Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin

Colossoma macropomum, known as “tambaqui”, is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and excellent adaptability to culture systems are some of its remarkable farming features. To support st...

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Autores principales:	Alexandre Wagner Silva Hilsdorf, Marcela Uliano-Silva, Luiz Lehmann Coutinho, Horácio Montenegro, Vera Maria Fonseca Almeida-Val, Danillo Pinhal
Formato:	article
Lenguaje:	EN
Publicado:	GigaScience Press 2021
Materias:	Electronic computers. Computer science QA75.5-76.95
Acceso en línea:	https://doaj.org/article/7e47366fdfe342c5a6a8592581da6fb6
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spelling	oai:doaj.org-article:7e47366fdfe342c5a6a8592581da6fb62021-12-02T18:53:30ZGenome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin10.46471/gigabyte.292709-4715https://doaj.org/article/7e47366fdfe342c5a6a8592581da6fb62021-09-01T00:00:00Zhttps://gigabytejournal.com/articles/29https://doaj.org/toc/2709-4715 Colossoma macropomum, known as “tambaqui”, is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and excellent adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39× coverage of long reads and polished to a consensus quality value (QV) of 36 with 130× coverage of short reads. The genome was assembled into 1269 scaffolds (a total of 1,221,847,006 bases), with a scaffold N50 size of 40 Mb, where 93% of all assembled bases were placed in the largest 54 scaffolds corresponding to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced, which will benefit groups interested in exploring the unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for the discovery of novel ecological and evolutionary insights, and is a helpful resource for aquaculture. Alexandre Wagner Silva HilsdorfMarcela Uliano-SilvaLuiz Lehmann CoutinhoHorácio MontenegroVera Maria Fonseca Almeida-ValDanillo PinhalGigaScience PressarticleElectronic computers. Computer scienceQA75.5-76.95ENGigaByte (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Electronic computers. Computer science QA75.5-76.95
spellingShingle	Electronic computers. Computer science QA75.5-76.95 Alexandre Wagner Silva Hilsdorf Marcela Uliano-Silva Luiz Lehmann Coutinho Horácio Montenegro Vera Maria Fonseca Almeida-Val Danillo Pinhal Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin
description	Colossoma macropomum, known as “tambaqui”, is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and excellent adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39× coverage of long reads and polished to a consensus quality value (QV) of 36 with 130× coverage of short reads. The genome was assembled into 1269 scaffolds (a total of 1,221,847,006 bases), with a scaffold N50 size of 40 Mb, where 93% of all assembled bases were placed in the largest 54 scaffolds corresponding to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced, which will benefit groups interested in exploring the unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for the discovery of novel ecological and evolutionary insights, and is a helpful resource for aquaculture.
format	article
author	Alexandre Wagner Silva Hilsdorf Marcela Uliano-Silva Luiz Lehmann Coutinho Horácio Montenegro Vera Maria Fonseca Almeida-Val Danillo Pinhal
author_facet	Alexandre Wagner Silva Hilsdorf Marcela Uliano-Silva Luiz Lehmann Coutinho Horácio Montenegro Vera Maria Fonseca Almeida-Val Danillo Pinhal
author_sort	Alexandre Wagner Silva Hilsdorf
title	Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin
title_short	Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin
title_full	Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin
title_fullStr	Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin
title_full_unstemmed	Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin
title_sort	genome assembly and annotation of the tambaqui (colossoma macropomum): an emblematic fish of the amazon river basin
publisher	GigaScience Press
publishDate	2021
url	https://doaj.org/article/7e47366fdfe342c5a6a8592581da6fb6
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Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin

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