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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.
We can see an increasing consumption of meat together with the corresponding behavioral adaptations in early hominins, such as Homo erectus. This new development was driven by one or more behavioral adaptations, such as a shift to a higher-quality diet, increased social interactions and/or changes in the life history strategies. The methods by which these hominins obtained meat—through scavenging the carcasses of large herbivores or hunting themselves—remain a topic of debate. They seem to have thrived in expanding grasslands, which offered few resources except for herds of large, gregarious mammals. In our study, we developed an agent-based model that simulates the behavior of a group of hunter-gatherers foraging in a reconstructed tropical grassland environment. The environmental parameters, including plant availability and prey population densities, are derived from the Serengeti National Park. In this model, agents gather or hunt various species either alone or as a group, using strategies early hominins may already have access to. The basic behavior and the implemented hunting strategies are based on data from recent hunter-gatherer societies living in tropical grasslands. Our model demonstrates how foragers may have thrived in tropical grasslands by either adopting fast hunting strategies, which often require access to sophisticated hunting tools, or by cooperating extensively, which would rely on an enhanced social structure to promote cooperative behavior. Our model can be used to study other scenarios by offering the option to change the environmental conditions and aspects of the agent behavior.