Department of Biogeography, Trier University, Trier 54296, Germany.
Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn 53113, Germany.
Genome Biol Evol. 2024 Aug 5;16(8). doi: 10.1093/gbe/evae155.
The viviparous eelpout Zoarces viviparus is a common fish across the North Atlantic and has successfully colonized habitats across environmental gradients. Due to its wide distribution and predictable phenotypic responses to pollution, Z. viviparus is used as an ideal marine bioindicator organism and has been routinely sampled over decades by several countries to monitor marine environmental health. Additionally, this species is a promising model to study adaptive processes related to environmental change, specifically global warming. Here, we report the chromosome-level genome assembly of Z. viviparus, which has a size of 663 Mb and consists of 607 scaffolds (N50 = 26 Mb). The 24 largest represent the 24 chromosomes of the haploid Z. viviparus genome, which harbors 98% of the complete Benchmarking Universal Single-Copy Orthologues defined for ray-finned fish, indicating that the assembly is highly contiguous and complete. Comparative analyses between the Z. viviparus assembly and the chromosome-level genomes of two other eelpout species revealed a high synteny, but also an accumulation of repetitive elements in the Z. viviparus genome. Our reference genome will be an important resource enabling future in-depth genomic analyses of the effects of environmental change on this important bioindicator species.
胎生杜父鱼 Zoarces viviparus 是一种分布广泛的北西洋鱼类，已成功适应了各种环境梯度的生境。由于其广泛的分布范围和对污染的可预测表型反应，胎生杜父鱼被用作理想的海洋生物指示生物，并被几个国家常规采样数十年，以监测海洋环境健康。此外，该物种是研究与环境变化相关的适应过程的有前途的模型，特别是全球变暖。在这里，我们报告了胎生杜父鱼的染色体水平基因组组装，其大小为 663Mb，由 607 个支架组成（N50=26Mb）。24 个最大的支架代表了胎生杜父鱼单倍体基因组的 24 条染色体，其中包含了为硬骨鱼定义的 98%的完整基准通用单拷贝直系同源物，这表明组装具有高度的连续性和完整性。胎生杜父鱼组装与另外两种杜父鱼物种的染色体水平基因组之间的比较分析表明，它们具有高度的同线性，但胎生杜父鱼基因组中也积累了大量的重复元件。我们的参考基因组将是一个重要的资源，使未来能够对这种重要的生物指示物种进行环境变化影响的深入基因组分析。
