High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

BMC Genomics

Methodology Article

Brian A Desany¹  Upeka Samarakoon²  John C Tan²  Asako Tan²  Brendan Collins²  Michael T Ferdig²  Allison Regier³  Scott J Emrich³ 

[1] 454 Life Sciences, a Roche company, 15 Commercial Street, 06405, Branford, CT, USA;Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, 46556, Notre Dame, IN, USA;Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, 46556, Notre Dame, IN, USA;Department of Computer Science and Engineering, University of Notre Dame, 46556, Notre Dame, IN, USA;

关键词: Single Nucleotide Polymorphism;    Single Nucleotide Polymorphism Marker;    Read Depth;    Parental Genome;    Base Call;   

DOI  :  10.1186/1471-2164-12-116

 received in 2010-07-23, accepted in 2011-02-17,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundKnowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites.ResultsWe present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome.ConclusionsBy sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.

【 授权许可】

Unknown   
© Samarakoon et al; licensee BioMed Central Ltd. 2011. 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.