Atlantic herring (Clupea harengus) population structure in the Northeast Atlantic Ocean.

The Atlantic herring Clupea harengus L has a vast geographical distribution and a complex population structure with a few very large migratory units and many small local populations. Each population has its own spawning ground and/or time, thereby maintaining their genetic integrity. Several herring populations migrate between common feeding grounds and over-wintering areas resulting in frequent mixing of populations. Thus, many herring fisheries are based on mixed populations of different demographic status. In order to avoid over-exploitation of weak populations and to conserve biodiversity, understanding the population structure and population mixing is important for maintaining biologically sustainable herring fisheries. The aim of this study was to investigate the genetic population structure of herring in the Faroese and surrounding waters, and to develop genetic markers for distinguishing between four herring management units (often called stocks), namely the Norwegian spring-spawning herring (NSSH), Icelandic summer-spawning herring (ISSH), North Sea autumn-spawning herring (NSAH), and Faroese autumn-spawning herring (FASH). Herring from the four stocks were sequenced at low coverage, and single nucleotide polymorphisms (SNPs) were called and used for population structure analysis and individual assignment. An ancestry-informative SNP panel with 118 SNPs was developed and tested on 240 individuals. The results showed that all four stocks appeared to be genetically differentiated populations, but at lower levels of differentiation between FASH and ISSH than the other two populations. Overall assignment rate with the SNP panel was 80.7%, and agreement between the genetic and traditional visual assignment was 75.5%. The NSAH and NSSH samples had the highest assignment rate (100% and 98.3%, respectively) and highest agreement between traditional and genetic assignment methods (96.6% and 94.9%, respectively). The FASH and ISSH samples had substantially lower assignment rates (72.9% and 51.7%, respectively) and agreement between traditional and genetic methods (39.5% and 48.4%, respectively).

Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly.

Atlantic herring (Clupea harengus) is one of the most abundant fish species in the world. It is an important economical and nutritional resource, as well as a crucial part of the North Atlantic ecosystem. In 2016, a draft herring genome assembly was published. Being a species of such importance, we sought to independently verify and potentially improve the herring genome assembly. We sequenced the herring genome generating paired-end, mate-pair, linked and long reads. Three assembly versions of the herring genome were generated based on a de novo assembly (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously published assembly (A3). The resulting assemblies were compared using parameters describing the size, fragmentation, correctness, and completeness of the assemblies. Results showed that the A2 assembly was less fragmented, more complete and more correct than A1. A3 showed improvement in fragmentation and correctness compared with A2 and the published assembly but was slightly less complete than the published assembly. Thus, we here confirmed the previously published herring assembly, and made improvements by further scaffolding the assembly and removing low-quality sequences using linked and long reads and merging of assemblies.