Sequencing the North Atlantic herring (Clupea harengus) genome and development of a genetic stock management tool

The Atlantic herring (Clupea harengus) is one of the most abundant fish species in the world and is an important economical and nutritional resource. The species is a highly migratory pelagic species with a complicated population structure. In order to keep the fisheries sustainable, knowledge of sub-populations, their migrations and mixing is important and would assist in the fight against illegal, unreported and unregulated fishing.In 2016 the the assembled herring genome was published. Nevertheless as this is a species of such economical and nutritional importance and to gain further information about population structure and standing variation, we have undertaken a second assembly on a different individual using a different mix of sequencing technologies.Here, we sequenced the herring genome with both Illumina and Oxford Nanopore Technologies platforms. The herring genome was assembled with three different assemblers and then scaffolded using long reads. To generate an assembly as complete and correct as possible we combined our assembly results with the previously published assembly to yield an improved herring genome assembly.