis of large-scale genomic datasets.

In a first analysis we addressed the use of conservation of sequence between highly diverged genomes to infer function. We provided evidence for a turnover of the patterns of negative selection. Hence, measures of constraint based on comparisons of diverged genomes might underestimate the functional proportion of the genome.

In the following analyses we focused on length variation as found in small-scale insertion and deletion (indel) polymorphisms and microsatellites. For indels in chicken, replication slippage is a likely mutation mechanism, as a large proportion of the indels are parts of tandem-duplicates. Using a set of microsatellite polymorphisms in chicken, where we avoid ascertainment bias, we showed that polymorphism is positively correlated with microsatellite length and AT-content. Furthermore, interruptions in the microsatellite sequence decrease the levels of polymorphism.

We also analysed the association between microsatellite polymorphism and recombination in the human genome. Here we found increased levels of microsatellite polymorphism in human recombination hotspots and also similar increases in the frequencies of single nucleotide polymorphisms (SNPs) and indels. This points towards natural selection shaping the levels of variation. Alternatively, recombination is mutagenic for all three kinds of polymorphisms.

Finally, I present the program ILAPlot. It is a tool for visualisation, exploration and data extraction based on BLAST.

Our combined results highlight the intricate connections between evolutionary phenomena. It also emphasises the importance of length variability in genome evolution, as well as the gradual difference between indels and microsatellites.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 60 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 348
Keyword
Biology, non-coding genome, selection, mutation, chicken, human, indel, microsatellite, sequence alignment, comparative genomics, bioinformatics, vertebrate, Biologi
Identifiers
urn:nbn:se:uu:diva-8240 (URN)978-91-554-6981-8 (ISBN)
Public defence
2007-10-31, Zootissalen, EBC, Villavägen 9, Uppsala, 09:00
Opponent
Supervisors
Available from: 2007-10-08 Created: 2007-10-08Bibliographically approved

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Brandström, MikaelEllegren, Hans

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