High-quality chromosome-level genome assembly of the melon-headed whale (Peponocephala electra)

The melon-headed whale ( Peponocephala electra ), a small toothed whale in the Delphinidae family, inhabits tropical and subtropical oceans. It is an attractive model species for studying secondary aquatic adaptation and evolution. Here, we successfully assembled a high-quality chromosome-level genome of P. electra using PacBio and Hi-C sequencing technologies. A 2.29 Gb 120 contig assembly with a contig N50 of 82.36 Mb and scaffold N50 of 102.72 Mb was obtained, with more than 96.93% (2.22 Gb) anchored to 22 pseudochromosomes. The genome assembly showed high completeness, with a BUSCO score of 96.6%. In total, 21 492 protein-coding genes were predicted in the newly assembled genome, 87.61% of which were functionally annotated. Repetitive elements accounted for 43.12% of the genome, dominated by long interspersed nuclear element (LINE) retrotransposons (25.10%). Based on phylogenetic analysis, P. electra and the long-finned pilot whale ( Globicephala melas ) formed a clade, which diverged 3.54–6.10 million years ago (Ma). We also identified gene family dynamics and positively selected genes specific to P. electra , which may be related to head and nervous system development. The high-quality reference genome of P. electra provides a valuable genomic resource for future studies of cetacean biology and evolution. The melon-headed