BUILDING THE FLOWERING PLANT 'Tree of Life’

BOTANIC GARDENS OF SYDNEY SCIENTISTS HAVE HELPED A GLOBAL TEAM OF RESEARCHERS – LED BY THE ROYAL BOTANIC GARDENS, KEW – TO ASSEMBLE THE MOST COMPREHENSIVE ANGIOSPERM ‘TREE OF LIFE’ EVER, SIGNIFYING A NEW MILESTONE IN UNDERSTANDING THE EVOLUTIONARY HISTORY OF FLOWERING PLANTS.

Flowering plants, also known as angiosperms, dominate the surface of Earth today and sustain the lives of countless other organisms, including most terrestrial animals.

About nine in ten land plants are flowering plants. With about 300,000 species worldwide (including over 20,000 in Australia), retracing angiosperms’ evolutionary history has long been a daunting task. A new global study published in Nature and involving 279 co-authors, including Botanic Gardens of Sydney, set a new milestone in building the flowering plant Tree of Life (phylogeny) using a new ground-breaking genomic sequencing technology.

An unprecedented, high-resolution window into flowering plant diversification nine in ten land plants are flowering plants.

To appreciate the significance of this new study, it is helpful to recall a key milestone published 30 years ago. In 1993, Mark Chase and 41 co-authors analysed the sequences of a single chloroplast gene named rbcL from 499 species of seed plants to reconstruct one of the very first comprehensive phylogenies of flowering plants based on DNA data. This paper laid the foundation for two decades of considerable progress in angiosperm molecular phylogenetics, leading to an entirely updated and more stable classification system.

Yet, with only 1428 base pairs, the power of rbcL to unravel relationships among flowering plant families was limited. Although standards in phylogenetics had progressed to use multiple genes and, over the past decade, entire chloroplast genomes, it is only very recently that genomic sequencing technology has allowed us to read the DNA of hundreds of genes at once from the much larger nuclear genome of plant cells. Our new study is based on the so-called Angiosperms353 bait set. Led by the Royal Botanic Gardens, Kew, the new flowering plant Tree of Life is based on these 353 genes sequenced across 9506 species, or nearly 1.8 billion base pairs, representing a 2500-fold increase in data volume since the milestone paper of 1993.

What did we find? Sampling included all currently recognised orders (64) and families (416) of flowering plants, but also 58% (7923) of all genera. The new study gave us the most comprehensive critical test to date of established phylogenetic relationships across multiple scales, based on entirely new data. Fortunately, many previous results were confirmed this way, but the new tree also unravelled unexpected relationships among some families. However, our study went much further by adding geological time to the new Tree of Life using a combination of 200 carefully curated fossil calibrations and so-called relaxed molecular clocks. This allowed unprecedented resolution into the early diversification of flowering plants, revealing explosive expansion of lineages shortly after their origin in the Late Jurassic and Early Cretaceous periods.

Big collaborations for big results

So how was such a grand project realised? Initiated as the Plant and Fungal Tree of Life (PAFTOL) project run by the Royal Botanic Gardens, Kew, with funding from the Calleva Foundation, the heart of this project has been a grand collaboration by the 279 co-authors, utilising the work of thousands of collectors and curators to sample as many flowering plant genera (almost 8000) as possible in the project timeframe. While led by Kew, a global network of scientists and curators was required to obtain samples from herbarium specimens, botanic gardens and in the field, to fill critical sampling gaps. In close collaboration with PAFTOL, the Genomics for Australian Plants (GAP) project was developed as a national collaboration to create a similar framework for the Australian flora.

The GAP project brought together researchers from all states and territories to sample over 95% of Australian flowering plant genera, utilising some data from the PAFTOL project, but sampling nearly 2000 additional species, and so becoming a major contributor to the overall PAFTOL aims.

Expanding the value of our collections

The National Herbarium of New South Wales holds more than one million plant specimens and represents a critical research resource for documenting plant diversity, species discovery and understanding the evolutionary history of our flora. Each plant specimen is accompanied by scientific data, including when and where it was collected.

The past ten years have seen vast technological changes in digitisation (capturing specimen data and images), DNA sequencing approaches and computing storage and power for analysis of increasingly large datasets. This has wildly augmented the value of and access to our collections.

New South Wales contributed 168 genera (across 25 families) to this study, the vast majority directly sampled from the herbarium and some from the living collections of the Botanic Gardens of Sydney. A unique collaboration saw 12 staff from our organisation working together to sample specimens and prepare them for sequencing. We developed a standardised methodology with stringent controls around sampling, data capture and tracking to ensure priority of care of our precious collection while taking advantage of the incredible new resource that access to the DNA of herbarium specimens provides.

Dr Hervé Sauquet, Head of Plant Discovery and Evolution Research, Principal Research Scientist; Dr Hannah McPherson, Collections Manager, National Herbarium of NSW; Dr Russell Barrett, Senior Research Scientist

The Nature paper reference: Zuntini AR (+ 278 co-authors including Barrett RL, Duretto MF, Jobson RW, Lu-Irving P, McColl K, McPherson H, Nge FJ, Renner M, Sauquet H, Tooth I, Wilson TC, Woods LA from Botanic Gardens of Sydney) (2024) ‘Phylogenomics and the rise of the angiosperms’, Nature 629, 843–850. doi.org/10.1038/s41586-024-07324-0

My proudest achievements are those that have resulted in or contributed to ‘plants in the ground’ outcomes.