Plant and Fungal Tree of Life

Plant and Fungal Trees of Life

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


Project information


Funded by

The staff and trustees of the Royal Botanic Gardens, Kew and the Kew Foundation would like to thank the Calleva Foundation and the Sackler Trust for generously funding the Plant and Fungal Trees of Life project.


Objectives and outputs

Summary:

Kew is committed to completing the Plant and Fungal Trees of Life by generating and compiling high throughput sequencing data for one representative of all 14,000 flowering plant genera and all 8,200 fungal genera by 2020.

Background:

Evolutionary trees are powerful tools for prediction, species discovery, monitoring and conservation. To better understand how the world’s plants and fungi are related to each other and how they have evolved, we aim to complete the Plant and Fungal Trees of Life (PAFTOL). Through comparative analysis of DNA sequence data, the backbones of these Trees of Life are already relatively well understood, and many components have been studied in great detail. However, DNA data are still lacking for many genera and the vast majority of species of plants and fungi, preventing their accurate placement within this evolutionary framework.

Objectives:

To complete the Plant and Fungal Trees of Life for all genera, we will utilise Kew’s collections to produce genome-scale DNA data for a representative of each genus of plant and fungi using high-throughput sequencing technologies. This comprehensive investigation of evolutionary relationships will provide a unifying framework for comparative plant and fungal research, greatly accelerating the discovery of new taxa, particularly in less well-known groups, as well as facilitating the exploration of properties and uses. The project is an essential step towards the compilation of genomic data for all known species using Kew’s collections.


Project outputs

Genomic data for one representative of all 14,000 flowering plant genera.

Image showing Ancistrochilus rothschildianus

Geomic data for one representative of all 8,200 fungal genera.

Image showing Chlorophyllum rhacodes

The PAFTOL Explorer, a novel web tool providing access to the latest versions of the trees of life, and sequence data.

Plant and Fungal Tree of Life

Creation of the Angiosperm353 probe kit, a universal toolkit for targeted sequencing of 353 genes from any flowering plant.

Image showing A scientist pipettes plant DNA in the Jodrell Laboratory

The publication of high impact science papers of relevance to the broadest scientific audience.

MPNS Resource

Engagement and dialogue around PAFTOL's research and approaches with both the public and scientific communities.

image showing the team in the lab demonstrating strawberry DNA extraction

Further information

Papers and publications:

Eiserhardt, W.L., Antonelli, A., Bennett, D.J., Botigué, L.R., Burleigh, J.G., Dodsworth, S., Enquist, B.J., Forest, F., Kim, J.T., Kozlov, A.M., Leitch, I.J., Maitner, B.S., Mirarab, S., Piel, W.H., Pérez‐Escobar, O.A., Pokorny, L., Rahbek, C., Sandel, B., Smith, S.A., Stamatakis, A., Vos, R.A., Warnow, T., & Baker, W.J. (2018). A roadmap for global synthesis of the plant tree of life. American Journal of Botany 105: 614-622. Available online

Johnson, M., Pokorny, L., Dodsworth, S., Botigue, L.R., Cowan, R.S., Devault, A., Eiserhardt, W.L., Epitawalage, N., Forest, F., Kim, J.T., Leebens-Mack, J.H.H., Leitch, I.J., Maurin, O., Soltis, D.E., Soltis, P.S., Wong, G.K., Baker, W.J., & Wickett, N. (2018). A Universal Probe Set for Targetted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering. bioRxiv 361618. Available online

Lewin, H.A., Robinson, G.E.,  Kress, W.J., Baker, W.J., Coddington, J., Crandall, K.A., Durbin, R., Edwards, S.V., Forest, F., Gilbert, M.T.P., Goldstein, M.M., Grigoriev, I.V., Hackett, K.J., Haussler, D., Jarvis, E.D., Johnson, W.E., Patrinos, A., Richards, S., Castilla-Rubio, J.C., van Sluys, M-A., Soltis, P.S., Xu, X., Yang, H. & Zhang,G. (2018). Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences of the United States of America 115: 4325-4333. Available online

Related links

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

Angiosperm353 bait kit

PhyloSynth

1000 Plants Iniative 

Earth Biogenome Project

Visual guide to collecting plant tissues for DNA