Improving the Chromosome-Level Genome Assembly of the Siamese Fighting Fish (Betta splendens) in a University Master's Course. Issue 7 (1st July 2020)

• Record Type: Journal Article
• Authors: Prost, Stefan; Petersen, Malte; Grethlein, Martin; Hahn, Sarah Joy; Kuschik-Maczollek, Nina; Olesiuk, Martyna Ewa; Reschke, Jan-Olaf; Schmey, Tamara Elke; Zimmer, Caroline; Gupta, Deepak K; Schell, Tilman; Coimbra, Raphael; De Raad, Jordi; Lammers, Fritjof; Winter, Sven; Janke, Axel
• Is Part Of: G3. Volume 10:Issue 7(2020)
• Page Start: 2179
• Page End: 2183
• Publication Date: 2020-07-01
• Subjects: chromosome-level genome assembly -- Betta splendens -- master's course; Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1534/g3.120.401205
• Languages: English
• ISSNs: 2160-1836

Abstract

Abstract: 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 behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x 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 the Hi-C 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 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. 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.