Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing

Abstract Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approach...

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Autores principales:	Tatiana Maroilley, Xiao Li, Matthew Oldach, Francesca Jean, Susan J. Stasiuk, Maja Tarailo-Graovac
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cc2274dbe4434c73b2ead9382c12c03a
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spelling	oai:doaj.org-article:cc2274dbe4434c73b2ead9382c12c03a2021-12-02T15:31:36ZDeciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing10.1038/s41598-021-97764-92045-2322https://doaj.org/article/cc2274dbe4434c73b2ead9382c12c03a2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97764-9https://doaj.org/toc/2045-2322Abstract Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.Tatiana MaroilleyXiao LiMatthew OldachFrancesca JeanSusan J. StasiukMaja Tarailo-GraovacNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tatiana Maroilley Xiao Li Matthew Oldach Francesca Jean Susan J. Stasiuk Maja Tarailo-Graovac Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing
description	Abstract Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.
format	article
author	Tatiana Maroilley Xiao Li Matthew Oldach Francesca Jean Susan J. Stasiuk Maja Tarailo-Graovac
author_facet	Tatiana Maroilley Xiao Li Matthew Oldach Francesca Jean Susan J. Stasiuk Maja Tarailo-Graovac
author_sort	Tatiana Maroilley
title	Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing
title_short	Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing
title_full	Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing
title_fullStr	Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing
title_full_unstemmed	Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing
title_sort	deciphering complex genome rearrangements in c. elegans using short-read whole genome sequencing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cc2274dbe4434c73b2ead9382c12c03a
work_keys_str_mv	AT tatianamaroilley decipheringcomplexgenomerearrangementsincelegansusingshortreadwholegenomesequencing AT xiaoli decipheringcomplexgenomerearrangementsincelegansusingshortreadwholegenomesequencing AT matthewoldach decipheringcomplexgenomerearrangementsincelegansusingshortreadwholegenomesequencing AT francescajean decipheringcomplexgenomerearrangementsincelegansusingshortreadwholegenomesequencing AT susanjstasiuk decipheringcomplexgenomerearrangementsincelegansusingshortreadwholegenomesequencing AT majatarailograovac decipheringcomplexgenomerearrangementsincelegansusingshortreadwholegenomesequencing
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Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing

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