Du Zhenyong, Gelembiuk Gregory, Moss Wynne, Tritt Andrew, Lee Carol Eunmi
Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA.
Genomics Proteomics Bioinformatics. 2024 Dec 3;22(5). doi: 10.1093/gpbjnl/qzae066.
Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as food sources for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations. Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio long-read and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome, consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb), was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transport-related gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transport-related genes and the significant clustering of these genes on each chromosome. This genome represents one of the most contiguous copepod genomes to date and is among the highest quality marine invertebrate genomes. As such, this genome provides an invaluable resource to help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments.
桡足类是地球上数量最为丰富的生物之一，在水生生态系统中发挥着关键作用。在桡足类中，近亲真宽水蚤物种复合体的种群数量在许多沿海栖息地中占据主导地位，并作为主要渔业的食物来源。有趣的是，某些种群具有在短时间尺度上侵入新盐度环境的非凡能力。尽管它们具有重要的生态意义，但对于哲水蚤目桡足类而言，高质量的基因组资源一直缺乏，这限制了我们全面剖析某些种群高度入侵性和适应能力背后的基因组结构的能力。在此，我们展示了哲水蚤目桡足类的首个染色体水平的基因组，该基因组来自近亲真宽水蚤物种复合体的大西洋分支（卡罗莱纳真宽水蚤）。这个基因组是利用通过30代全同胞交配产生的近交系的高覆盖度PacBio长读长和Hi-C序列组装而成的。该基因组由529.3 Mb组成（重叠群N50 = 4.2 Mb，支架N50 = 140.6 Mb），被锚定到四条染色体上。基因组注释预测有20,262个蛋白质编码基因，基于对另外12个节肢动物基因组的比较分析，其中与离子运输相关的基因家族大幅扩展。此外，我们发现了离子运输相关基因的全基因组历史基因体甲基化特征以及这些基因在每条染色体上的显著聚类。这个基因组是迄今为止最连续的桡足类基因组之一，也是最高质量的海洋无脊椎动物基因组之一。因此，这个基因组提供了一个宝贵的资源，有助于深入了解这种桡足类适应快速变化环境的能力。
