Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi.

Abstract

The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980Mb E. newberryi reference genome has an N50 of 34Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the northern tidewater goby, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.