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

Carolina Heloisa Souza-Borges, Ricardo Utsunomia, Alessandro M Varani, Marcela Uliano-Silva, Lieschen Valeria G Lira, Arno J Butzge, John F Gomez Agudelo, Shisley Manso, Milena V Freitas, Raquel B Ariede, Vito A Mastrochirico-Filho, Carolina Penaloza, Agustín Barria, Fábio Porto-Foresti, Fausto Foresti, Ricardo Hattori, Yann Guiguen, Ross D Houston, Diogo Teruo Hashimoto

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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 sequencing of males and females to characterize its sex system, and RNA sequencing to highlight candidate genes of M. macrocephalus sex determination.

RESULTS: The reference genome of M. macrocephalus is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. In the sex chromosome, based on patterns of recombination suppression, coverage, FST, and sex-specific SNPs, we distinguished a putative W-specific region that is highly differentiated, a region where Z and W still share some similarities and is undergoing degeneration, and the PAR. The sex chromosome gene repertoire includes genes from the TGF-β family (amhr2, bmp7) and the Wnt/β-catenin pathway (wnt4, wnt7a), some of which are 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.

Original languageEnglish
Pages (from-to)1-19
Number of pages19
JournalGigaScience
Volume13
Early online date26 Nov 2024
DOIs
Publication statusE-pub ahead of print - 26 Nov 2024

Keywords / Materials (for Non-textual outputs)

  • Animals
  • Sex Chromosomes/genetics
  • Male
  • Female
  • Sex Determination Processes/genetics
  • Fishes/genetics
  • Characiformes/genetics
  • Genome
  • Chromosome Mapping

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