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

Isabella R Sessi; James B Henderson; Jessica A Martin; Alice Skehel; Gabriela Pozo; Jonathan A Guillén Alcides; Vera de Ferran; John P Dumbacher; Jaime A Chaves

doi:10.1093/g3journal/jkag004

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

Journal article

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

Isabella R Sessi, James B Henderson, Jessica A Martin, Alice Skehel, Gabriela Pozo, Jonathan A Guillén Alcides, Vera de Ferran, John P Dumbacher and Jaime A Chaves

G3: Genes, Genomes, Genetics, Vol.16(3), pp.1-11

2026

DOI: https://doi.org/10.1093/g3journal/jkag004

PMCID: PMC12958810

PMID: 41589066

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Abstract

endangered species

Long reads

genome assembly

invasive species

Galápagos Islands

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 36.07x, 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) GCA_964196065.2 (Arànega et al., 2024), 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 ONT-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.

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Title: First Whole-Genome Assembly of the Galápagos Petrel (Pterodroma phaeopygia) Using Oxford Nanopore Sequencing to Advance Conservation Genomics in a Critically Endangered Seabird
Authors: Isabella R Sessi - California Academy of Sciences
James B Henderson - California Academy of Sciences
Jessica A Martin - San Francisco State University
Alice Skehel - University of the Sunshine Coast, Queensland, School of Science, Technology and Engineering
Gabriela Pozo - Universidad San Francisco de Quito
Jonathan A Guillén Alcides
Vera de Ferran - San Francisco State University
John P Dumbacher - San Francisco State University
Jaime A Chaves (Corresponding Author) - Universidad San Francisco de Quito
Publication details: G3: Genes, Genomes, Genetics, Vol.16(3), pp.1-11
Publisher: Oxford University Press
Date published: 2026
DOI: 10.1093/g3journal/jkag004
ISSN: 2160-1836
PMID: 41589066; PMC12958810
Copyright note: © The Author(s) 2026. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Data Availability: Raw sequencing data is available on NCBI under BioProject PRJNA1275046 and BioSample SAMN49010279: GAPE_003. The genome assembly is deposited under the same BioProject on NCBI. All NCBI submissions will be made public at the time of publication. GFF files are available at GSA FigShare: https://doi.org/10.25387/g3.29648078.
Grant note: This project is based upon work supported by the National Science Foundation under Grant Number 2233210 (BRC-BIO: GalapaGenomes).
Organisation Unit: School of Science, Technology and Engineering
Language: English
Record Identifier: 991208975602621
Output Type: Journal article

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