Jacobs David K, Kinziger Andrew, Abrecht Mira, McCraney W Tyler, Hà Benjamin A, Spies Brenton T, Heath-Heckman Elizabeth, Marimuhtu Mohan P A, Nguyen Oanh, Fairbairn Colin W, Seligmann William E, Escalona Merly, Miller Courtney, Shaffer H Bradley
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA.
Department of Fisheries Biology, Cal Poly Humboldt, Arcata, California, USA.
J Hered. 2025 Mar 1;116(2):170-178. doi: 10.1093/jhered/esae053.
The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby, NTG) 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 980 Mb E. newberryi reference genome has an N50 of 34 Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO (Benchmarking Universal Single-Copy Orthologs) 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 NTG, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.
联邦濒危姐妹物种纽氏真圆腹雅罗鱼（Eucyclogobius newberryi，北潮汐虾虎鱼，NTG）和克里斯蒂娜真圆腹雅罗鱼（E. kristinae，南潮汐虾虎鱼）构成了加利福尼亚特有的真圆腹雅罗鱼属，该属历史上曾出现在加利福尼亚沿海的所有县。仅间歇性与大海相连的孤立泻湖是它们的主要栖息地。繁殖在泻湖封闭期间进行，最大限度地减少了海洋扩散，并形成了加利福尼亚海岸遗传分化最严重的脊椎动物属。我们使用高保真长读长和Hi-C染色质邻近测序技术，为纽氏真圆腹雅罗鱼提供了一个新的基因组组装。9.8亿碱基对的纽氏真圆腹雅罗鱼参考基因组的N50为3400万碱基对，有22个注释良好的支架，占基因组的88%，完整的BUSCO（基准通用单拷贝直系同源基因）评分为96.7%。该基因组将有助于开展针对细分种群中的选择、漂变和集合种群遗传学的研究，以及极度濒危的克里斯蒂娜真圆腹雅罗鱼的存续研究，在该研究中，重新引入将是恢复保护行动的一个关键要素。它还为恢复北潮汐虾虎鱼中遗传上不同的管理单元提供了关键工具，以及对虾虎鱼进行更广泛的生态和进化研究，虾虎鱼是世界上物种最丰富的鱼类家族。
