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

IF 11.8 2区 生物学 Q1 MULTIDISCIPLINARY SCIENCES
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
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引用次数: 0

Abstract

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.

从头组装并鉴定巨头鱼高度退化的 ZW 性染色体。
背景:巨头鱼(Megaleporinus macrocephalus,piauçu)是一种新热带鱼类,属于Characoidei科,具有完善的异形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。我们利用 PacBio reads 和 Hi-C 为巨头鱼组装了染色体水平的参考基因组。我们生成了家系分离信息以构建遗传图谱,对雄性和雌性进行集合测序以描述其性别系统的特征,并通过RNA测序突出了大口鲶性别决定的候选基因:结果:大头蝠参考基因组长度为1,282,030,339 bp,等位基因和支架N50分别为5.0 Mb和45.03 Mb。在性染色体中,根据重组抑制模式、覆盖率、FST和性别特异性SNPs,我们区分出了一个高度分化的假定W特异性区域、一个Z和W仍有一些相似性并正在退化的区域以及PAR。性染色体基因库包括来自 TGF-β 家族(amhr2、bmp7)和 Wnt/β-catenin 通路(wnt4、wnt7a)的基因,其中一些基因的表达存在差异:piauçu染色体级基因组具有很高的质量,为推动该群体的研究提供了宝贵的资源。我们的发现为鱼类 Z 和 W 性染色体的进化动态提供了见解,强调了正在进行的退化过程,并显示了特定基因组区域中 Z 和 W 序列之间复杂的相互作用。值得注意的是,amhr2和bmp7是巨头鱼性别决定的潜在候选基因。
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来源期刊
GigaScience
GigaScience MULTIDISCIPLINARY SCIENCES-
CiteScore
15.50
自引率
1.10%
发文量
119
审稿时长
1 weeks
期刊介绍: GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.
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