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Published VersionCC BY V4.0, Open Access
Journal article
High-quality de novo genome assembly for the Galápagos endemic lava gull using Oxford Nanopore Technologies
G3: Genes, Genomes, Genetics, Vol.16(3), pp.1-9
2026
PMID: 41419217
Abstract
High-quality reference genomes permit deeper investigation into species' evolution and provide insight into species management and conservation. Next-generation sequencing technologies, such as Oxford Nanopore Technologies, allow researchers to generate high-accuracy long-read genetic data in real-time from anywhere in the world, increasing accessibility to sequence data without exportation of the sample. The lava gull (Leucophaeus fuliginosus), an endemic bird species of the Galápagos archipelago, is the world's rarest gull with an estimated population of 300 to 600 individuals. Little genetic research has been done on this species due to its solitary nature and small population size. Here we present a chromosome-level reference genome assembly of an adult female lava gull, generated using ultra-long reads from the Oxford Nanopore Ultra-Long DNA Sequencing Kit and a PromethION 2 Solo device. Initial sequencing generated 1.78 million reads, consisting of 29.6 gigabases (Gbp), with a mean Q-score of 17.8 at an average 22.5× coverage. Our final assembly has a total length of 1.31 Gbp, with 450 scaffolds, and a scaffold N50 of 85.1 Mbp and contig N50 of 42.8 Mbp. The generation of a high-quality whole genome for the lava gull is an important step for investigation into the species' phylogeography and population genetics.
Details
- Title
- High-quality de novo genome assembly for the Galápagos endemic lava gull using Oxford Nanopore Technologies
- Authors
- Jessica A Martin (Author) - San Francisco State UniversityJames B Henderson - California Academy of SciencesVera de Ferran - San Francisco State UniversityGabriela Pozo - Universidad San Francisco de QuitoAlice Skehel - University of the Sunshine CoastAthena Lam - California Academy of SciencesJohn P Dumbacher - California Academy of SciencesJaime A Chaves (Corresponding Author) - Universidad San Francisco de Quito
- Publication details
- G3: Genes, Genomes, Genetics, Vol.16(3), pp.1-9
- Publisher
- Oxford University Press
- Date published
- 2026
- DOI
- 10.1093/g3journal/jkaf259
- ISSN
- 2160-1836
- PMID
- 41419217
- Copyright note
- © The Author(s) 2025. 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
- All raw sequencing data are deposited at NCBI under PRJNA1275045, BioProject SAMN49010278, and BioSample SAMN49010278 : LVGU_060. The genome assembly is deposited under the same BioProject on NCBI and will be made public at the time of publication. https://dataview.ncbi.nlm.nih.gov/object/PRJNA1275045?reviewer=3bu7kcf60sgf0f7k39oj81j4u1. GFF files have been submitted to GSA Figshare following the website submission instructions. The publicly accessible datasets used in this study (lesser black-backed gull, yellow-legged gull, laughing gull, European herring gull, black-headed gull, little vermilion flycatcher, dark-eyed junco, and Galápagos petrel) can be found on GenBank and are cited within this paper.
- Grant note
- This project is based upon work supported by the National Science Foundation under Grant Number 2233210 (BRC-BIO: GalapaGenomes) to J.A.C.
- Organisation Unit
- School of Science, Technology and Engineering
- Language
- English
- Record Identifier
- 991216651302621
- Output Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web Of Science research areas
- Genetics & Heredity