Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes

Yang Zhou; Jiazheng Jin; Xuemei Li; Gregory Gedman; Sarah Pelan; Arang Rhie; Chuan Jiang; Olivier Fedrigo; Kerstin Howe; Adam M Phillippy; Erich D Jarvis; Frank Grutzner; Qi Zhou; Guojie Zhang

doi:10.1093/gigascience/giae112

Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes

Gigascience. 2025 Jan 6:14:giae112. doi: 10.1093/gigascience/giae112.

Authors

Yang Zhou^{1

2

3}, Jiazheng Jin², Xuemei Li⁴, Gregory Gedman⁵, Sarah Pelan⁶, Arang Rhie⁷, Chuan Jiang⁸, Olivier Fedrigo⁹, Kerstin Howe⁶, Adam M Phillippy⁷, Erich D Jarvis^{5

10}, Frank Grutzner¹¹, Qi Zhou^{12

13

14}, Guojie Zhang^{14

15

16}

Affiliations

¹ State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen 518083, China.
² BGI Research, Wuhan 430074, China.
³ BGI Research, Hangzhou 310030, China.
⁴ College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
⁵ Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
⁶ Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK.
⁷ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
⁸ College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
⁹ The Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.
¹⁰ Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
¹¹ School of Biological Sciences, The Environment Institute, The University of Adelaide, Adelaide 5005, Australia.
¹² The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
¹³ Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Hangzhou 310052, China.
¹⁴ Centre for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
¹⁵ Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China.
¹⁶ Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.

PMID: 39778707
DOI: 10.1093/gigascience/giae112

Abstract

Background: 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.

Results: 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.

Conclusion: The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.

Keywords: echidna; monotreme; multiple sex chromosomes; sex chromosome evolution.

MeSH terms

Animals
Evolution, Molecular*
Female
Genome
Male
Phylogeny
Sex Chromosomes* / genetics
Tachyglossidae* / genetics

Abstract

MeSH terms

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