Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Background: Yellow perch, Perca flavescens, is an ecologically and commercially important species native to a large portion of the northern United States and southern Canada. It is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquaculture management practices. Findings: 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 perchgenome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perchcount, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). Genome annotation identified 41.7% (366 Mb) of repeated elements and 24,486 genes including 16,579 genes (76.3%) significantly matching with proteins in public databases. We also provide a first characterization of the yellow perchsex determination locus that contains a male-specific duplicate of the anti-Mullerian hormonetype 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 test which accurately differentiates XY genetic males (amhr2by+) from XX genetic females (amhr2by-). Conclusions: Our high-quality genome assembly is an important genomic resource for future studies on yellow perchecology, toxicology, fisheries, and aquaculture research. In addition, the characterization of the amhr2by gene as a candidate sex determining gene in yellow perchprovides a new example of the recurrent implication of the transforming growth factor betapathway in fish sex determination, and highlights gene duplicationas an important genomic mechanism for the emergence of new master sex determination genes.