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Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing

The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and...

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Autores principales: Ozerov, Mikhail Yu., Flajšhans, Martin, Noreikiene, Kristina, Vasemägi, Anti, Gross, Riho
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642921/
https://www.ncbi.nlm.nih.gov/pubmed/32917720
http://dx.doi.org/10.1534/g3.120.401711
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author Ozerov, Mikhail Yu.
Flajšhans, Martin
Noreikiene, Kristina
Vasemägi, Anti
Gross, Riho
author_facet Ozerov, Mikhail Yu.
Flajšhans, Martin
Noreikiene, Kristina
Vasemägi, Anti
Gross, Riho
author_sort Ozerov, Mikhail Yu.
collection PubMed
description The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N(50) = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.
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spelling pubmed-76429212020-11-13 Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing Ozerov, Mikhail Yu. Flajšhans, Martin Noreikiene, Kristina Vasemägi, Anti Gross, Riho G3 (Bethesda) Genome Report The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N(50) = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis. Genetics Society of America 2020-09-11 /pmc/articles/PMC7642921/ /pubmed/32917720 http://dx.doi.org/10.1534/g3.120.401711 Text en Copyright © 2020 Ozerov et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Ozerov, Mikhail Yu.
Flajšhans, Martin
Noreikiene, Kristina
Vasemägi, Anti
Gross, Riho
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing
title Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing
title_full Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing
title_fullStr Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing
title_full_unstemmed Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing
title_short Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing
title_sort draft genome assembly of the freshwater apex predator wels catfish (silurus glanis) using linked-read sequencing
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642921/
https://www.ncbi.nlm.nih.gov/pubmed/32917720
http://dx.doi.org/10.1534/g3.120.401711
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