Scott Edmunds

![T2T
Series](http://gigasciencejournal.com/blog/wp-content/uploads/2024/08/t2t-instagram-square-300x300.png){.wp-image-5889
.aligncenter fetchpriority="high" decoding="async" width="638"
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*GigaScience's T2T Series has now
[launched](https://academic.oup.com/gigascience/pages/t2t-series-closing-the-gaps-from-telomere-to-telomere),
with our first papers showcasing new Telomere-to-Telomere methods and
genomic data sets.*

While the first draft of the Human Genome was declared complete in April
2003, it took a further two decades for the
[publication](http://doi.org/10.1126/science.abj6987) of the first
complete, gapless sequence of a human genome in March 2022. The work was
done by the [Telomere to Telomere (T2T)
consortium](https://sites.google.com/ucsc.edu/t2tworkinggroup?pli=1),
which was a years-long global collaboration led by geneticists at UC
Santa Cruz, University of Washington, and the National Institutes of
Health. This T2T approach has now moved onto to other species' genomes
(for example see the [recently published first
outputs](https://doi.org/10.1038/s41586-024-07473-2) from the
[T2T-Primates](https://github.com/marbl/Primates) project of the
consortium), and what was originally just the name of the consortium has
now become a badge for a certain level of quality that enables new
understanding of biology and improvements in genome annotation.

With the interest in this new level of genome sequence, the new data and
tools coming from this research, and the new biological insight coming
from previously ignored corners of the genome, *GigaScience* is [pleased
to announce](http://gigasciencejournal.com/blog/t2t-series/) the launch
of new [thematic
series](https://academic.oup.com/gigascience/pages/collections) covering
T2T Genomics. [This T2T
series](https://academic.oup.com/gigascience/pages/t2t-series-closing-the-gaps-from-telomere-to-telomere)
providing a home for these discussions, updated datasets, and showcasing
of the new technologies and methods that have driven this new standard
in genomics.

The first batch of papers are [now
out](https://academic.oup.com/gigascience/pages/t2t-series-closing-the-gaps-from-telomere-to-telomere)
and demonstrate the scope of the series, and rapid development of this
field. With an interesting balance of new methods and papers presenting
new data. From new tools for [mapping and visualization of the
low-complexity regions](https://doi.org/10.1093/gigascience/giad101)
that previously were too challenging to assemble, to new computational
approaches to sort and assemble equally challenging [sex-limited
chromosomes](https://doi.org/10.1093/gigascience/giae015). And following
our first fully-resolved genome of the protozoal agent [*Cryptosporidium
parvum*](https://doi.org/10.1093/gigascience/giac010), we've now
published much longer and difficult to assemble plant genomes such as
the [cupuassu tree (*Theobroma
grandiflorum*)](https://doi.org/10.1093/gigascience/giae027) and the
Chinese medicine plant [Qianhu (*Peucedanum praeruptorum*
Dunn)](https://doi.org/10.1093/gigascience/giae025). Providing novel
molecular insights into the many bioactive and commercially important
genes . With many more plant and animal species genomes currently under
review, watch this space for the final chapter of these reference
genomes to be published.

We would like to thank our Guest Editors Jue Ruan (Chinese Academy of
Agricultural Sciences) and Fritz J Sedlazeck (Baylor College of
Medicine), who both have hands-on involvement in this rapidly moving
field, and have helped draw up guidelines of what can be considered for
the series.

Please [contact
us](http://gigasciencejournal.com/blog/t2t-series/editorial@gigasciencejournal.com)
if you have work of interest you would like to discuss, or you can
submit through our submission system and make a note of this series in
the covering letter.

#### **Further Reading: ** {#further-reading}

Nurk S, et al. The complete sequence of a human genome. *Science*. 2022
Apr;376(6588):44-53. doi:
[10.1126/science.abj6987](http://doi.org/10.1126/science.abj6987).

Menon VK, et al. Fully resolved assembly of *Cryptosporidium parvum*.
*Gigascience*. 2022 Feb 15;11:giac010.
<https://doi.org/10.1093/gigascience/giac010>

Silva JM et al. AlcoR: alignment-free simulation, mapping, and
visualization of low-complexity regions in biological data.
*Gigascience*. 2023 Dec 28;12:giad101.
<https://doi.org/10.1093/gigascience/giad101>

Wang XB et al. An effective strategy for assembling the sex-limited
chromosome. *Gigascience*. 2024 Jan 2;13:giae015.
<https://doi.org/10.1093/gigascience/giae015>

Bai M et al. The telomere-to-telomere (T2T) genome of *Peucedanum
praeruptorum* Dunn provides insights into the genome evolution and
coumarin biosynthesis. *Gigascience*. 2024 Jan 2;13:giae025.
<https://doi.org/10.1093/gigascience/giae025>

Alves RM et al. Genomic decoding of *Theobroma grandiflorum* (cupuassu)
at chromosomal scale: evolutionary insights for horticultural
innovation. *Gigascience*. 2024 Jan 2;13:giae027.
<https://doi.org/10.1093/gigascience/giae027>

T2T Series: Closing the Gaps from Telomere-to-Telomere
<https://academic.oup.com/gigascience/pages/t2t-series-closing-the-gaps-from-telomere-to-telomere>

The post [Launch of the T2T Series: Closing the Gaps from
Telomere-to-Telomere](http://gigasciencejournal.com/blog/launch-of-the-gigascience-t2t-series/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<em>
 GigaScience’s T2T Series has now launched, with our first papers showcasing new Telomere-to-Telomere methods and genomic data sets.
</em>
While the first draft of the Human Genome was declared complete in April 2003, it took a further two decades for the publication of the first complete, gapless sequence of a human genome in March 2022.

Launch of the T2T Series: Closing the Gaps from Telomere-to-Telomere

<figure class="wp-block-image size-large is-resized">
<img
src="http://gigasciencejournal.com/blog/wp-content/uploads/2023/04/t2t-instagram-square-1-1024x1024.png"
class="wp-image-4895" loading="lazy" decoding="async"
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*Series Editors: Jue Ruan (Agricultural Genomics Institute at Shenzhen,
Chinese Academy of Agricultural Sciences) and Fritz J Sedlazeck (Human
Genome Sequencing Center, Baylor College of Medicine) *

   
While the first draft of the Human Genome was announced back in June
2000 and declared complete in April 2003, it took 20 years for the
[publication](http://doi.org/10.1126/science.abj6987) of the first
complete, gapless sequence of a human genome in March 2022. The work was
done by the [Telomere to Telomere (T2T)
consortium](https://sites.google.com/ucsc.edu/t2tworkinggroup?pli=1),
which was a years-long global collaboration led by geneticists at UC
Santa Cruz, University of Washington, and the National Institutes of
Health. This T2T approach has now rolled out to other species' genomes,
and has become a bit of a badge for a certain level of quality that
enables new understanding of biology and improvements in genome
annotation. At *GigaScience* we've already seen fully-resolved genomes
coming in, for example that of the protozoal agent [*Cryptosporidium
parvum*](https://doi.org/10.1093/gigascience/giac010); however, given
the current uncertainty within the broader community on what constitutes
a "true" T2T sequence, completely defined standards remain unclear.

With the interest in this new level of genome sequence, the data and
tools, and the evolving nature of accepted cutoffs, *GigaScience* is
pleased to announce a new [thematic
series](https://academic.oup.com/gigascience/pages/collections). This
series is focused on T2T papers to provide a home for these discussions,
updated datasets, including new technologies and methods that have
driven this new standard in genomics. 

Working on the definition of what T2T standards are (and to aid
potential submitters on what is suitable for submission), our Guest
Editors [Jue
Ruan](https://agis.caas.cn/en/research/principalinvestigator/237653.htm)
and [Fritz J Sedlazeck](https://www.hgsc.bcm.edu/people/sedlazeck-f)
both have hands-on involvement in this rapidly moving field and have
helped draw up guidelines of what can be called a T2T genome and
considered for the series. Feeling these should be gap-free assemblies
(although a few gaps can potentially be allowed, especially in rRNA
regions and sex chromosomes), have very high Q and BUSCO scores, and
with minimal structural artefacts (in the raw data vs assembly).
Nevertheless, in such a rapidly moving area of research especially
across multiple phylums these requirements need some adaptations
depending on ploidy, repetitiveness and other factors given a .
particularly complicated or  insightful findings.

On top of defining thresholds the Guest Editors have interesting
frontline insight in the field as a whole, and there is a lot that can
potentially be discussed and shared. There is much biological
information to be gleaned from newly resolved regions,
annotations/genes, etc. As Dr. Sedlazeck highlighted "The access in
these novel regions will enable new insights for biology and evolution,
but demand novel analytical approaches". Exploratory articles
highlighting the importance of these new regions or improving the
annotations are particularly encouraged, especially as the latter is
still a huge pain point. 

Please [contact us](editorial@gigasciencejournal.com) if you have work
of interest you would like to discuss, or you can submit through our
submission and make a note of this series in the covering letter.

**Further Reading:**  
Nurk S, et al. The complete sequence of a human genome. *Science*. 2022
Apr;376(6588):44-53. doi:
[10.1126/science.abj6987](http://doi.org/10.1126/science.abj6987).

Menon VK, et al. Fully resolved assembly of *Cryptosporidium parvum*.
*Gigascience*. 2022 Feb 15;11:giac010.
<https://doi.org/10.1093/gigascience/giac010>

The post [Announcing the GigaScience T2T Series: Closing the Gaps from
Telomere-to-Telomere](http://gigasciencejournal.com/blog/t2t-series/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


*Series Editors: Jue Ruan (Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences) and Fritz J Sedlazeck (Human Genome Sequencing Center, Baylor College of Medicine) *    While the first draft of the Human Genome was announced back in June 2000 and declared complete in April 2003, it took 20 years for the publication of the first complete, gapless sequence of a human genome in March 2022.

Publicaciones de Rogue Scholar

Launch of the T2T Series: Closing the Gaps from Telomere-to-Telomere

Announcing the GigaScience T2T Series: Closing the Gaps from Telomere-to-Telomere