Loss of Major Histocompatibility Complex I and II Function in the Genome of Glacier Lanternfish Provides Insight Into Evolution of Vertebrate Immune Systems.

Lanternfishes (Myctophidae) are one of the most abundant and species diverse orders inhabiting the mesopelagic zone. Exploitation of marine resources has recently attracted increased interest. It is therefore essential to improve our understanding of the meso- and deep-pelagic ecosystems with respect to conservation and management strategies. Genomic resources are paramount to enable in-depth studies of population structuring and understanding the inherent genetic diversity, but also to enable studies of processes such as local adaptation and selection. Here, we present a genome assembly of the glacier lanternfish (Benthosema glaciale) generated with long-read PacBio and Hi-C contact map data. By comparing additional available genomes from the Myctophiformes order, we explore their adaptive immune strategies. Our findings reveal that multiple lineages within this order have lost a significant proportion of genes related to adaptive immunity (Electrona, Protomyctophum and Benthosema). We find simultaneous loss of both classical major histocompatibility complex (MHC) class I and class II function coinciding with reduction in genetic diversity with respect to immunoglobulin and T-cell receptors. In contrast, the sister branch represented by Gymnoscopelus and Nannobrachium appears to have maintained the standard configuration of the jawed vertebrate adaptive immune system apart from large gene expansions in MHC class II. Our results demonstrate that the Benthosema-belonging lineage (Myctophinae) has completely lost the core functions of the adaptive immune system. How, when, and why this occurred warrants further investigations.