Hans Zauner

**This week we published a new, high-quality genome sequence of one of
Australia's most iconic animals, the short beaked echidna. The almost
gapless [genome sequence of this egg-laying
mammal](https://doi.org/10.1093/gigascience/giae112) helps researchers
to track genomic reshuffling events that gave rise to a perplexing  sex
determination system.**

At first glance they may be mistaken for a weird-looking hedgehog.
However, the short-beaked echidna (*Tachyglossus aculeatus*) belongs to
a unique group of egg-laying mammals called "monotremes" (with the
platypus as the other prominent member). The international team of
authors that embarked on this project include Guojie Zhang  and Qi Zhou
at the [Centre for Evolutionary & Organismal Biology at Zhejiang
University](https://evolution.zju.edu.cn/en/index.html), Yang Zhou from
BGI-Research and Frank Grutzner from Adelaide University. The work is
part of the international [Vertebrate Genome
Project](https://vertebrategenomesproject.org/), and hosted in the [VGP
Genome Ark Database](https://www.genomeark.org/).

::: {#attachment_5984 .wp-caption .aligncenter style="width: 334px"}
![short beaked echidna (photo by Allan Whittome,
cc0)](http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/Low-Res_Echidna_burningwell-CC0-300x225.jpg){.wp-image-5984
fetchpriority="high" decoding="async"
aria-describedby="caption-attachment-5984" width="324" height="243"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/Low-Res_Echidna_burningwell-CC0-300x225.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/Low-Res_Echidna_burningwell-CC0.jpg 700w"
sizes="(max-width: 324px) 100vw, 324px"}

The short-beaked echidna (Tachyglossus aculeatus)
:::

Among other unusual features (egg-laying mammals -- ***helllooo???***),
the unique position of monotremes in the tree of life is also reflected
in their genomes, and in particular in the way sex is determined
genetically. In most sex determination systems, sex chromosomes
typically come as a pair, such as in the familiar X/Y system in humans
and in most other mammals. In this familiar setup, sperm carry either an
X or a Y chromosome. Together with the X chromosome that the egg
contributes, females typically have two X chromosomes, and males one X
and one Y.

### Sex chromosomes galore

In contrast, the situation is far more complex in monotremes, featuring
multiple X and Y chromosomes. As if this was not complicated enough
already, there are also differences between the two monotreme groups,
differentiating echidnas and the platypus. In male echidna there are
nine sex chromosomes, in platypus even ten (five X and five Y in male
platypus, and five X but only four Y chromosomes in male echidna). How
on earth is genetic disaster avoided during meiosis, when sex
chromosomes need to be passed on to egg and sperm cells? The trick is
that these sex chromosomes [pair in a head-to-tail manner and form
chains](https://doi.org/10.1186/gb-2007-8-11-r243). This allows for them
to be distributed in an orderly manner to the germ cells.

::: {#attachment_5987 .wp-caption .aligncenter style="width: 310px"}
![Model for the sex chromosome evolution in
monotremes.](http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/model-300x148.jpg){.size-medium
.wp-image-5987 decoding="async"
aria-describedby="caption-attachment-5987" width="300" height="148"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/model-300x148.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/model-1024x505.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/model-768x378.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/model.jpg 1455w"
sizes="(max-width: 300px) 100vw, 300px"}

Model for the sex chromosome evolution in monotremes. (from Zhou et al,
CC-BY)
:::

The details of this process, and the intriguing question of how and why
this complicated system originated in the first place, is still under
investigation. The new echidna genome sequence presented in GigaScience
helps to trace the genetic events that led to this remarkable
chromosomal arrangement. [A previous version of an echidna
genome](https://doi.org/10.1038/s41586-020-03039-0) has been published
before, but the new high quality sequence with very few gaps allows
researchers to infer events like chromosomal rearrangements in the
ancestry line of monotremes.

Zhang says:

*"The high quality reference genome of echidna allows us to infer which
chromosomes are shared between echidna and platypus since they diverged
from other mammals and which were newly evolved more recently after the
two monotreme split".*

### The origins of the echidna sex chromosomes

The evolutionary lineages of echidnas and platypus have diverged around
55 million years ago and there is evidence that chromosome fusion or
fission events might have occurred since the divergence of platypus and
echidna. Using both the new echidna and an existing platypus genome
sequence, the GigaScience authors reconstructed the likely chromosome
composition of the monotreme ancestor, using also chromosomal assemblies
of placentals (human, bovine and sloth), marsupials (opossum and
Tasmanian devil), and reptilian outgroups (chicken, turtle and common
wall lizard).

Analysis of the sex chromosomes revealed that the ancestral X chromosome
of monotremes had exchanged segments with ancestral non-sex chromosomes
(autosomes), which gave rise to the complex system.

::: {#attachment_5986 .wp-caption .aligncenter style="width: 310px"}
![Figure 2 of Zhou et al
(cc-BY)](http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/Fig2-300x193.jpg){.wp-image-5986
.size-medium decoding="async" aria-describedby="caption-attachment-5986"
width="300" height="193"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/Fig2-300x193.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/Fig2-768x493.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2025/01/Fig2.jpg 874w"
sizes="(max-width: 300px) 100vw, 300px"}

Karyotype evolution in monotremes. Figure 2 of Zhou et al (cc-BY)
:::

### Gene family expansion

In addition to these structural changes in genome organisation, the
authors also found signals of gene family expansion, meaning that
additional copies of specific genes arose during the evolution of
monotremes. One such event concerns a gene called SYCP3Y. This gene
encodes a component of the synaptonemal complex, which is a protein
structure that connects chromosome pairs during meiosis. SYCP3Y is
duplicated from autosomes and expanded in both platypus and echidna,
suggesting that the gene expansion may be associated with the evolution
of the sex chromosome complex or play a role in its organization.

Overall, the new results provide a detailed evolutionary history of the
highly unusual multiple sex chromosome system in monotremes and
demonstrate how today's high-resolution genomic methods can uncover
evolutionary events that shaped the mammalian tree of life millions of
years ago.

**Share the press release:**

<https://www.eurekalert.org/news-releases/1069499>

### References:

Zhou Y et al., Chromosome-level echidna genome illuminates evolution of
multiple-sex-chromosome system in monotremes. GigaScience. 2025.
<https://doi.org/10.1093/gigascience/giae112>

Data in GigaDB: Zhou Y, Jin J, Li X, et al. Supporting data for
"Chromosome-Level Echidna Genome Illuminates Evolution of Multiple Sex
Chromosome System in Monotremes.". GigaScience Database 2024.
<https://doi.org/10.5524/102609>

Rhie, A., McCarthy, S.A., Fedrigo, O. et al. Towards complete and
error-free genome assemblies of all vertebrate species. Nature 592,
737--746 (2021). <https://doi.org/10.1038/s41586-021-03451-0>

Kerstin Howe, William Chow, Joanna Collins, Sarah Pelan, Damon-Lee
Pointon, Ying Sims, James Torrance, Alan Tracey, Jonathan Wood,
Significantly improving the quality of genome assemblies through
curation, GigaScience, Volume 10, Issue 1, January 2021, giaa153,
<https://doi.org/10.1093/gigascience/giaa153>

Sheri Sanders. DNA Day 2019: How to sequence the genomes of the weird
and wonderful. In
GigaBlog. [https://doi.org/10.59350/7×637-mb215](https://doi.org/10.59350/7x637-mb215){target="_blank"
rel="noopener"}

 

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Supporting data for "Chromosome-level echidna genome illuminates evolution of multiple-sex-chromosome system in monotremes"

Towards complete and error-free genome assemblies of all vertebrate species

Significantly improving the quality of genome assemblies through curation

DNA Day 2019: How to sequence the genomes of the weird and wonderful

<strong>
 This week we published a new, high-quality genome sequence of one of Australia’s most iconic animals, the short beaked echidna. The almost gapless genome sequence of this egg-laying mammal helps researchers to track genomic reshuffling events that gave rise to a perplexing  sex determination system.
</strong>
At first glance they may be mistaken for a weird-looking hedgehog.

Rogue Scholar Posts

Sex chromosome madness in the iconic echidna