The Rosenstiel School, University of Miami, Florida, USA.
Department of Veterinary and Biomedical Sciences, University of Minnesota, Minnesota, USA.
Genome Biol Evol. 2022 Aug 3;14(8). doi: 10.1093/gbe/evac111.
Genetic data from nonmodel species can inform ecology and physiology, giving insight into a species' distribution and abundance as well as their responses to changing environments, all of which are important for species conservation and management. Moreover, reduced sequencing costs and improved long-read sequencing technology allows researchers to readily generate genomic resources for nonmodel species. Here, we apply Oxford Nanopore long-read sequencing and low-coverage (∼1x) whole genome short-read sequencing technology (Illumina) to assemble a genome and examine population genetics of an abundant tropical and subtropical fish, the hardhead silverside (Atherinomorus stipes). These fish are found in shallow coastal waters and are frequently included in ecological models because they serve as abundant prey for commercially and ecologically important species. Despite their importance in sub-tropical and tropical ecosystems, little is known about their population connectivity and genetic diversity. Our A. stipes genome assembly is about 1.2 Gb with comparable repetitive element content (∼47%), number of protein duplication events, and DNA methylation patterns to other teleost fish species. Among five sampled populations spanning 43 km of South Florida and the Florida Keys, we find little population structure suggesting high population connectivity.
非模式物种的遗传数据可以为生态学和生理学提供信息，深入了解物种的分布和丰度及其对环境变化的反应，所有这些对于物种保护和管理都很重要。此外，测序成本的降低和长读测序技术的改进使得研究人员能够轻松地为非模式物种生成基因组资源。在这里，我们应用 Oxford Nanopore 长读测序和低覆盖度（约 1x）全基因组短读测序技术（Illumina）来组装基因组，并研究一种丰富的热带和亚热带鱼类——硬头银鲈（Atherinomorus stipes）的种群遗传学。这些鱼类分布在浅海沿岸水域，由于它们是商业和生态上重要物种的丰富猎物，因此经常被纳入生态模型。尽管它们在亚热带和热带生态系统中很重要，但人们对它们的种群连通性和遗传多样性知之甚少。我们组装的 A. stipes 基因组约为 1.2 Gb，与其他硬骨鱼类的重复元件含量（约 47%）、蛋白质重复事件数量和 DNA 甲基化模式相当。在佛罗里达州南部和佛罗里达群岛 43 公里范围内采样的五个种群中，我们发现种群结构很小，表明种群连通性很高。
