Zhou Yang, Jin Jiazheng, Li Xuemei, Gedman Gregory, Pelan Sarah, Rhie Arang, Jiang Chuan, Fedrigo Olivier, Howe Kerstin, Phillippy Adam M, Jarvis Erich D, Grutzner Frank, Zhou Qi, Zhang Guojie
State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen 518083, China.
BGI Research, Wuhan 430074, China.
Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giae112.
A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology. However, they also exhibit rearrangements in several chromosomes, especially in the sex chromosome chain. Therefore, the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex.
Here, we present a new long reads-based chromosome-level short-beaked echidna (Tachyglossus aculeatus) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between 1 Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes.
The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.
对基因组进化进行全面分析是理解生物多样性的基础。标志性的单孔目动物（鸭嘴兽和针鼹）具有非凡的生物学特性。然而，它们在几条染色体上也表现出重排，尤其是在性染色体链中。因此，缺乏染色体水平的针鼹基因组限制了我们对单孔目动物基因组进化的深入了解，特别是对多性染色体复合体的了解。
在此，我们展示了一个基于长读长的新的染色体水平的短吻针鼹（Tachyglossus aculeatus）基因组，该基因组有助于推断单孔目祖先（2n = 64）和每个现存物种中的染色体重排。对更完整的性染色体的分析揭示了1条Y染色体与多条X染色体之间的同源性，这表明是祖先的X染色体与祖先的常染色体发生了相互易位，从而形成了该复合体。我们还在性染色体上鉴定出了数十个扩增基因，其中有几个祖先基因在雄性减数分裂期间表达，这表明在多性染色体配对过程中存在选择性限制。
新的针鼹基因组为进一步研究该物种独特的生物学特性和保护提供了重要依据。
