Dynamics of a Human Interparalog Gene Conversion Hotspot
- 1 Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
- 2 McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER UK
- 3 Unitat de Biologia Evolutiva, Facultat de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
Abstract
Gene conversion between paralogs can alter their patterns of sequence identity, thus obscuring their evolutionary relationships and affecting their propensity to sponsor genomic rearrangements. The details of this important process are poorly understood in the human genome because allelic diversity complicates the interpretation of interparalog sequence differences. Here we exploit the haploid nature of the Y chromosome, which obviates complicating interallelic processes, together with its known phylogeny, to understand the dynamics of conversion between two directly repeated HERVs flanking the 780-kb AZFa region on Yq. Sequence analysis of a 787-bp segment of each of the HERVs in 36 Y chromosomes revealed one of the highest nucleotide diversities in the human genome, as well as evidence of a complex patchwork of highly directional gene conversion events. The rate of proximal-to-distal conversion events was estimated as 2.4 × 10-4 to 1.2 × 10-3 per generation (3.9 × 10-7 to 1.9 × 10-6 per base per generation), and the distal-to-proximal rate as about one-twentieth of this. Minimum observed conversion tract lengths ranged from 1 to 158 bp and maximum lengths from 19 to 1365 bp, with an estimated mean of 31 bp. Analysis of great ape homologs shows that conversion in this hotspot has a deep evolutionary history.
Footnotes
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[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession numbers AY500148–AY500151 and AY549481–AY549491. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: C. Tyler-Smith, Q. Mehdi, P. Shen, and Z. Rosser.]
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Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2177404.
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↵4 Present address: Unitat de Biologia Evolutiva, Facultat de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
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↵5 Present address: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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↵6 Corresponding author. E-MAIL maj4{at}leicester.ac.uk; FAX 44-116-252-3378.
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- Accepted February 16, 2004.
- Received November 18, 2003.
- Cold Spring Harbor Laboratory Press
