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

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.

doi:10.1101/2024.03.07.583869

bioRxiv · 10.1101/2024.03.07.583869

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

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.

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Abstract

BackgroundMegaleporinus 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. ResultsM. 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. ConclusionsThe 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.

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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.. 2024-03-12. De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus. https://doi.org/10.1101/2024.03.07.583869

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