| Autor: |
Stefan Prost, Malte Petersen, Martin Grethlein, Sarah Joy Hahn, Nina Kuschik-Maczollek, Martyna Ewa Olesiuk, Jan-Olaf Reschke, Tamara Elke Schmey, Caroline Zimmer, Deepak K. Gupta, Tilman Schell, Raphael Coimbra, Jordi De Raad, Fritjof Lammers, Sven Winter, Axel Janke |
| Jazyk: |
angličtina |
| Rok vydání: |
2020 |
| Předmět: |
|
| Zdroj: |
G3: Genes, Genomes, Genetics, Vol 10, Iss 7, Pp 2179-2183 (2020) |
| Druh dokumentu: |
article |
| ISSN: |
2160-1836 |
| DOI: |
10.1534/g3.120.401205 |
| Popis: |
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. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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