Manta and devil ray genome assemblies uncover signatures of pelagic adaptation

Manta and devil rays (Mobulidae) are iconic marine megafauna highly adapted to life in the open ocean, with forward-facing mouths, enlarged pectoral fins and specialised filter-feeding apparatus. These innovations have enabled mobulids to occupy vast pelagic habitats, yet the genetic changes underlying them remain poorly understood. Here we use a combination of chromatin conformation capture, PacBio HiFi and Nanopore long-reads to generate highly contiguous annotated chromosome-level reference genomes for two mobulid species: the Atlantic pygmy devil ray (Mobula hypostoma) and the Atlantic manta ray (Mobula yarae). The assemblies span 3.5 and 4.0 Gb, with contig N50s of 23.3 and 7.3 Mb, respectively. We combine these into a Progressive Cactus whole genome alignment with benthic batoid outgroups to characterise the landscape of structural variation and identify candidate molecular regions associated with pelagic adaptation. This approach revealed that over 1.5 million structural rearrangements occurred along the ancestral mobulid lineage, with deletions encompassing three times more sequence compared to the benthic sister lineage. Genes affected by mobulid specific deletions were significantly enriched for neurogenesis pathways linked to craniofacial patterning, with several deletions overlapping the putative promoter sequences of craniofacial and roof of mouth development genes. Our findings highlight candidate developmental pathways through which ancestral deletions may have driven mobulid adaptations, while the high-quality genome resources provide a foundation for comparative and functional studies in Chondrichthyes.