First whole-genome assembly of the Galápagos Petrel (Pterodroma phaeopygia) using Oxford Nanopore sequencing to advance conservation genomics in a critically endangered seabird.

The Galápagos Petrel (Pterodroma phaeopygia) is a critically endangered procellariiform seabird endemic to the Galápagos Islands. Once abundant, its populations have sharply declined due to invasive predators, habitat degradation, and destruction of nest burrows. Although the species is distributed across several islands, the demographics of each population and their genetic relationships are poorly understood. To facilitate future studies of population structure and connectivity, we present the first high-quality reference genome for the Galápagos Petrel. The genome was assembled solely from ultra-long Oxford Nanopore sequence data collected from an adult female sampled on San Cristóbal Island. Sequencing was performed at the Galapagos Science Center, building local capacity for the generation of genomic data in remote regions. The final nuclear genome assembly spans 1.35 Gb in length, with average coverage of 36.07×, scaffold N50 of 74.2 Mb, and a BUSCO completeness of 99.95%. The genome comprises 41 pseudo-chromosomes, with 23 spanning from telomere to telomere and 16, including W and Z chromosomes, containing a single telomere. Chromosomal-level scaffolding by reference was performed using the genome of Cory's Shearwater (Calonectris borealis), a closely related species. This reference genome provides a foundational tool for comparative genomics, conservation biology, and functional studies of island-endemic avifauna, and demonstrates that recent advances in basecalling and error correction now enable Oxford Nanopore Technologies-only datasets to achieve assemblies comparable in quality to those generated using short-read or PacBio HiFi data. It will also facilitate future efforts to characterize genetic diversity, structural variation, and adaptive responses in this critically endangered species.