Abstract Detail

Phylogeny and evolution of angiosperms in the era of next generation sequencing

Baker, William J. [1], Barber, Vanessa [1], Barker, Abigail [1], Botigué, Laura R.  [2], Brewer, Grace [1], Cowan, Robyn S. [1], Dodsworth, Stephen [1], Epitawalage, Niroshini [1], Eiserhardt, Wolf L.T. [1], Forest, Felix [1], Johnson, Matthew [3], Kim, Jan [1], Leitch, Ilia [1], Maurin, Olivier [1], Pokorny, Lisa [1], Wickett, Norman [4].

Completing the Plant Tree of Life.

Evolutionary trees are powerful tools for prediction, species discovery, monitoring and conservation. Through comparative analysis of DNA sequence data, the backbone of the plant tree of life is relatively well understood, and many subcomponents have been studied in great detail. However, DNA data are still lacking for numerous plant and fungal genera and the vast majority of species, preventing their accurate placement within an evolutionary framework, in turn hindering downstream science. To better understand how the world’s plants and fungi have evolved, we have initiated the Plant and Fungal Trees of Life (PAFTOL) project at the Royal Botanic Gardens, Kew. We aim to utilise our collections and work with collaborators to generate extensive new data for at least one representative species of every genus of plant and fungi using high-throughput DNA sequencing technologies, producing a unifying framework for comparative research. In this talk, we report on progress in the plant component of PAFTOL. We have established a targeted sequence capture (HybSeq) approach and have designed a single probe (bait) kit that can isolate up to 353 nuclear genes across all angiosperm families. Data obtained with this kit effectively resolves both deep and species-level relationships and is currently being evaluated as a “next generation” barcode. The angiosperm-wide bait kit is publicly available and is being adopted by numerous researchers. A refined bioinformatic pipeline is also in preparation. Our pilot project, which included at least one representative of every angiosperm family, is complete and we now aim to generate data for 25% of the 14,000 angiosperm genera within the coming year. Focused studies on families such as orchids, palms, sedges, daisies and legumes are also underway. Securing samples to complete this project is a key challenge, requiring detailed gap analyses and the establishment of rigorous sampling standards. 57% of the samples required for PAFTOL already exist in Kew’s living collection, seed bank, DNA bank and tissue bank. The remaining samples will be sourced primarily from the Kew Herbarium, in which ca. 95% of all angiosperm genera are represented. Our sequence capture protocol is highly effective with degraded herbarium DNA, with good results obtained from specimens up to ca. 200 years old. PAFTOL aspires to be highly open and collaborative, sharing data and tools at the earliest opportunity, and integrating with the broader global genomic agenda. Researchers who share an interest in our project are warmly invited to get in touch.

Related Links:
PAFTOL website

1 - Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
2 - Centre for Research in Agricultural Genomics, Barcelona, Spain
3 - Texas Tech University, Biological Sciences, 2901 Main Street, Ms3131, Lubbock, TX, 79409, United States
4 - Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL, 60022, United States

Keywords:
angiosperms
Phylogenomics
tree of life
HybSeq
Targeted Sequence Capture
museomics
herbarium DNA
Genomics
Next generation sequencing.

Presentation Type: Symposium Presentation
Session: SY6, Phylogeny and evolution of angiosperms in the era of next generation sequencing
Location: 102/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 2:15 PM
Number: SY6003
Abstract ID:300
Candidate for Awards:None