A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes.

IF 11.8 2区生物学 Q1 MULTIDISCIPLINARY SCIENCES

GigaScience Pub Date : 2025-01-06 DOI:10.1093/gigascience/giaf079

Qunfei Guo, Youliang Pan, Wei Dai, Fei Guo, Tao Zeng, Wanyi Chen, Yaping Mi, Yanshu Zhang, Shuaizhen Shi, Wei Jiang, Huimin Cai, Beiying Wu, Yang Zhou, Ying Wang, Chentao Yang, Xiao Shi, Xu Yan, Junyi Chen, Chongyang Cai, Jingnan Yang, Xun Xu, Ying Gu, Yuliang Dong, Qiye Li

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引用次数: 0

Abstract

Background: Vertebrate sex is typically determined either by genetic factors, such as sex chromosomes, or by environmental cues like temperature. Therefore, the agamid dragon lizard Pogona vitticeps is remarkable in this regard, as it exhibits both ZZ/ZW genetic and temperature-dependent sex determination. However, complete sequence and full gene content of P. vitticeps sex chromosomes remain unclear, hindering the investigation of sex-determining cascade in this model lizard.

Results: Using CycloneSEQ and DNBSEQ sequencing technologies, we generated a near-complete chromosome-scale genome assembly for a ZZ male P. vitticeps. Compared with previous reference genome (GCF_900067755.1/Pvi1.1), this ∼1.8-Gb new assembly displayed >5,700-fold improvement in contiguity (contig N50: 202.5 Mb vs. 35.5 kb) and achieved complete chromosome anchoring (16 vs. 13,749 scaffolds). We found that over 80% of the P. vitticeps Z chromosome remains as a pseudo-autosomal region, where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as AMH, AMHR2, and BMPR1A. Finally, by tracking the evolutionary origin and developmental expression of SDR genes, we proposed a model for the origin of P. vitticeps sex chromosomes that considered the Z-linked AMH as the master sex-determining gene.

Conclusions: In this study, we fully characterized the Z sex chromosome of P. vitticeps, identified AMH as the candidate sex-determining gene, and proposed a new model for the origin of P. vitticeps sex chromosomes. The near-complete P. vitticeps reference genome will also benefit future study of reptile evolution.

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一个近乎完整的胡须龙vitticeps Pogona基因组组装提供了对Pogona性染色体起源的见解。

背景：脊椎动物的性别通常是由遗传因素（如性染色体）或环境因素（如温度）决定的。因此，在这方面，agamid龙蜥Pogona vitticeps是值得注意的，因为它同时表现出ZZ/ZW遗传和温度依赖的性别决定。然而，由于目前尚不清楚这种模式蜥蜴性染色体的完整序列和全基因含量，阻碍了这种模式蜥蜴性别决定级联的研究。结果：利用CycloneSEQ和DNBSEQ测序技术，我们获得了一个接近完整的ZZ雄性葡萄籽的染色体规模的基因组组装。与之前的参考基因组（GCF_900067755.1/Pvi1.1）相比，这个1.8 gb的新组装显示出bbb5700倍的连续性提高（contig N50: 202.5 Mb对35.5 kb），并实现了完整的染色体锚定（16对13,749个支架）。我们发现超过80%的葡萄P. vitticeps Z染色体仍然是一个假常染色体区域，在那里重组不受抑制。性别分化区（SDR）很小，主要由转座子占据，但它聚集了参与男性发育的基因，如AMH、AMHR2和BMPR1A。最后，通过追踪SDR基因的进化起源和发育表达，我们提出了一个将z连锁AMH作为主要性别决定基因的葡萄拟南藜性染色体起源模型。结论：本研究充分表征了葡萄葡萄的Z性染色体，确定AMH为候选性别决定基因，提出了葡萄葡萄性染色体起源的新模型。这一接近完整的参考基因组也将有利于未来爬行动物进化的研究。

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来源期刊

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.