High-resolution genotyping and mapping of recombination and gene conversion in the protozoan Theileria parva using whole genome sequencing

BMC Genomics

Research Article

Martin Ebeling¹  Erich Küng¹  Ulrich Certa¹  Lucy Poveda²  Weihong Qi²  Richard P Bishop³  Subhash Morzaria³  Sonal Henson³  Paul R Spooner³  Roger Pelle³  Claudia A Daubenberger⁴ 

[1] F. Hoffmann-La Roche AG, 4070, Basel, Switzerland;Functional Genomics Center Zurich, UZH/ETHZ, Winterthurerstrasse 190, 8057, Zurich, Switzerland;International Livestock Research Institute, 00100, Nairobi, Kenya;Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland;University of Basel, Peterplatz 1, 4003, Basel, Switzerland;

关键词: Gene Conversion;    Single Nucleotide Polymorphism Marker;    Recombinant Clone;    Variable Number Tandem Repeat;    Single Nucleotide Polymorphism Locus;   

DOI  :  10.1186/1471-2164-13-503

 received in 2012-02-11, accepted in 2012-09-13,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundTheileria parva is a tick-borne protozoan parasite, which causes East Coast Fever, a disease of cattle in sub-Saharan Africa. Like Plasmodium falciparum, the parasite undergoes a transient diploid life-cycle stage in the gut of the arthropod vector, which involves an obligate sexual cycle. As assessed using low-resolution VNTR markers, the crossover (CO) rate in T. parva is relatively high and has been reported to vary across different regions of the genome; non-crossovers (NCOs) and CO-associated gene conversions have not yet been characterised due to the lack of informative markers. To examine all recombination events at high marker resolution, we sequenced the haploid genomes of two parental strains, and two recombinant clones derived from ticks fed on cattle that had been simultaneously co-infected with two different parasite isolates.ResultsBy comparing the genome sequences, we were able to genotype over 64 thousand SNP markers with an average spacing of 127 bp in the two progeny clones. Previously unrecognized COs in sub-telomeric regions were detected. About 50% of CO breakpoints were accompanied by gene conversion events. Such a high fraction of COs accompanied by gene conversions demonstrated the contributions of meiotic recombination to the diversity and evolutionary success of T. parva, as the process not only redistributed existing genetic variations, but also altered allelic frequencies. Compared to COs, NCOs were more frequently observed and more uniformly distributed across the genome. In both progeny clones, genomic regions with more SNP markers had a reduced frequency of COs or NCOs, suggesting that the sequence divergence between the parental strains was high enough to adversely affect recombination frequencies. Intra-species polymorphism analysis identified 81 loci as likely to be under selection in the sequenced genomes.ConclusionsUsing whole genome sequencing of two recombinant clones and their parents, we generated maps of COs, NCOs, and CO-associated gene conversion events for T. parva. The data comprises one of the highest-resolution genome-wide analyses of the multiple outcomes of meiotic recombination for this pathogen. The study also demonstrates the usefulness of high throughput sequencing typing for detailed analysis of recombination in organisms in which conventional genetic analysis is technically difficult.

【 授权许可】

Unknown   
© Henson et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.