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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| Format: | Article |
| Language: | English |
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GigaScience Press
2021-09-01
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| Series: | GigaByte |
| Online Access: | https://gigabytejournal.com/articles/29 |
| _version_ | 1797871220835745792 |
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| 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 |
| collection | DOAJ |
| 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.
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| first_indexed | 2024-04-10T00:39:39Z |
| format | Article |
| id | doaj.art-7e47366fdfe342c5a6a8592581da6fb6 |
| institution | Directory Open Access Journal |
| issn | 2709-4715 |
| language | English |
| last_indexed | 2024-04-10T00:39:39Z |
| publishDate | 2021-09-01 |
| publisher | GigaScience Press |
| record_format | Article |
| series | GigaByte |
| spelling | doaj.art-7e47366fdfe342c5a6a8592581da6fb62023-03-14T06:59:00ZengGigaScience PressGigaByte2709-47152021-09-0110.46471/gigabyte.29Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River BasinAlexandre Wagner Silva Hilsdorf 0https://orcid.org/0000-0001-9565-8072Marcela Uliano-Silva 1https://orcid.org/0000-0001-6723-4715Luiz Lehmann Coutinho 2https://orcid.org/0000-0002-7266-8881Horácio Montenegro 3https://orcid.org/0000-0002-8142-896XVera Maria Fonseca Almeida-Val 4Danillo Pinhal 5https://orcid.org/0000-0003-1075-0182Integrated Center of Biotechnology, University of Mogi das Cruzes, P.O. Box 411, Mogi das Cruzes, SP 08780-911, BrazilWellcome Sanger Institute, Saffron Walden, Hinxton, Cambridgeshire CB10 1SA, UKAnimal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP 13418-900, BrazilAnimal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP 13418-900, BrazilBrazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, AM 69067-375, BrazilDepartment of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP 18618-689, Brazil 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. https://gigabytejournal.com/articles/29 |
| spellingShingle | 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 GigaByte |
| title | 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_short | 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 |
| url | https://gigabytejournal.com/articles/29 |
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