The Wellcome Sanger Institute’s Tree of Life program is redesigning how its genome notes are published, with a target of increasing output from about 30 reports a month to 200. The plan combines automated genome-quality checks, immediate online publication and post-publication open peer review; 200 reports per month is a program target, not a rate shown to have been achieved.
Why the Tree of Life workflow is being overhauled
Sequencing capacity has begun to outpace the publication process used to document reference genomes. The Tree of Life program wants its reports to keep pace with the genomes produced by its sequencing machines, rather than allowing completed assemblies to wait in a conventional publication queue.
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F1000 and the Wellcome Sanger Institute designed the new workflow for Wellcome Open Research. It is built around the highly structured format of a Tree of Life genome note, which makes it possible to automate repeatable checks without removing expert oversight.
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The stated goal is a rise from approximately 30 genome notes per month to 200 per month. Those figures were reported in 2026 and describe the program’s existing rate and target; they are not an independent audit showing that the higher rate has already been reached.
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What a genome note is and where it fits
A genome note is a rapidly published, citable report accompanying a completed reference genome. It gives researchers a formal record they can interpret, reference and reuse while also documenting the people and organizations involved in producing the resource.
The Darwin Tree of Life program, led by the Wellcome Sanger Institute, aims to sequence every findable species in the United Kingdom and Ireland. The program is part of the broader Earth BioGenome Project, described in the report as an effort to sequence all life on Earth. The stated UK-and-Ireland ambition is approximately 30,000 findable species for publication and indexing.
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The Tree of Life Gateway, launched in May 2021, contained more than 1,900 genome notes from universities, museums and horticultural organizations across the UK and Ireland when the overhaul was reported. That total reflects contributions from multiple institutions, not only sequencing performed at the Sanger Institute.
How the new publication pipeline works
- A structured genome note is prepared. The standardized format supplies the information needed to describe a reference genome and makes the submission suitable for consistent automated checking.
- Computer-aided review runs on the submission. The system records a defined set of assembly and annotation indicators before or as the note is prepared for online release.
- The note is published online. The quality results are embedded directly in the article, so readers can see the checks alongside the genome description rather than relying on an opaque editorial decision.
- Human review follows publication. Wellcome Open Research’s post-publication open peer-review process uses an invited expert reviewer or a peer-review panel.
- The result remains citable and indexable. The report says the combination of automated benchmarking and independent human review has been approved by indexers such as PubMed.
This sequence changes the timing of review, not the principle that published research should be examined by qualified scientists. A genome note can become available quickly, while the open review record supplies a visible route for expert assessment after publication.
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Which quality checks are recorded
Automated review records five categories of genome quality information. The values are placed in the published article so researchers evaluating or reusing a genome can inspect the evidence directly.
| Recorded category | What the workflow exposes |
|---|---|
| Genome continuity | Information about how continuous the assembled genome is. |
| Structural accuracy | A benchmark of the assembly’s structural correctness. |
| Base accuracy | A benchmark of accuracy at the DNA-base level. |
| Functional completeness | Evidence about how completely biological functions are represented in the annotation. |
| Chromosome status | Whether chromosome-level status has been recorded for the genome. |
These checks are not presented as a substitute for interpretation. They give reviewers and readers a consistent technical record, while the invited expert or panel can assess the broader scientific context through open peer review.
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Why publication before peer review does not mean “no review”
In this model, online publication and computer-aided assessment come first, followed by an open review process. That ordering is intended to make the genome resource available sooner and to expose the review history rather than keeping all evaluation behind a closed editorial gate.
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1Scan for outdated or missing drivers - takes under a minute2Clear out junk files and repair common Windows errors3Fix the driver behind crashes, sound loss and screen glitchesJames Cleaver, head of publishing at F1000, said the structured nature of the notes created an opportunity to redesign the workflow by combining publishing technology with human expertise. He also emphasized that human oversight remains central to the integrity and reliability of the research.
For readers, the practical distinction is timing and transparency: the genome note can be accessed and cited while the review is still taking place, and the article carries the automated metrics that underpin the technical assessment.
What researchers and collaborators gain
- Earlier access: completed reference genomes can enter the public literature without waiting for a lengthy pre-publication cycle.
- Visible technical context: continuity, structural accuracy, base accuracy, functional completeness and chromosome status appear in the article itself.
- Open review: an invited expert or panel reviews the published note through the Wellcome Open Research process, creating a public assessment trail.
- Formal credit: genome notes provide a citable record that credits collectors and taxonomists as well as genome-sequencing teams.
- Reuse at program scale: a common format makes thousands of species records easier to find, compare and reference across the Tree of Life Gateway.
Mark Blaxter, head of the Tree of Life program at the Wellcome Sanger Institute, said the institute releases its reference genomes to the global community and that genome notes provide a rapidly published, citable resource that recognizes both field collaborators and sequencing teams.
How to interpret the numbers
The headline increase is a capacity objective: approximately 30 notes per month today, with a target of 200. The Gateway’s more than 1,900 notes are a contemporaneous count reported in 2026, and the approximately 30,000-species figure describes the program’s stated UK-and-Ireland publication and indexing ambition. None of these numbers, on their own, demonstrates that every planned species has been sequenced or that the 200-per-month rate is already operating.
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The overhaul therefore addresses a specific bottleneck: converting completed genome assemblies into standardized, citable publications. Its proposed solution is to automate repeatable quality reporting, publish the note promptly and retain independent human review as an open, post-publication stage.
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