First Whole-Genome Assembly of the Galapagos Petrel (Pterodroma phaeopygia) Using Oxford Nanopore Sequencing to Advance Conservation Genomics in a Critically Endangered Seabird

Abstract

The Galapagos petrel (Pterodroma phaeopygia) is a critically endangered procellariiform seabird endemic to the Galapagos 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 Galapagos petrel. The genome was assembled from ultra-long Oxford Nanopore sequence data collected from an adult female sampled on San Cristobal Island. Sequencing was performed at the Galapagos Science Center, enabling local capacity-building and compliance with strict sample import-export regulations of endangered species. The final nuclear genome assembly spans 1.35 Gb in length, with average coverage of 36.07x, scaffold N50 of 74.2 Mb, and a BUSCO aves lineage 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 Corys shearwater (Calonectris borealis) GCA_964196065.2 (Aranega et al., 2024), a related species. The Galapagos petrel reference genome represents a foundational tool for comparative genomics, conservation biology, and functional studies of island-endemic avifauna. It will also facilitate future efforts to characterize genetic diversity, structural variation, and adaptive responses in this critically endangered species.