Long-read sequence capture elucidates the evolution of the hemoglobin gene clusters in codfishes

Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. This approach does not capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. In this study, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology, leading to the successful sequencing and assembling of the two hemoglobin (Hb) gene clusters LA (~100kb) and MN (~200kb) across eight species of codfishes that are separated by up to 70 million years of evolution. The highly continuous assemblies – capturing both intergenic and coding sequences – revealed overall conserved genetic organization and synteny of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. Taken together, our study highlights the efficiency of targeted long-read capture for comparative genomic studies by shedding light on the evolutionary history of the Hb gene family across the highly divergent group of codfishes.