Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a...

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Autores principales:	Daren C Card, Drew R Schield, Jacobo Reyes-Velasco, Matthew K Fujita, Audra L Andrew, Sara J Oyler-McCance, Jennifer A Fike, Diana F Tomback, Robert P Ruggiero, Todd A Castoe
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ab826c0aab824688ab6d55777aefb7a6
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spelling	oai:doaj.org-article:ab826c0aab824688ab6d55777aefb7a62021-11-25T06:01:40ZTwo low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.1932-620310.1371/journal.pone.0106649https://doaj.org/article/ab826c0aab824688ab6d55777aefb7a62014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25192061/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.Daren C CardDrew R SchieldJacobo Reyes-VelascoMatthew K FujitaAudra L AndrewSara J Oyler-McCanceJennifer A FikeDiana F TombackRobert P RuggieroTodd A CastoePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 9, p e106649 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daren C Card Drew R Schield Jacobo Reyes-Velasco Matthew K Fujita Audra L Andrew Sara J Oyler-McCance Jennifer A Fike Diana F Tomback Robert P Ruggiero Todd A Castoe Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
description	As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
format	article
author	Daren C Card Drew R Schield Jacobo Reyes-Velasco Matthew K Fujita Audra L Andrew Sara J Oyler-McCance Jennifer A Fike Diana F Tomback Robert P Ruggiero Todd A Castoe
author_facet	Daren C Card Drew R Schield Jacobo Reyes-Velasco Matthew K Fujita Audra L Andrew Sara J Oyler-McCance Jennifer A Fike Diana F Tomback Robert P Ruggiero Todd A Castoe
author_sort	Daren C Card
title	Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
title_short	Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
title_full	Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
title_fullStr	Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
title_full_unstemmed	Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
title_sort	two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/ab826c0aab824688ab6d55777aefb7a6
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Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

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