Abstract
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 40Mb, 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.
Highlights
The Amazon Basin harbors enormous freshwater ichthyo diversity throughout its rivers and tributaries, with 2406 validated freshwater native fish species from 232,936 georeferenced records [1]
Colossoma macropomum (NCBI:txid42526, fishbase ID:263) is the largest Characiformes representative found across the Amazon River and its tributaries, with individuals reaching 1 meter in length and 30 kg in weight (Figure 1) [2]
Genomic DNA was isolated from caudal fin-clip samples from a C. macropomum specimen obtained from the germplasm bank maintained by the National Center for Research and Conservation of Freshwater Aquatic Biodiversity of the Brazilian Ministry of the Environment
Summary
The Amazon Basin harbors enormous freshwater ichthyo diversity throughout its rivers and tributaries, with 2406 validated freshwater native fish species from 232,936 georeferenced records [1]. Colossoma macropomum (NCBI:txid42526, fishbase ID:263) is the largest Characiformes representative found across the Amazon River and its tributaries, with individuals reaching 1 meter in length and 30 kg in weight (Figure 1) [2] Considering the great need for increased genetic resources for the tambaqui to assist fishery management and aquaculture [16], here we present the first high-quality reference genome for C. macropomum This complete set of DNA provides a valuable resource for the study of evolutionary and functional genomics in bony fishes, providing a window of opportunity to reveal singularities of the tambaqui genome, as well as to help develop molecular techniques to improve selective breeding programs. COI: Cytochrome c oxidase I; TROP: Alpha tropomyosin; fkh: fork head domain protein; RAG2: recombination activating gene 2; sina: absentia 1A
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