Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome

C. Isabel Wagner; Martina Elisabeth Luise Kopp; James Thorburn; Catherine Jones; Galice Hoarau; Leslie R. Noble

doi:10.1093/g3journal/jkad146

Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome

C. Isabel Wagner^* (Corresponding Author), Martina Elisabeth Luise Kopp, James Thorburn, Catherine Jones, Galice Hoarau, Leslie R. Noble^* (Corresponding Author)

^*Corresponding author for this work

Aberdeen Centre For Environmental Sustainability

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

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Abstract

Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish’s genome, of which 31,979 are functionally annotated.

Original language	English
Article number	jkad146
Number of pages	10
Journal	G3: Genes, Genomes, Genetics Mission
Volume	13
Issue number	9
Early online date	3 Jul 2023
DOIs	https://doi.org/10.1093/g3journal/jkad146
Publication status	Published - 30 Aug 2023

Bibliographical note

Funding
This project was funded by Nord University, Faculty of Biosciences and Aquaculture, Norway. The Norwegian Sequencing Centre, University of Oslo, Norway, which performed some of the DNA sequencing for this study, is supported by both the "Functional Genomics" and "Infrastructure" programs of the Research Council of Norway and the South-Eastern Norway Regional Health Authorities

Acknowledgements
The authors would like to thank Aurélien Delaval, Sven Gust and Clive Fox who supported the field work of this study, and Lars Martin Jakt for support with bioinformatics. For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) license to any Author Accepted Manuscript version arising from this submission.

Data Availability Statement

For a detailed bench protocol for high-molecular weight DNA extractions and a Python3 script for assembly statistics see Supplementary Files 1 and 2. The raw sequencing data (Hi-C, PacBio CLR, and Illumina short reads) and final assembly can be found on NCBI under BioProject PRJNA978993. Repeat content information are included in Supplementary File 3, and annotation information in Supplementary File 8; further information regarding annotation can be found in Supplementary Files 4 to 7. Supplementary Files are available on the GSA figshare: https://doi.org/10.25387/g3.23260280.

Supplemental material available at G3 online.

Keywords

Squalus acanthias
nuclear genome
de-novo assembly
Selachii
Shark

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Wagner_etal_GGG_Characteristics_of_the_VOR
© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 1.96 MBLicence: CC BY

Cite this

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abstract = "Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish{\textquoteright}s genome, of which 31,979 are functionally annotated.",

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Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome

Abstract

Bibliographical note

Data Availability Statement

Keywords

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