Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

Brandon D Pickett; Sheena Talma; Jessica R Glass; Daniel Ence; Timothy P Johnson; Paul D Cowley; Perry G Ridge; John S K Kauwe

doi:10.46471/gigabyte.44

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish

GigaByte. 2022 Mar 17:2022:gigabyte44. doi: 10.46471/gigabyte.44. eCollection 2022.

Authors

Brandon D Pickett¹, Sheena Talma², Jessica R Glass^{3

4}, Daniel Ence⁵, Timothy P Johnson⁶, Paul D Cowley³, Perry G Ridge¹, John S K Kauwe^{1

7}

Affiliations

¹ Department of Biology, Brigham Young University, Provo, Utah, USA.
² Department of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South Africa.
³ South African Institute for Aquatic Biodiversity, Makhanda, South Africa.
⁴ College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA.
⁵ School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, USA.
⁶ Tim Johnson Gallery, Mesa, Arizona, USA.
⁷ Brigham Young University - Hawai'i, Laie, Hawai'i, USA.

Abstract

The roundjaw bonefish, Albula glossodonta, is the most widespread albulid in the Indo-Pacific and is vulnerable to extinction. We assembled the genome of a roundjaw bonefish from Hawai'i, USA, which will be instrumental for effective transboundary management and conservation when paired with population genomics datasets. The 1.05 gigabase pair (Gbp) contig-level assembly had a 4.75 megabase pair (Mbp) NG50 and a maximum contig length of 28.2 Mbp. Scaffolding yielded an LG50 of 20 and an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. The genome comprised 6.5% repetitive elements and was annotated with 28.3 K protein-coding genes. We then evaluated population genetic connectivity between six atolls in the Western Indian Ocean with 38,355 SNP loci across 66 A. glossodonta individuals. We discerned shallow population structure and observed genetic homogeneity between atolls in Seychelles and reduced gene flow between Seychelles and Mauritius. The South Equatorial Current might be the limiting mechanism of this reduced gene flow. The genome assembly will be useful for addressing taxonomic uncertainties of bonefishes globally.

Grants and funding

BDP was supported by a Conservation Scholarship from Fly Fishers International. ST was supported by the South African Institute for Aquatic Biodiversity, the Mandela Rhodes Foundation, the Marine Research Grant from the Western Indian Ocean Marine Science Association, and the Yale University Department of Ecology and Evolutionary Biology.