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

BACKGROUND: Knowledge 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 th...

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Autores principales: Samarakoon, Upeka, Regier, Allison, Tan, Asako, Desany, Brian A, Collins, Brendan, Tan, John C, Emrich, Scott J, Ferdig, Michael T
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055840/
https://www.ncbi.nlm.nih.gov/pubmed/21324207
http://dx.doi.org/10.1186/1471-2164-12-116
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author Samarakoon, Upeka
Regier, Allison
Tan, Asako
Desany, Brian A
Collins, Brendan
Tan, John C
Emrich, Scott J
Ferdig, Michael T
author_facet Samarakoon, Upeka
Regier, Allison
Tan, Asako
Desany, Brian A
Collins, Brendan
Tan, John C
Emrich, Scott J
Ferdig, Michael T
author_sort Samarakoon, Upeka
collection PubMed
description BACKGROUND: Knowledge 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. RESULTS: We 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. CONCLUSIONS: By 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.
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spelling pubmed-30558402011-03-12 High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum Samarakoon, Upeka Regier, Allison Tan, Asako Desany, Brian A Collins, Brendan Tan, John C Emrich, Scott J Ferdig, Michael T BMC Genomics Methodology Article BACKGROUND: Knowledge 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. RESULTS: We 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. CONCLUSIONS: By 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. BioMed Central 2011-02-17 /pmc/articles/PMC3055840/ /pubmed/21324207 http://dx.doi.org/10.1186/1471-2164-12-116 Text en Copyright ©2011 Samarakoon et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Methodology Article
Samarakoon, Upeka
Regier, Allison
Tan, Asako
Desany, Brian A
Collins, Brendan
Tan, John C
Emrich, Scott J
Ferdig, Michael T
High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
title High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
title_full High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
title_fullStr High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
title_full_unstemmed High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
title_short High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum
title_sort high-throughput 454 resequencing for allele discovery and recombination mapping in plasmodium falciparum
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055840/
https://www.ncbi.nlm.nih.gov/pubmed/21324207
http://dx.doi.org/10.1186/1471-2164-12-116
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