Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP, 14884-900, Brazil.
School of Sciences, São Paulo State University (Unesp), Bauru, SP, 17033-360, Brazil.
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae085.
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.
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.
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.
Megaleporinus macrocephalus（piauçu）是一种新热带鱼类，属于 Characoidei，具有完善的异型 ZZ/ZW 性别决定系统，因此是研究鱼类 W 和 Z 染色体的良好模型。我们使用 PacBio reads 和 Hi-C 组装了 M. macrocephalus 的染色体水平参考基因组。我们生成了家族分离信息来构建遗传图谱，对雄性和雌性进行池测序以表征其性别系统，并进行 RNA 测序以突出 M. macrocephalus 性别决定的候选基因。
M. macrocephalus 的参考基因组长 1282030339bp，具有 5.0Mb 和 45.03Mb 的 contig 和 scaffold N50。在性染色体上，根据重组抑制、覆盖度、FST 和性别特异性 SNPs 的模式，我们区分了一个具有高度分化的推定 W 特异性区域，一个 Z 和 W 仍有一些相似之处且正在退化的区域，以及 PAR。性染色体基因谱包括 TGF-β 家族（amhr2、bmp7）和 Wnt/β-catenin 途径（wnt4、wnt7a）的基因，其中一些基因表达存在差异。
piauçu 的染色体水平基因组质量高，为该组的研究提供了有价值的资源。我们的发现揭示了鱼类 Z 和 W 性染色体的进化动态，强调了正在进行的退化过程，并表明在特定基因组区域中 Z 和 W 序列之间存在复杂的相互作用。值得注意的是，amhr2 和 bmp7 可能是 M. macrocephalus 性别决定的候选基因。
