A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea

Abstract

Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed using DNA from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the cold Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. Structurally, the genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig size of 686 Mb with a N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize in detail large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step towards developing pan-genomic resources for Atlantic cod.

SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea

“…Manhattan plots of outlier analyses based on median log10(p value). The SNPs are distributed according to LG and their position within the LGs along the X axis 124,125 . The solid line is standard p value cutoff 124 .…”

“…www.nature.com/scientificreports www.nature.com/scientificreports/ using the R package "qqman" 124 . Homology searching was done through BLAST search of the available flanking sequences 125 for each detected outlier loci on the NCBI and Ensembl public databases 126 . Functions of annotated outlier loci were determined using UniProt database.…”

Supergene origin and maintenance in Atlantic cod

“…Despite the suggestion of a lekking mating system[41], mating between the two ecotypes appears to occur and thus explains the presence of individuals that are heterozygous for the LG 1 haplotypes as well as the very weak separation outside of the four differentiated regions[29]. The differentiated region on LG 1 thus matches the definition of a supergene[6] and is commonly referred to by this term[33–35, 42, 43]. A number of genes from within this supergene have been proposed as candidate genes under selection, including the Ca6 gene that plays a role in pH-level reduction in the swim bladder and might thus be important for feeding at greater depths in the migratory ecotype.…”

“…Similar to the different frequencies of LG 1 haplotypes between migratory and stationary ecotypes, one of the two alternative haplotypes on LG 2 is far more frequent in Atlantic cod from the Baltic sea compared to the nearest North Atlantic populations and has been suggested to carry genes adapted to low salinity[28, 37]. The alternative haplotypes on LGs 7 and 12 also differ in their frequencies among Atlantic cod populations, with one of the two haplotypes in each case being nearly absent in the Irish and Celtic Sea, which are among the southernmost populations in the Northeast Atlantic, possibly in relation to adaptation to the higher temperatures experienced by these populations[42, 44, 45]. While the ”supergene” status of the haplotypes on LGs 2, 7, and 12 will depend on further investigations of their ecological role, they, too, are commonly referred to by this term in the literature[33–35, 42], and we will do so hereafter.…”

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals structural genome variation in rainbow trout

“…The rainbow trout genome contains large polymorphic inversions on chromosomes Omy05 and Omy20 (Pearse et al 2019). Recently, a second de-novo assembly for Atlantic cod has been useful for characterizing known inversions and identifying additional smaller inversions in the cod genome (Kirubakaran et al 2020). By generating a second de-novo assembly for rainbow trout from a distinctly different genetic line we aim to further characterize the two known inversions in the rainbow trout genome and identify additional putative large-scale structural variants between the Swanson and Arlee lines.…”