Plant and Fungal Trees of Life (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

Principal investigators

Dr William Baker
Dr Félix Forest
Dr Ilia Leitch
Dr Paul Kersey

Project staff

Data production team
Dr Olivier Maurin
Dr Jim Clarkson
Dr Alexandre Zuntini 
Robyn Cowan

Data analysis team
Dr Paul Bailey

Project manager
Vanessa Barber

Project alumni
Dr Lisa Pokorny
Dr Sidonie Bellot
Dr Laura Botigue
Grace Brewer
Dr Steven Dodsworth
Niroshini Epitawalage
Dr Wolf Eiserhardt
Dr Jan Kim

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 probe set, and final pooling, can be found in Johnson,M.G., Pokorny, L., Dodsworth, S. et al. (2018).

Angiosperms353 probe set
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 probe 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 six months after production. 

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

Fungal methods
We are currently developing our methods for fungi.

Data

Data generated by the PAFTOL is accessible through the Kew Tree of Life Explorer

We currently have special projects on the following plant families and if you would like to find out more about our progress, or how to contribute, please email the associated contact:

Acanthaceae, Achariaceae, Aizoaceae, Anacardiaceae, Amaryllidaceae, Apiales, Aquifoliales, Araceae, Arecaceae, Asphodelaceae, Asteraceae, Caryophyllales, Celastrales, Chrysobalanaceae, Connaraceae, Cunoniaceae, Cyperaceae, Dioscoreales, Orchidaceae, Ericales, Euphorbiaceae, Fabaceae, Fabaceae (Phaseolineae), Gentianales, Iridaceae, Lamiales, Laurales (Monimiaceae), Linderniaceae, Magnoliales, Malpighiales, Malvales, Moraceae, Myristicaceae, Myrtales, Ochnaceae, Oxalidales, Poaceae, Podostemaceae, Portulacineae, Primulaceae, Proteales, Sapindaceae, Sapindales, Solanaceae, Thymelaeaceae & Urticaceae.

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

• PhyloSynth
• GoFlag - Genealogy of Flagellate Plants
• Genomics for Australian Plants
• Earth Biogenome Project
• Darwin Tree of Life project

All PAFTOL publications are listed in our Research Repository.