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

Prost, S.; Petersen, M.; Grethlein, M.; Hahn, S. J.; Kuschik-Maczollek, N.; Olesiuk, M. E.; Reschke, J.-O.; Schmey, T. E.; Zimmer, C.; Gupta, D. K.; Schell, T.; Coimbra, R.; De Raad, J.; Lammers, F.; Winter, S.; Janke, A.

doi:10.1101/2020.03.06.981332

bioRxiv · 10.1101/2020.03.06.981332

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

Prost, S.·Petersen, M.·Grethlein, M.·Hahn, S. J.·Kuschik-Maczollek, N.·Olesiuk, M. E.·Reschke, J.-O.·Schmey, T. E.·Zimmer, C.·Gupta, D. K.·Schell, T.·Coimbra, R.·De Raad, J.·Lammers, F.·Winter, S.·Janke, A.

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Abstract

BackgroundEver 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 Masters 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. FindingsThe 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. ConclusionWe present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university Masters course. The use of ~35x 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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Prost, S., Petersen, M., Grethlein, M., Hahn, S. J., Kuschik-Maczollek, N., Olesiuk, M. E., Reschke, J.-O., Schmey, T. E., Zimmer, C., Gupta, D. K., Schell, T., Coimbra, R., De Raad, J., Lammers, F., Winter, S., Janke, A.. 2020-03-09. Improving the chromosome-level genome assembly of the Siamese fighting fish (Betta splendens) in a university Master's course.. https://doi.org/10.1101/2020.03.06.981332

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