The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross

<p>Abstract</p> <p>Background</p> <p>Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand the...

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Main Authors: Tan Asako, Patel Jigar J, Gonzales Joseph M, Samarakoon Upeka, Checkley Lisa, Ferdig Michael T
Format: Article
Language:English
Published: BMC 2011-09-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/12/457
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spelling doaj-8a5beb8ae1414b6ba11b3c793129d7052020-11-25T01:47:05ZengBMCBMC Genomics1471-21642011-09-0112145710.1186/1471-2164-12-457The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic crossTan AsakoPatel Jigar JGonzales Joseph MSamarakoon UpekaCheckley LisaFerdig Michael T<p>Abstract</p> <p>Background</p> <p>Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, <it>Plasmodium falciparum</it>, to identify and analyze the inheritance of 170 genome-wide CNVs.</p> <p>Results</p> <p>We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton <it>de novo </it>CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation.</p> <p>Conclusions</p> <p>CNVs are a significant source of segregating and <it>de novo </it>genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.</p> http://www.biomedcentral.com/1471-2164/12/457
collection DOAJ
language English
format Article
sources DOAJ
author Tan Asako
Patel Jigar J
Gonzales Joseph M
Samarakoon Upeka
Checkley Lisa
Ferdig Michael T
spellingShingle Tan Asako
Patel Jigar J
Gonzales Joseph M
Samarakoon Upeka
Checkley Lisa
Ferdig Michael T
The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross
BMC Genomics
author_facet Tan Asako
Patel Jigar J
Gonzales Joseph M
Samarakoon Upeka
Checkley Lisa
Ferdig Michael T
author_sort Tan Asako
title The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross
title_short The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross
title_full The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross
title_fullStr The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross
title_full_unstemmed The landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross
title_sort landscape of inherited and <it>de novo </it>copy number variants in a <it>plasmodium falciparum </it>genetic cross
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2011-09-01
description <p>Abstract</p> <p>Background</p> <p>Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, <it>Plasmodium falciparum</it>, to identify and analyze the inheritance of 170 genome-wide CNVs.</p> <p>Results</p> <p>We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton <it>de novo </it>CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation.</p> <p>Conclusions</p> <p>CNVs are a significant source of segregating and <it>de novo </it>genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.</p>
url http://www.biomedcentral.com/1471-2164/12/457
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