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bioRxiv · 10.1101/2025.07.21.665996

High-Quality De Novo Genome Assembly for the Galapagos Endemic Lava Gull Using Oxford Nanopore Technologies

Martin, J. A.·Henderson, J. B.·de Ferran, V.·Pozo, G.·Skehel, A.·Lam, A.·Dumbacher, J. P.·Chaves, J. A.
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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. The lava gull (Leucophaeus fuliginosus), an endemic bird species of the Galapagos archipelago, is the worlds 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 22.5x 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.

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Martin, J. A., Henderson, J. B., de Ferran, V., Pozo, G., Skehel, A., Lam, A., Dumbacher, J. P., Chaves, J. A.. 2025-07-24. High-Quality De Novo Genome Assembly for the Galapagos Endemic Lava Gull Using Oxford Nanopore Technologies. https://doi.org/10.1101/2025.07.21.665996

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