A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

The sequence of Ciona savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference s...

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Detalles Bibliográficos
Autores principales: Small, Kerrin S, Brudno, Michael, Hill, Matthew M, Sidow, Arend
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868934/
https://www.ncbi.nlm.nih.gov/pubmed/17374142
http://dx.doi.org/10.1186/gb-2007-8-3-r41
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author Small, Kerrin S
Brudno, Michael
Hill, Matthew M
Sidow, Arend
author_facet Small, Kerrin S
Brudno, Michael
Hill, Matthew M
Sidow, Arend
author_sort Small, Kerrin S
collection PubMed
description The sequence of Ciona savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved.
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spelling pubmed-18689342007-05-16 A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome Small, Kerrin S Brudno, Michael Hill, Matthew M Sidow, Arend Genome Biol Method The sequence of Ciona savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved. BioMed Central 2007 2007-03-20 /pmc/articles/PMC1868934/ /pubmed/17374142 http://dx.doi.org/10.1186/gb-2007-8-3-r41 Text en Copyright ©2007 Small 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 Method
Small, Kerrin S
Brudno, Michael
Hill, Matthew M
Sidow, Arend
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
title A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
title_full A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
title_fullStr A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
title_full_unstemmed A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
title_short A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
title_sort haplome alignment and reference sequence of the highly polymorphic ciona savignyi genome
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868934/
https://www.ncbi.nlm.nih.gov/pubmed/17374142
http://dx.doi.org/10.1186/gb-2007-8-3-r41
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