Scott Edmunds

<figure class="wp-block-image size-large is-resized is-style-default">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/eggblog_sex_chr-1024x746.jpg"
class="wp-image-3737" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/eggblog_sex_chr-1024x746.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/eggblog_sex_chr-300x219.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/eggblog_sex_chr-768x559.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/eggblog_sex_chr-1536x1119.jpg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/eggblog_sex_chr-2048x1492.jpg 2048w"
sizes="(max-width: 768px) 100vw, 768px" width="768" height="560"
alt="sex chromosome duck genome" />
</figure>

Today is a big day for the genomics of egg-laying animals, with the
coordinated publication of three papers on animal sex chromosome
evolution and diversity in *GigaScience*, *Nature*, and *Genome
Research* by the Qi Zhou lab at Zhejiang University. Also co-lead by
Frank Grutzner from Adelaide and *GigaScience* [Editorial Board
Member](https://academic.oup.com/gigascience/pages/Editorial_Board)
Guojie Zhang of Copenhagen University, this collection of studies
includes two chromosome-level monotreme genomes (platypus and echidna)
[in *Nature*](https://doi.org/10.1038/s41586-020-03039-0), and two
chromosome scale bird genomes for the Pekin Duck in
*[GigaScience](https://academic.oup.com/gigascience/article/10/1/giaa142/6039068?searchresult=1)*
and Emu in *[Genome Research](http://dx.doi.org/10.1101/gr.271569.120)*.
These three works systematically depict the dazzling diversity of animal
sex chromosomes, and use Hi-C technology to gain new insight into the
origin and evolution of sex chromosomes at the level of the
three-dimensional genome.

**New advances in genomics finally fit the bill** 
Monotremes are unusual species which display a unique mix of mammalian
and reptilian features and form the most distantly related group of
living mammals. While the some of these species may have a superficial
resemblance in the way they look and lay eggs, it is a fun coincidence
that the duck and duck-billed platypus both join the chromosome-scale
genome club on the same day. This work discovering other characteristics
of birds, with monotremes found to express one of the three
*vitellogenin* genes which encode the major egg proteins responsible for
making the yolk in chicken, while these genes have become lost in other
mammals. On top of these fascinating physical traits, monotremes and
birds are equally interesting models of sex-chromosome evolution, and
this has been the overlapping focus of these three new papers. Bringing
together the recent huge improvements in sequencing with new
computational methods specifically developed for this work, this has
allowed the researchers to obtain the highest quality chromosome-level
genome assemblies that now enable the resolution of these previously too
challenging-to-assemble sex chromosomes.

Monotremes have a complex sex chromosome system consisting of five pairs
of sex chromosomes, and their X chromosomes share no homology with
human's X-chromosome, having more in common with the avian Z-chromosome
(see more in [this
interview](https://natureecoevocommunity.nature.com/posts/embrace-cytogenetics-in-a-genomics-era-a-platypus-story)
with Qi Zhou talking about the Nature paper). Alongside characterizing
these in monotremes, for the first time the Z and W sex chromosomes have
also been assembled in the duck, discovering they have more than twice
the number of W-chromosome genes than the chicken. As with monotremes,
bird genomes can have some very interesting characteristics from an
evolutionary perspective, with some of them even demonstrating fusions
between autosomal and sex chromosome elements. In 2019 we published an
example of this mechanism of sex-determination and speciation, [via a
paper](https://doi.org/10.1093/gigascience/giz111) that discovered novel
neo-sex chromosomes in the eastern yellow robin (see
[GigaBlog](http://gigasciencejournal.com/blog/robin-sex-chromosomes/)).

Looking deeper at the work in our [new *GigaScience*
paper](https://academic.oup.com/gigascience/article/10/1/giaa142/6039068?searchresult=1),
Pekin duck on top of being one of the most commercially important
poultry species, has a higher tolerance to avian influenza than chicken.
Making it also an important model organism for the study of virus
transmission and control. From the perspective of evolutionary biology,
Pekin duck, chicken, goose, quail and other poultry form the
Gallonanserae Superorder, which is one of the three major branches of
modern birds. Obtaining a high-quality duck genome at chromosome level
therefore is of great significance for studying the domestication of
poultry and filling an important gap in resolving phylogeny of
vertebrates and birds in projects such as the [VGP (Vertebrate Genome
Project)](https://vgp.github.io/) and [B10K](https://b10k.genomics.cn/)
(Bird 10,000 Genomes project, as we've covered [here
before](http://gigasciencejournal.com/blog/sequencing-order-b10k-reaching-skies-decode-bird-genomes/)).

::: {.wp-block-image}
<figure class="aligncenter size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/robert-woeger-w3xQ2pM6Pwg-unsplash1-1024x683.jpg"
class="wp-image-3731" loading="lazy" decoding="async" width="600"
height="342" alt="duck genome breed" />
</figure>
:::

**Duck genome tales** 
In 2013 researchers at our co-publishers BGI [published the first
draft](https://doi.org/10.1038/ng.2657) of the Pekin duck genome.
However, due to the lack of genetic map and usage of short reads, most
of the genome sequences and genes in the draft, especially the highly
repetitive sex chromosome sequence, were in a state of fragmentation,
Meaning the exact chromosomal position was not clear. This new update
uses third generation pacbio long reading sequencing technology,
combined with the state-of-the-art 10x, Bionano and Hi-C chromatin
conformation capture technology to assemble and annotate the new
reference genome, and located more than 95% of the sequences to specific
chromosome positions. The [new genome](http://doi.org/10.5524/100831)
(named ZJU1.0) has achieved a 60-fold increase in N50 continuity (76.3MB
vs. 1.2MB) compared with the previously published version released in
[GigaDB (BGI1.0)](http://dx.doi.org/10.5524/101001), and also corrected
the incomplete and incorrect annotations caused by repetitive sequences.

**Avian genomes soar into the third dimension** 
The new Pekin duck and emu genomes are among the first of a new
generation of high-quality avian genomes assembled at chromosome level.
With assembly quality of these genomes equal to or better than that of
the most studied avian models of chicken and zebrafinch. Furthermore,
through the comparative analysis of 3D genome data, the researchers
divided the 3D spatially associated domain (TAD) of Pekin duck, and
found that most of the regulatory domains were highly conserved between
chicken and duck, reflecting the strong selection effect of natural
selection on regulatory domains. Although there were a lot of
rearrangements between chicken and duck genomes, these rearrangements
tended not to destroy the internal structure of these regulatory
domains.

**The evolution of duck sex** 
Importantly this work marks the first publication of the Z and W sex
chromosome sequences of the duck. Previous studies have shown that genes
related to sex traits, such as egg laying traits, tend to be enriched on
sex chromosomes. Therefore, these newly published sequences will provide
important references for the domestication of sex related traits in
Pekin duck. In addition, the number of W chromosome genes in Peking duck
is more than twice that in chicken. Studying the function these female
specific genes in the Peking duck will also be a very important research
directions in the future.

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/giaa142fig5-1024x302.jpg"
class="wp-image-3734" loading="lazy" decoding="async"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/giaa142fig5-1024x302.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/giaa142fig5-300x89.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/giaa142fig5-768x227.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/giaa142fig5-1536x454.jpg 1536w, http://gigasciencejournal.com/blog/wp-content/uploads/2021/01/giaa142fig5.jpg 1581w"
sizes="(max-width: 768px) 100vw, 768px" width="768" height="227"
alt="duck genome and sex chromosome evolution" />
<figcaption>Evolutionary strata analyses of the duck sex
chromosomes</figcaption>
</figure>

These unique evolutionary characteristics of the duck may be related to
the early differentiation of bird species, so their sex chromosomes have
independent evolutionary history. Being big fans of bird genomes, and
being involved in the [coordinated publication of the Avian Phylogenomic
Project](http://gigasciencejournal.com/blog/sequencing-order-b10k-reaching-skies-decode-bird-genomes/)
genomes it is great to see another one take flight. With the coordinated
publications today being another milestone in the study of vertebrate
genomes and sex chromosome evolution.

## References {#references .wp-block-heading}

Li J et al., A new duck genome reveals conserved and convergently
evolved chromosome architectures of birds and mammals. *GigaScience*,
[doi:10.1093/gigascience/giaa142](https://doi.org/10.1093/gigascience/giaa142)

Liu J et al., A new emu genome illuminates the evolution of genome
configuration and nuclear architecture of avian chromosomes. *Genome
Res.* 2021.
[doi:10.1101/gr.271569.120](http://dx.doi.org/10.1101/gr.271569.120)

Zhou, Y., et al. Platypus and echidna genomes reveal mammalian biology
and evolution. Nature (2021).
[doi:10.1038/s41586-020-03039-0](https://doi.org/10.1038/s41586-020-03039-0)

The post [Cracking sex chromosome evolution via egg-laying birds and
mammals](http://gigasciencejournal.com/blog/sex-chromosome-evolution/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

Platypus and echidna genomes reveal mammalian biology and evolution

Today is a big day for the genomics of egg-laying animals, with the coordinated publication of three papers on animal sex chromosome evolution and diversity in

 GigaScience

,

 Nature

, and

 Genome Research

by the Qi Zhou lab at Zhejiang University.

Cracking sex chromosome evolution via egg-laying birds and mammals

*![Penguin
genomes](http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/GentooPenguins-Antartica-LGoodman-Small-240x300.jpg){.alignright
.wp-image-3080 loading="lazy" decoding="async" width="266" height="333"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/GentooPenguins-Antartica-LGoodman-Small-240x300.jpg 240w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/GentooPenguins-Antartica-LGoodman-Small-768x960.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/GentooPenguins-Antartica-LGoodman-Small-819x1024.jpg 819w"
sizes="(max-width: 266px) 100vw, 266px"}The Penguin Genome Consortium
sequences all living penguin species genomes to understand the evolution
of life on the ice.*

[Published today in
*GigaScience*](https://academic.oup.com/gigascience/article/8/9/giz117/5571031?searchresult=1)
is an article that presents the first effort to capture the entirety of
the genomic landscape of all living penguin species. The Penguin Genome
Consortium ---bringing together researchers from China, Denmark, New
Zealand, Australia, Argentina, South Africa, the UK, the US, France and
Germany--- has produced 19 high-coverage penguin genome sequences that,
together with two genomes [previously published in
*GigaScience*](https://doi.org/10.1186/2047-217X-3-27), encompass all
surviving penguin species. This extensive study provides an unparalleled
amount of information that covers an entire biological order. Completing
a useful chunk of the [B10K Avian
Genomes](http://gigasciencejournal.com/blog/sequencing-order-b10k-reaching-skies-decode-bird-genomes/),
and which will promote research in a wide variety of areas from
evolution to the impact of human activities and environmental changes.

Penguins ([Sphenisciformes](https://en.wikipedia.org/wiki/Penguin)) are
a diverse order of species that span the Southern hemisphere, ranging
from the Galápagos Islands on the equator, to the oceanic temperate
forests of New Zealand, to the rocky coastlines of the sub-Antarctic
islands, finally reaching the sea-ice around Antarctica. This iconic
bird group have transitioned from flying seabirds to powerful,
flightless marine divers. With their specialized skin and feathers and
an enhanced thermoregulation system they are able to inhabit
environments from the extreme cold Antarctic sea ice to the tropical
Galápagos Islands.

::: {#attachment_3083 .wp-caption .aligncenter style="width: 691px"}
![Penguin
genomes](http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-1_small-1024x753.jpg){.wp-image-3083
loading="lazy" decoding="async"
aria-describedby="caption-attachment-3083" width="681" height="501"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-1_small-1024x753.jpg 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-1_small-300x221.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-1_small-768x565.jpg 768w"
sizes="(max-width: 681px) 100vw, 681px"}

Penguin planet: the 20 extant species featured in this study (taken from
figure 1 of the paper).
:::

These birds also serve as the figurative "canary in a coal mine";
warning of environmental and climate change. Many penguin populations
have experienced rapid declines in recent decades, some having extreme
population drops, such as the crash of the King penguin population,
which has declined by 88% in just 3 decades. And more penguin species
are predicted to decline in the near future. The dwindling populations
have been linked to climate warming, environmental degradation,
exploitation of the marine environment, fisheries bycatch, pollution,
and the introduction of exotic predators. Penguins have thus become the
focus of many ecosystem monitoring studies. Having high-quality genomes
sequences of all extant penguin species serves as an outstanding new
resource for understanding the specific reasons for species population
loss.

![Penguin
genome](http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/ChinstrapOnTheRocks-small-300x236.jpg){.wp-image-3082
.alignright loading="lazy" decoding="async" width="462" height="363"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/ChinstrapOnTheRocks-small-300x236.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/ChinstrapOnTheRocks-small-768x605.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/ChinstrapOnTheRocks-small-1024x807.jpg 1024w"
sizes="(max-width: 462px) 100vw, 462px"}Author Theresa Cole from the
University of Otago in New Zealand says of this work: "The population
history of different penguin species can be seen in their genome. We
will provide new insights into the population history of all penguins
over dramatic climate events, to predict population trends under future
climate change scenarios. This research will help us understand how
future climate change may affect other species, to help us develop
conservation strategies."

As with the work done on Darwin's finches, studying the radiation of the
20 penguin species provides similar enlightening case study for
researching unique penguin morphological and physiological adaptations.
The consortium are also sequencing the genomes of recently extinct
penguin taxa, as well as undertaking population genomic studies using
multiple genomes per species.

Senior author Guojie Zhang from the University of Copenhagen, BGI, and
Kunming Institute of Zoology says of this: "The penguin ancestor
experienced rapid radiation leading to the current approximate 20 extant
species, accompanied by many ancient lineages that are now extinct. The
radiation of penguin thus provides an excellent example for the study of
speciation."

There were logistical challenges to get hold of high-quality specimens
for all of these species as many come from some of the most inhospitable
and far-flung corners of the globe. However, an additional challenge was
cultural rather than technical. The process by which this consortium
handled these sensitive issues serves as a model for building trust and
collaboration with cultures that have equally important links to other
native species.

Co-author Bruce McKinlay from the New Zealand Department of Conservation
highlights this, saying: "Genome research in New Zealand is currently
moving into novel cultural contexts, especially for penguins, which are
Taonga or treasured possessions in Māori culture. As such, our
consortium have undertaken rigorous indigenous consultation to sequence
the genomes from six New Zealand Taonga species. We believe these
genomes will be important for a cultural context."

::: {#attachment_3081 .wp-caption .alignleft style="width: 315px"}
![Penguin
genome](http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-3-300x170.png){.wp-image-3081
loading="lazy" decoding="async"
aria-describedby="caption-attachment-3081" width="305" height="173"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-3-300x170.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-3-768x436.png 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Penguin-Paper-Figure-3.png 939w"
sizes="(max-width: 305px) 100vw, 305px"}

The penguin family tree taken from the paper.
:::

The goal of the first stage of the Penguin Genome Consortium project was
purely to sequence high-quality genomes, but initial validation studies
have demonstrated these genomes are already producing valuable insight
into evolutionary history of the penguin tree of life and the
evolutionary patterns of their adaptation to Antarctica. For example, an
initial phylogenetic tree presented in this study demonstrates that
penguins have adapted to Antarctica on multiple occasions.

This and further comparative and evolutionary genomic analyses are
currently being carried out, and the penguin genome consortium welcomes
new members interested in joining the open consortium and contributing
to this work. While this work is still underway early access to the 19
penguin genomes data has been provided, while the researchers ask groups
intending to use this data for similar cross-species comparisons to
follow the long running
[Bermuda](https://doi.org/10.1093/gigascience/giw003), [Fort
Lauderdale](https://www.genome.gov/10506537/reaffirmation-and-extension-of-nhgri-rapid-data-release-policies)
and [Toronto](https://www.nature.com/articles/461168a) rules. All of the
individual Penguin genomes are available from GigaDB, and are linked to
a [top-level DOI](http://dx.doi.org/10.5524/100649) cited in the paper.
As with the related [Avian Phylogenomic Project
genomes](http://dx.doi.org/10.1186/2047-217X-3-26) we published in 2014,
we've been [releasing the genomes via our
twitter](http://gigasciencejournal.com/blog/a-flock-of-bird-data-comes-to-roost/)
feed to get a high-flying response from the genomics community.

### **References**

Pan et al. High-coverage genomes to elucidate the evolution of penguins.
2019. *GigaScience* doi:
[[http://dx.doi.org/10.1093/gigascience/giz117](https://academic.oup.com/gigascience/article/8/9/giz117/5571031?searchresult=1)]{.underline}

Li et al. Two Antarctic penguin genomes reveal insights into their
evolutionary history and molecular changes related to the Antarctic
environment. *Gigascience*. 2014 Dec 12;3(1):27. doi:
[10.1186/2047-217X-3-27.](https://doi.org/10.1186/2047-217X-3-27)

The post [March of the Multiple Penguin
Genomes](http://gigasciencejournal.com/blog/penguin-genome/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


The Penguin Genome Consortium sequences all living penguin species genomes to understand the evolution of life on the ice.

Published today in

 GigaScience

is an article that presents the first effort to capture the entirety of the genomic landscape of all living penguin species.

March of the Multiple Penguin Genomes

Hans Zauner

::: {#attachment_3045 .wp-caption .alignleft style="width: 195px"}
![Robin sex
chromsomes](http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/EYRPaulsPainting-216x300.jpg){.wp-image-3045
loading="lazy" decoding="async"
aria-describedby="caption-attachment-3045" width="185" height="257"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/EYRPaulsPainting-216x300.jpg 216w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/EYRPaulsPainting.jpg 482w"
sizes="(max-width: 185px) 100vw, 185px"}

*Painting of the Eastern Yellow Robin by Prof Paul Sunnucks.*
:::

**[Today in *Gigascience*](https://doi.org/10.1093/gigascience/giz111)
we published an avian genome assembly with a twist. An Australian team
at Monash University discovered unusual, so-called neo-sex chromosomes
in the genome of the Eastern Yellow Robin. Being big fans of bird
genomes (see our [support of the Avian Phylogenomic and B10K
projects](http://gigasciencejournal.com/blog/sequencing-order-b10k-reaching-skies-decode-bird-genomes/))
it is great to see another one take flight. The surprise finding and the
new genome assembly will help the researchers to better understand  the
genetics of ongoing speciation processes, also involving co-adaption
between the mitochondrial and nuclear genomes.**

If you are a birder and wish to spot an Eastern Yellow Robin
(*Eopsaltria australis*) you have to travel to Australia, where you'll
find the bird around coastal areas in the east of the continent. Just
watch out for a little fellow with a distinctive yellow breast.

::: {#attachment_3044 .wp-caption .alignright style="width: 310px"}
![Bird sex
chromosomes](http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Distributionmap-300x234.jpg){.wp-image-3044
.size-medium loading="lazy" decoding="async"
aria-describedby="caption-attachment-3044" width="300" height="234"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Distributionmap-300x234.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/Distributionmap.jpg 661w"
sizes="(max-width: 300px) 100vw, 300px"}

*Map illustrating mito-nuclear discordance (adapted from Fig. 1 of
Morales et al, 2017)*.
:::

The [*Persistence and Adaptation Research
Team* ](https://sites.google.com/site/sunnucksresearchgroup/home) (PART)
at Monash University have chosen the Eastern Yellow Robin as a model and
decided to sequence its genome. "Our research group focuses on applying
evolutionary concepts to wildlife management to improve the persistence
of populations, including how organisms adapt to their environment",
Professor Paul Sunnucks, one of the study's authors, explains. One major
reason why the Eastern Yellow Robin is a particularly interesting system
to study evolutionary processes: The species may be in the process of
splitting into two, allowing the scientists to get a glimpse of a
speciation event as it happens. A smoking gun are peculiar genetic
findings that the PART team have discovered over the course of the last
couple of years.  The previous research showed that there are two
genetically distinct lineages of the bird, separated by a mountain
range. These two lineages live in different areas with distinct
climates: The birds at the coast live in temperate conditions, whereas
it is dry inland.

**Occasional encounters 
**Some members of the two lineages do come into contact sometimes and
even interbreed. However, depending on which genetic markers the
scientists look at, they get a different genetic picture of these
encounters, as the PART researchers explain on their [project home
page](https://sites.google.com/monash.edu/eyr):

The mitochondrial genome, which is exclusively inherited by the mother,
seems to indicate that there is virtually no gene flow between the two
Yellow Robin lineages. However, analyses of nuclear genes reveal that
they do mix at least occasionally. The straightforward interpretation is
that males and females apparently behave differently in this species.

However, the difference between mitochondrial and nuclear genomes is not
so clear-cut, says Dr Alexandra Pavlova:

> "A subset of a nuclear genome, mapping to chromosome 1A of Zebra Finch
> and enriched for genes with functions in the mitochondria, appears to
> have been co-evolved and co-inherited together with the mitochondrial
> genome. This makes the Eastern Yellow Robin an emerging model for
> fascinating evolutionary processes related to evolutionary
> interactions between the mitochondrial and nuclear genomes."

The [993 Mb genome assembly that the authors now present in
*GigaScience*](https://academic.oup.com/gigascience/article/8/9/giz111/5559526?searchresult=1)
(and open data released in our repository GigaDB,
[here](http://dx.doi.org/10.5524/100639)) was achieved by combining
Illumina and Nanopore data.

**Surprising sex chromosomes** 
Various analyses, including the anchoring of segments to the published
zebra finch genome combined with read depth estimation and k-mer
analyses, provided evidence for the presence of neo-sex chromosomes that
involve large parts of Chromosome 1A. Professor Sunnucks says:

> "We had suspected some sort of chromosome reorganization, but the fact
> that it turned out to be neo-sex chromosomes was a complete surprise!
> Neo-sex chromosomes are newly-created or augmented sex chromosomes.
> They can arise by a range of mechanisms including the emergence of
> novel sex-determining genes, as well as many different patterns of
> chromosomal rearrangements, notably fusions between autosomes and sex
> chromosomes."

How exactly the previously autosomal regions turned into neo-sex
chromosomes is not clear yet, but the authors write in the paper that
one relatively simple model is that one copy of chromosome 1A fused with
the W chromosome, and the second copy of chromosome 1A became inherited
in a neo-Z fashion.

::: {#attachment_3043 .wp-caption .alignright style="width: 310px"}
![Robin sex
chromosomes](http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/EYRChrisTsaros.jpg){.wp-image-3043
loading="lazy" decoding="async"
aria-describedby="caption-attachment-3043" width="300" height="321"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/EYRChrisTsaros.jpg 695w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/09/EYRChrisTsaros-280x300.jpg 280w"
sizes="(max-width: 300px) 100vw, 300px"}

*Photo by Chris Tzaros*
:::

Prof. Sunnucks puts the findings in context:

> "Most sex chromosomes are many tens of millions of years old, by which
> time it is difficult to observe sex chromosome evolution in action.
> The neo-sex part of the Eastern Yellow Robin genome is very large and
> so probably quite recent (we will try to quantify that): it should be
> subject to ongoing sex-chromosome evolution, including of dispensable
> genes and some that might be critically important."

The PART collaboration has come a long way already with this genome
project, Alexandra Pavlova recalls:

> "The Eastern Yellow Robin project started at Monash University with
> the publication of the first Eastern Yellow Robin paper in Evolution
> ([Pavlova et al.
> 2013](https://onlinelibrary.wiley.com/doi/full/10.1111/evo.12107)). In
> that paper we demonstrated mito-nuclear discordance, ruled out neutral
> reasons for this pattern and concluded that sex-specific selection
> must be operating in this species."

**A problem: Most available bird genomes are from males** 
One of the difficulties the authors had to deal with during this genome
project was that the majority of available bird genomes are those of
male birds, says first author Dr Han Ming Gan (who is now at Deakin
University), adding that the female-specific chromosome is a
particularly difficult region to work with:

> "Because the W chromosome is not recombining, it rapidly accumulates
> repetitive material and deleterious mutations, presenting special
> challenges for genome assembly. "

Another coauthor, Hernán Morales, points out why the neo-sex chromosomes
of the Eastern Yellow Robin are quite unique, and how the finding fits
into the larger picture of co-adaptive processes in this species:

> "Among the few known bird neo-sex chromosomes, the Eastern Yellow
> Robin one is unique in involving chromosome 1A with its unparalleled
> concentration of nuclear genes with mitochondrial function. This is
> particularly alluring because in birds, females are heterogametic as
> well as the source of mitochondrial DNA, so the female-only neo-sex
> chromosome will always be coinherited with the mitochondrial genome
> from mother to daughter to granddaughter and so on, providing for
> possible intense mitochondrial-nuclear coadaptation."

As usual,  with a  genome assembly in hand, the work is not done, but
opens the path for new research. Dr Pavlova outlines some of the future
plans:

> "This includes chromosome-level genome assembly, in-depth work testing
> whether mitolineages or hybridization impact bird respiration and
> metabolism, monumental efforts to estimate the fitness in the wild of
> birds with different genome compositions, and comparative genomics to
> understand the evolution of neo-sex chromosomes in the Eastern Yellow
> Robin and its relatives in the Australian Robin family Petroicidae and
> beyond."

At *GigaScience*, we are big fans of bird genomes  -- for example,
during our last ICG prize track, Stefan Prost from the Senckenberg
Museum in Frankfurt (Germany) [presented a genomic study on five
birds-of-paradise
species ](http://gigasciencejournal.com/blog/birds-of-paradise-genomes/)which
also revealed interesting evolutionary  insights (see Stefan's talk
[here](https://www.youtube.com/watch?v=ULiT2kJkquA)). We are excited how
genomics contributes to our understanding of bird evolution.

### **References**

***Gigascience* article: 
**Han Ming Gan, Stephanie Falk, Hernán E Morales, Christopher M Austin,
Paul Sunnucks, Alexandra Pavlova. Genomic evidence of neo-sex
chromosomes in the eastern yellow robin, *GigaScience* 2019. giz111,
<https://doi.org/10.1093/gigascience/giz111>

**Supporting data: 
**Gan HM; Falk S; Morales HE; Austin CM; Sunnucks P; Pavlova A (2019):
Supporting data for "Genomic evidence of neo-sex chromosomes in the
Eastern Yellow Robin" GigaScience Database.
http://dx.doi.org/10.5524/100639

Pavlova, A., J. N. Amos, L. Joseph, K. Loynes, J. J. Austin, J. S.
Keogh, G. Stone, J. A. Nicholls, and P. Sunnucks. 2013. Perched at the
mito-nuclear crossroads: divergent mitochondrial lineages correlate with
environment in the face of ongoing nuclear gene flow in an Australian
bird. Evolution 67:3412--3428.

Morales, H., A. Pavlova, L. Joseph, and P. Sunnucks. 2015. Positive and
purifying selection in mitochondrial genomes of a bird with mitonuclear
discordance. Molecular Ecology **24**:2820--2837.

Morales, H., P. Sunnucks, L. Joseph, and A. Pavlova. 2017. Perpendicular
axes of differentiation generated by mitochondrial introgression.
Molecular Ecology **26**:3241--3255.

Morales, H. E., A. Pavlova, P. Sunnucks, R. Major, J. N. Amos, L.
Joseph, A. R. Lemmon, J. A. Endler, and K. Delhey. 2017. Neutral and
selective drivers of colour evolution in a widespread Australian
passerine. Journal of Biogeography **44**:522--536.

Sunnucks, P., H. E. Morales, A. M. Lamb, A. Pavlova, and C. Greening.
2017. Integrative approaches for studying mitochondrial and nuclear
genome co-evolution in oxidative phosphorylation. Frontiers in Genetics
8:25.

Morales, H. E., A. Pavlova, N. Amos, R. Major, A. Killian, C. Greening,
and P. Sunnucks. 2018. Concordant divergence of mitogenomes and a
mitonuclear gene cluster in bird lineages inhabiting different climates.
Nature Ecology and Evolution **2**:1258--1267.

Lamb, A. M., H. M. Gan, C. Greening, L. Joseph, Y. P. Lee, A.
Morán-Ordóñez, P. Sunnucks, and A. Pavlova. 2018. Climate-driven
mitochondrial selection: a test in Australian songbirds. Molecular
Ecology **27**:898--918.

The post [Sequencing The Eastern Yellow Robin: Sex chromosomes with a
twist](http://gigasciencejournal.com/blog/robin-sex-chromosomes/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.

Painting of the Eastern Yellow Robin by Prof Paul Sunnucks.


 Today in
 
 Gigascience
 
 we published an avian genome assembly with a twist. An Australian team at Monash University discovered unusual, so-called neo-sex chromosomes in the genome of the Eastern Yellow Robin. Being big fans of bird genomes (see our support of the Avian Phylogenomic and B10K projects) it is great to see another one take flight.

Messaggi di Rogue Scholar

Cracking sex chromosome evolution via egg-laying birds and mammals

March of the Multiple Penguin Genomes

Sequencing The Eastern Yellow Robin: Sex chromosomes with a twist