De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

Background Megaleporinus macrocephalus (piauçu) 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-β family (amhr2 , bmp7 ) and Wnt/β-catenin pathway ( wnt4 , wnt7a ), and some of them were differentially expressed. Conclusions The chromosome-level genome of piauçu 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 . ### Competing Interest Statement The authors have declared no competing interest. * BMPs : Bone morphogenetic proteins BUSCO : Benchmarking Universal Single Copy Orthologs CLR : continuous long reads ddRADseq : Double Digest Restriction Site Associated DNA Sequencing DE : differentially expressed FISH : Fluorescence in situ hybridization Fst : fixation index GO : gene ontology HMW : high molecular weight JBAT : Juicebox Assembly Tools LG : Linkage Group LINE : long interspersed nuclear elements LOD : Logarithm of Odds LTR : long terminal repeats MSD : master sex determining NCBI : National Center for Biotechnology Information PacBio : Pacific Biosciences PAR : Pseudoautosomal region PCA : Principal component analysis QV : Consensus Quality Value sat DNA : Satellite DNAs SINE : short interspersed nuclear elements SMRT : single molecule real time T2T : Telomere to Telomere consortium TE : transposable elements.