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Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing

Ozerov, Mikhail and Flajshans, Martin and Noreikiene, Kristina and Vasemägi, Anti and Gross, Riho (2020). Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing. G3. 10 , 3897-3906
[Journal article]

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Abstract

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 N50 = 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.

Authors/Creators:Ozerov, Mikhail and Flajshans, Martin and Noreikiene, Kristina and Vasemägi, Anti and Gross, Riho
Title:Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing
Year of publishing :2020
Volume:10
Page range:3897-3906
Number of Pages:10
ISSN:2160-1836
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biological Systematics
Keywords:Silurus glanis, wels catfish:whole genome sequencing, de novo assembly, 10X Genomics Chromium linked-reads, teleost
URN:NBN:urn:nbn:se:slu:epsilon-p-108957
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-108957
Additional ID:
Type of IDID
DOI10.1534/g3.120.401711
ID Code:19129
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Aquatic Resources
Deposited By: SLUpub Connector
Deposited On:08 Dec 2020 16:03
Metadata Last Modified:15 Jan 2021 19:44

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