Borges, C. H. d. S.; Utsunomia, R.; Varani, A. M.; Uliano da Silva, M.; Guerra, L. V.; Butzge, A. J.; Gomez Agudelo, J. F.; Manso, S.; Freitas, M. V.; Ariede, R. B.; Mastrochirico-Filho, V. A.; Penaloza, C.; Barria, A.; Porto-Foresti, F.; Foresti, F.; Hattori, R. S.; Guiguen, Y.; Houston, R. D.; Hashimoto, D. T.

Background: Megaleporinus macrocephalus (piaucu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex-determination system and thus, constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus. We generated family segregation information to construct a genetic map, pool-seq of males and females to characterize its sex system, and RNA-seq to highlight candidate genes of M. macrocephalus sex determination. Results: M. macrocephalus reference genome is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. Based on patterns of recombination suppression, coverage, Fst, and sex-specific SNPs, three major regions were distinguished in the sex chromosome: W-specific (highly differentiated), Z-specific (in degeneration), and PAR. The sex chromosome gene repertoire was composed of genes from the TGF-beta family (amhr2, bmp7) and Wnt/beta-catenin pathway (wnt4, wnt7a), and some of them were differentially expressed. Conclusions: The chromosome-level genome of piaucu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, amhr2 and bmp7 are potential candidate genes for sex determination in M. macrocephalus.