Plant and Fungal Trees of Life (PAFTOL)

Discovering and disseminating the evolutionary history of all plant and fungal genera

Evolutionary trees are powerful tools for prediction, species discovery, monitoring and conservation. They help us understand how the world’s plants and fungi are related to each other and how they have evolved. Through comparative analysis of DNA sequence data, the backbone of the Tree of Life is already relatively well understood, and many components have been studied in great detail. However, data are still lacking for many genera and the majority of species of plants and fungi, preventing their accurate placement within this evolutionary framework. Exploiting Kew’s unrivalled collections, the Plant and Fungal Tree of Life project (PAFTOL) is now completing the tree, by generating and compiling high throughput DNA sequence data for one representative of all 14,000 flowering plant genera and all 8,200 fungal genera by 2020.

About PAFTOL

Expected outputs

Genomic data for one representative of all 14,000 flowering plant genera.
Genomic data for one representative of all 8,200 fungal genera.
Creation of the Angiosperm353 probe kit, a universal toolkit for targeted sequencing of 353 genes from any flowering plant.
The publication of high impact science papers of relevance to the broadest scientific audience.
Up-to-date tree of life (and all underpinning data) made publicly available online.
Engagement and dialogue around PAFTOL's research and approaches with both the public and scientific communities.

Funded by

The Calleva Foundation
The Sackler Trust
Garfield Weston

PAFTOL plants staff

Principal investigators

Dr William (Bill) Baker

Dr Félix Forest

Dr Ilia Leitch

Dr Paul Kersey

Project staff

Data production team

Dr Olivier Maurin

Dr Jim Clarkson

Dr Alexandre Zuntini

Dr Niroshini Epitawalage

Grace Brewer

Robyn Cowan

Dr Wolf Eiserhardt

Data analysis team

Dr Jan Kim

Dr Paul Bailey

Project manager

Vanessa Barber

Project alumni

Dr Lisa Pokorny

Dr Sidonie Bellot

Dr Steven Dodsworth

Dr Laura Botigue

Data and methods

Methods

Sampling methods
PAFTOL’s samples come from fresh tissue from the living collections at the Royal Botanic Gardens, Kew, herbaria material sampled from Kew's Herbarium and other herbaria around the world, and existing DNA extractions and tissue samples from Kew's DNA and Tissue bank.

For step-by-step instructions on how to collect fresh tissue samples download PAFTOL's sampling guide.

Laboratory methods
Details of PAFTOL’s lab methods, covering DNA extraction, sonication, library preparation, evaluation and quantification, hybridisation to the Angiosperms353 baits, and final pooling, can be found in Johnson,M.G., Pokorny, L., Dodsworth, S. et al. (2018).

Angiosperms353 Bait kit
The Angiosperms353 probe set has been demonstrated to enrich hundreds of putatively single-copy protein-coding genes, identified by the One Thousand Plant Transcriptomes Initiative, across a broad range of flowering plants. Probes were designed from 353 loci, each with 5-15 representative sequences from across all angiosperms which were selected using a novel “k-medoids clustering approach” to maximize taxonomic breadth of the design (Johnson,M.G., Pokorny, L., Dodsworth, S. et al. 2018)

The bait set is broadly applicable for phylogenetic research across all flowering plants, and is available from Arbor Biosciences at a low per-reaction cost.

Computational methods
PAFTOL aims to share its data as openly and as early as possible. All data that are generated with support from PAFTOL project resources (funding, staff time, etc.) will be freely and immediately shared among its members and is available upon request. Data generated by the PAFTOL project will be made publicly available no later than 6 months after production.

GitHub: “HybSeq Target Capture of 353 Protein Coding Genes in Any Angiosperm”

Collaborations

PAFTOL is actively working with other projects and initiatives that share our goals: