Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)

Abstract The diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome...

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Autores principales:	Iria Fernandez-Silva, James B. Henderson, Luiz A. Rocha, W. Brian Simison
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f2ebfb266b534c02926db4712f6b97bb
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spelling	oai:doaj.org-article:f2ebfb266b534c02926db4712f6b97bb2021-12-02T15:07:48ZWhole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)10.1038/s41598-018-19430-x2045-2322https://doaj.org/article/f2ebfb266b534c02926db4712f6b97bb2018-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-19430-xhttps://doaj.org/toc/2045-2322Abstract The diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only. Our best candidate assembly had a scaffold N50 of 8.97 Mb, contig N50 of 189,827, and 97.4% complete for BUSCO v2 (Actinopterygii set) and 95.6% complete for CEGMA matches. These contiguity and accuracy scores are higher than those of any other fish assembly released to date that did not apply linkage map information, including those based on more expensive long-read sequencing data. Our analysis of how different data types improve assembly quality will help others choose the most appropriate de novo genome sequencing strategy based on resources and target applications. Furthermore, the draft genome of the Pearlscale Pygmy angelfish will play an important role in future studies of coral reef fish evolution, diversity and conservation.Iria Fernandez-SilvaJames B. HendersonLuiz A. RochaW. Brian SimisonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Iria Fernandez-Silva James B. Henderson Luiz A. Rocha W. Brian Simison Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
description	Abstract The diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only. Our best candidate assembly had a scaffold N50 of 8.97 Mb, contig N50 of 189,827, and 97.4% complete for BUSCO v2 (Actinopterygii set) and 95.6% complete for CEGMA matches. These contiguity and accuracy scores are higher than those of any other fish assembly released to date that did not apply linkage map information, including those based on more expensive long-read sequencing data. Our analysis of how different data types improve assembly quality will help others choose the most appropriate de novo genome sequencing strategy based on resources and target applications. Furthermore, the draft genome of the Pearlscale Pygmy angelfish will play an important role in future studies of coral reef fish evolution, diversity and conservation.
format	article
author	Iria Fernandez-Silva James B. Henderson Luiz A. Rocha W. Brian Simison
author_facet	Iria Fernandez-Silva James B. Henderson Luiz A. Rocha W. Brian Simison
author_sort	Iria Fernandez-Silva
title	Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
title_short	Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
title_full	Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
title_fullStr	Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
title_full_unstemmed	Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
title_sort	whole-genome assembly of the coral reef pearlscale pygmy angelfish (centropyge vrolikii)
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/f2ebfb266b534c02926db4712f6b97bb
work_keys_str_mv	AT iriafernandezsilva wholegenomeassemblyofthecoralreefpearlscalepygmyangelfishcentropygevrolikii AT jamesbhenderson wholegenomeassemblyofthecoralreefpearlscalepygmyangelfishcentropygevrolikii AT luizarocha wholegenomeassemblyofthecoralreefpearlscalepygmyangelfishcentropygevrolikii AT wbriansimison wholegenomeassemblyofthecoralreefpearlscalepygmyangelfishcentropygevrolikii
_version_	1718388424848703488

Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)

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