Tree of Life Gateway – Celebrating 1000 Published Genome Notes on Wellcome Open Research
| 27 August, 2025 | Jack Nash |
In May 2021, Wellcome Open Research launched the Tree of Life Gateway. This Gateway serves as an open publishing hub for the Darwin Tree of Life, Aquatic Symbiosis Genomics, and 25 Genomes for 25 Years projects, all supported by the Wellcome Sanger Institute.
The primary goal of the Gateway is to publish the genome sequences of the eukaryotic species sequenced by the Tree of Life.
In December 2024, the Gateway published the 1,000th Genome Note, a significant milestone for everyone involved. In the following blog post, we discuss how these Genome Notes are important markers of progress in sequencing all of life with Professor Mark Blaxter, Head of the Tree of Life Programme, and celebrate Notes that describe genomes of iconic species native to the UK.
In conversation with Mark Blaxter, Head of the Tree of Life Programme at the Wellcome Sanger Institute
What have you learned from leading the Tree of Life projects so far?
That organisms’ genomes are as wonderful and varied as the species they come from. Whether it is the tiny genome of an intracellular parasite (microsporidia, which infect many insects) or the giant genome of the mistletoe (30 times the size of our human genome), there are always new stories. Did you know that wild dog roses are pentaploid (have five copies of each chromosome – most species, like us, have just two)? This made for difficulties in genome assembly, but the final result is now a detailed map of the biology behind the wild dog rose’s unusual genome organisation.
Where are you currently in the Tree of Life programme timeline?
10,000 species have been collected and more than 5,000 processed for sequencing. We have released over 3,000 completed reference genomes from the Darwin Tree of Life project (focussed on species found in Britain and Ireland), Aquatic Symbiosis Genomics, Project Psyche (European butterflies and moths), Vertebrate Genome project, 959 Nematode Genomes, and other large-scale projects.
What were the biggest challenges you’ve encountered during the project?
Every new phylum of life was a challenge! For each, we had to modify our methods for collecting and shipping, for extracting DNA and RNA, and tweak our genome assembly computational pipelines to deal with the real biological differences we found.
Was there something from the project that surprised you, or was unexpected?
When we sequence an individual collected from the wild, we try our best to ensure it is “clean” – not carrying obvious contaminants. However when we sequence these specimens, we have found that many carry parasites, pathogens and other bacterial and eukaryotic “cobionts”. This “cobiont by-catch” is turning out to be fascinating and includes both the expected (all aphids carry a bacterium that helps them live on the thin gruel that is plant sap) and the unexpected (for example, a parasitic jellyfish-relative we found hiding in the genome data for the horse mackerel).
Can you share any specific success stories or positive outcomes?
We have just released our 2,000th Darwin Tree of Life project genome – from a beautiful colonial hydroid (jellyfish) named Sertularella gayi. Hydroids are major components of marine and freshwater systems, where they filter their food from the water column. They are underrepresented in traditional morphological surveys, but the genome will aid in giving better depth to environmental DNA approaches, as now hydroid-derived sequences can be recognised.
There are many examples of reference genomes being used in conservation, for example, aiding the management of otter recovery plans and tracking the success of white-tailed sea eagles.
What are the next major milestones for the programme?
We have 10,000 species collected, and our sights are set on achieving 5,000 reference genomes in 2026.
How do you see the Tree of Life programme evolving in the future?
The Sanger Institute established the Tree of Life programme to support delivery of the Earth BioGenome Project – to sequence all of Earth’s eukaryotic biodiversity. This is still our goal, and we see the future as a combination of continuous improvement of our systems and production at the Sanger Institute and the seeding of new centres globally to join us to “sequence life for the future of life”. We cannot do all 1.6 million species ourselves, but a consortium of tens or hundreds of labs could, and we are working alongside the Earth BioGenome Project to make this happen.
An example is Project Psyche, a new initiative that aims to sequence all 11,000 of Europe’s Lepidoptera (butterflies and moths) in the next 5-8 years. Moths and butterflies are important pollinators, can be nasty pests, and also act as markers of the effects of climate change on wild and managed ecosystems. The pan-European collaboration will use our genomes to explore these topics and more.
Highlights from the Tree of Life Gateway
With over 1,000 genomes published in the Tree of Life gateway in the past four years, browsing the gateway offers a fascinating insight into the broad array of species, some of which can be found across the Britain and Ireland. These include:
Red fox (Vulpes vulpes)
Known for its recognisable red coat, this opportunistic omnivore can be found in many habitats across Britain and Ireland. Their genome can be found as a Genome Note on Wellcome Open Research as part of the Tree of Life programme.
Read the Genome Note for Vulpes vulpes.
European Badger (Meles meles)
Did you know that European Badgers are Britain’s largest land predator? This nocturnal black and white striped mammal uses its large front paws to dig for food, consuming hundreds of earthworms per night. The genome of the European Badger has been sequenced as part of the Tree of Life programme.
Read the Genome Note for Meles meles.
Common adder (Vipera berus)
Native to Britain, but not Ireland, the common adder is Britain’s only venomous snake. Adders are the most northerly-occurring snake species in the world, with some living as far north as the Arctic Circle. They are easily identified by their distinctive zig-zag pattern along their backs. The genome of the Common Adder has been sequenced as part of the Tree of Life programme.
Read the Genome Note for Vipera berus.
How can you support the Tree of Life programme?
We invite all genomics researchers to contribute to peer reviewing Genome Notes for the Tree of Life programme as community reviewers by assessing the genome sequences published in the Tree of Life Gateway.
If you are interested in joining the Tree of Life Gateway community reviewer group, please sign up here or contact us at info@wellcomeopenresearch.org.
Image credits
Vulpes vulpes: Dušan Veverkolog/Unsplash
Meles meles: Vincent van Zalinge/Unsplash
Vipera berus: Photorama/ Pixabay