Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+ ) from XX genetic females (amhr2by- ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

中文翻译：

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基于黄鲈、Perca flavescens 的染色体规模基因组组装，表征抗苗勒管激素 II 型受体基因的 Y 特异性重复/插入。

黄鲈（Perca flavescens）是美国北部和加拿大南部大部分地区的重要生态和经济物种，也是水产养殖的有前途的候选物种。然而，没有可用的黄鲈参考基因组来促进渔业和水产养殖管理实践的改进。通过结合 Oxford Nanopore Technologies 长读长、10X Genomics Illumina 短链读长和 Hi-C 生成的染色体接触图，我们生成了 877.4 Mb 的高连续性染色体尺度黄鲈基因组组装。与已知的二倍体染色体黄鲈计数一致，它包含 24 个染色体大小的支架，覆盖了整个组装的 98.8%（N50 = 37.4 Mb，L50 = 11）。我们还提供了黄鲈性别决定基因座的首次表征，该基因座包含插入 Y 染色体（染色体 9）近端的抗苗勒激素 II 型受体基因 (amhr2by) 的男性特异性重复。使用此性别特异性信息，我们开发了一种简单的 PCR 基因分型分析，可准确区分 XY 遗传雄性 (amhr2by+) 和 XX 遗传雌性 (amhr2by-)。我们高质量的基因组组装是未来黄鲈生态学、毒理学、渔业和水产养殖研究的重要基因组资源。此外，将 amhr2by 基因表征为黄鲈的候选性别决定基因，为转化生长因子β途径在鱼类性别决定中的反复影响提供了一个新的例子，