Improving the chromosome-level genome assembly of the Siamese fighting fish (Betta splendens) in a university master’s course

  • Background: Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university Master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behaviour. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published HiC data. Findings: The use of nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using previously published HiC data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 95.8% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. Conclusion: We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university Master’s course. The use of ~35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.

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Author:Stefan ProstORCiD, Malte PetersenORCiDGND, Martin GrethleinORCiD, Sarah Joy Hahn, Nina Kuschik-Maczollek, Martyna Ewa Olesiuk, Jan-Olaf ReschkeORCiD, Tamara Elke SchmeyORCiD, Caroline Zimmer, Deepak Kumar GuptaORCiD, Tilman SchellORCiDGND, Raphael T. F. CoimbraORCiD, Jordi de RaadORCiD, Fritjof LammersORCiDGND, Sven WinterORCiDGND, Axel JankeORCiD
Parent Title (English):bioRxiv
Document Type:Preprint
Date of Publication (online):2020/03/09
Date of first Publication:2020/03/09
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2023/05/25
Page Number:9
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 59 Tiere (Zoologie) / 590 Tiere (Zoologie)
Licence (German):License LogoCreative Commons - CC BY-NC-ND - Namensnennung - Nicht kommerziell - Keine Bearbeitungen 4.0 International