Patel Hardip R, Alreja Kirat, Reis Andre L M, Chang J King, Chew Zahra A, Jung Hyungtaek, Hammond Jillian M, Deveson Ira W, Ruiz-Herrera Aurora, Marin-Gual Laia, Holleley Clare E, Zhang Xiuwen, Lister Nicholas C, Whiteley Sarah, Xiong Lei, Dissanayake Duminda S B, Waters Paul D, Georges Arthur
National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia.
Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giaf085.
The central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated near telomere-to-telomere phased assembly of the genome of a female ZW central bearded dragon.
Genome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps, and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single-copy BUSCO genes, and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model ribosomal DNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome. This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudo-autosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies, and their resultant transcription factors and intermediaries determine sex in the bearded dragon.
This high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally.
中部鬃狮蜥（Pogona vitticeps）广泛分布于澳大利亚中东部，易于圈养。它具有诸多特性，其中特别之处在于，在较高孵化温度下，其基因型为ZZ的雄性会发生性反转，转变为表型雌性。在此，我们报告了一只雌性ZW中部鬃狮蜥基因组的一份注释后的近端粒到端粒的分阶段组装结果。
基因组组装长度为1.75 Gbp，支架N50为266.2 Mbp，N90为28.1 Mbp，有26个缺口，GC含量为42.2%。大部分（99.6%）的参考组装被构建成6条大染色体和10条小染色体，包括Z和W小染色体，与核型相对应。该基因组组装超过了地球生物基因组计划（6CQ40）推荐的标准：0.003%的折叠序列、0.03%的错误扩展、99.8%的k-mer完整性、97.9%的完整单拷贝BUSCO基因，以及平均93.5%的转录组数据可映射回基因组组装。线粒体基因组（16,731 bp）和模型核糖体DNA重复单元（长度9.5 Kbp）被组装出来。雄性脊椎动物性别基因Amh和Amhr2在Z染色体的小非重组区域被发现有拷贝，而W染色体上没有。这一点，再加上之前发现的由假常染色体性别基因Nr5a1导致的Z和W转录异构体组成差异，表明这些基因、它们的常染色体拷贝以及它们产生的转录因子和中间产物之间的复杂相互作用决定了鬃狮蜥的性别。
这种高质量的组装将作为一种资源，有助于并加速对该物种异常生殖特性的研究，以及更广泛地用于鬣蜥科和爬行动物的比较研究。
