Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.

Restriction-site associated DNA (RAD) sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis of non-model organisms including genotype-phenotype association mapping, phylogeography, population genetic...

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Autores principales:	Simon W Baxter, John W Davey, J Spencer Johnston, Anthony M Shelton, David G Heckel, Chris D Jiggins, Mark L Blaxter
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d114109ef41f4ab1ab9e3d003464fb45
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spelling	oai:doaj.org-article:d114109ef41f4ab1ab9e3d003464fb452021-11-18T06:55:12ZLinkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.1932-620310.1371/journal.pone.0019315https://doaj.org/article/d114109ef41f4ab1ab9e3d003464fb452011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21541297/?tool=EBIhttps://doaj.org/toc/1932-6203Restriction-site associated DNA (RAD) sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis of non-model organisms including genotype-phenotype association mapping, phylogeography, population genetics and scaffolding genome assemblies through linkage mapping. We constructed a RAD library using genomic DNA from a Plutella xylostella (diamondback moth) backcross that segregated for resistance to the insecticide spinosad. Sequencing of 24 individuals was performed on a single Illumina GAIIx lane (51 base paired-end reads). Taking advantage of the lack of crossing over in homologous chromosomes in female Lepidoptera, 3,177 maternally inherited RAD alleles were assigned to the 31 chromosomes, enabling identification of the spinosad resistance and W/Z sex chromosomes. Paired-end reads for each RAD allele were assembled into contigs and compared to the genome of Bombyx mori (n = 28) using BLAST, revealing 28 homologous matches plus 3 expected fusion/breakage events which account for the difference in chromosome number. A genome-wide linkage map (1292 cM) was inferred with 2,878 segregating RAD alleles inherited from the backcross father, producing chromosome and location specific sequenced RAD markers. Here we have used RAD sequencing to construct a genetic linkage map de novo for an organism that has no previous genome data. Comparative analysis of P. xyloxtella linkage groups with B. mori chromosomes shows for the first time, genetic synteny appears common beyond the Macrolepidoptera. RAD sequencing is a powerful system capable of rapidly generating chromosome specific data for non-model organisms.Simon W BaxterJohn W DaveyJ Spencer JohnstonAnthony M SheltonDavid G HeckelChris D JigginsMark L BlaxterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e19315 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Simon W Baxter John W Davey J Spencer Johnston Anthony M Shelton David G Heckel Chris D Jiggins Mark L Blaxter Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
description	Restriction-site associated DNA (RAD) sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis of non-model organisms including genotype-phenotype association mapping, phylogeography, population genetics and scaffolding genome assemblies through linkage mapping. We constructed a RAD library using genomic DNA from a Plutella xylostella (diamondback moth) backcross that segregated for resistance to the insecticide spinosad. Sequencing of 24 individuals was performed on a single Illumina GAIIx lane (51 base paired-end reads). Taking advantage of the lack of crossing over in homologous chromosomes in female Lepidoptera, 3,177 maternally inherited RAD alleles were assigned to the 31 chromosomes, enabling identification of the spinosad resistance and W/Z sex chromosomes. Paired-end reads for each RAD allele were assembled into contigs and compared to the genome of Bombyx mori (n = 28) using BLAST, revealing 28 homologous matches plus 3 expected fusion/breakage events which account for the difference in chromosome number. A genome-wide linkage map (1292 cM) was inferred with 2,878 segregating RAD alleles inherited from the backcross father, producing chromosome and location specific sequenced RAD markers. Here we have used RAD sequencing to construct a genetic linkage map de novo for an organism that has no previous genome data. Comparative analysis of P. xyloxtella linkage groups with B. mori chromosomes shows for the first time, genetic synteny appears common beyond the Macrolepidoptera. RAD sequencing is a powerful system capable of rapidly generating chromosome specific data for non-model organisms.
format	article
author	Simon W Baxter John W Davey J Spencer Johnston Anthony M Shelton David G Heckel Chris D Jiggins Mark L Blaxter
author_facet	Simon W Baxter John W Davey J Spencer Johnston Anthony M Shelton David G Heckel Chris D Jiggins Mark L Blaxter
author_sort	Simon W Baxter
title	Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
title_short	Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
title_full	Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
title_fullStr	Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
title_full_unstemmed	Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
title_sort	linkage mapping and comparative genomics using next-generation rad sequencing of a non-model organism.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/d114109ef41f4ab1ab9e3d003464fb45
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_version_	1718424258544140288

Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.

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