Sequencing the genomes of Australian plants

By Dr Alexander Schmidt-Lebuhn, Dr Katharina NargarOctober 27th, 2020

As part of the Genomics for Australian Plants consortium, we are sequencing the genomes of the Queen of Sheba orchid and Hoary Sunray daisy.

It’s barely 25 years since researchers began sequencing the entire genomes of species. The first full genome sequenced belonged to the bacterium Haemophilus influenzae. It is just two million letters (or base pairs) long.

Genome sequences are like a reference library for research. They support scientific advances as diverse as producing vaccines, calculating the lifespans of marine turtles and conserving plants.

As part of the Genomics for Australian Plants consortium, we are adding two extraordinary plants to the list of species sequenced, the Queen of Sheba orchid and the Hoary Sunray daisy. Their genomes are approximately 4.3 and 0.9 billion base pairs long, respectively. (For comparison, the human genome is 3 billion base pairs long.)

A stunning orchid

For an orchid, the Queen of Sheba has a bizarre and beautiful colour scheme and an unusual symmetry. It mimics other flowers that provide a food reward to pollinators, to trick the pollinators into visiting the non-rewarding orchid flowers. (Photo copyright David Blumer.)

The Queen of Sheba orchid (Thelymitra variegata) is one of the most stunning of Australia’s more than 1,300 native orchid species. Along with many Australian orchids, we are worried about the long-term survival of this species.

Teams at Kings Park in Perth and Royal Botanic Gardens Victoria recently succeeded in growing this species from seed. Like all orchids, its seeds require the presence of a specific fungus in order to germinate. The Queen of Sheba also requires particular nutrients to be present in the soil. We will generate the reference genome using plants being grown at Kings Park.

The Hoary Sunray

A field of Hoary Sunray daisies.

The Hoary Sunray has slender leaves concentrated near the base of the plant. It carries solitary flower-heads on long stalks. The flower-heads have a yellow centre and either yellow or white petal-like, papery bracts to attract pollinators.

The Hoary Sunray (Leucochrysum albicans) is an everlasting paper daisy. It has two varieties, a widespread yellow form and a rarer white form. Gardeners sometimes plant these daisies as a native ornamental and in the wild they grow from southernmost Queensland to Tasmania.

In mid October, Hoary Sunrays flowered en masse in nature reserves in Canberra following winter rains. The local plants are the rare white variety, which is surviving relatively well in the Canberra area and in small populations in Tasmania.

Sequencing the genomes of reference plants

Hoary Sunray daisies mass-flowering in Canberra following winter rainfall.

The main reason we are sequencing the genomes of this orchid and daisy is to generate reference genomes for major Australian plant groups.

Many existing genome sequences belong to animal species. They include model organisms, such as the fruit fly and the zebra fish, which scientists use to study the functions of genes. Non-model species and the majority of plants are still underrepresented relative to their diversity.

The Hoary Sunray is part of the everlasting paper daisy tribe (Gnaphalieae). This group has more than 2000 species worldwide, including around 500 species in Australia. They occur in habitats from the arid zone to the Australian Alps and make up about half of Australia’s native daisy diversity.

The Queen of Sheba is part of a group of ground orchids that are also very diverse in Australia. They represent approximately 75 per cent of Australia’s orchid diversity.

The Queen of Sheba orchid has some unique features, in particular its floral traits. As a result, this species is of high scientific and horticultural value. (Photo copyright David Blumer.)

Because there are no reference genomes for these groups yet, the genome sequences of the Hoary Sunray and the Queen of Sheba will support many aspects of research, such as understanding the evolution and diversity of our flora.

These genome sequences also have potential to aid environmental monitoring and detection of illicit trade of orchids.

A high value species

The Queen of Sheba and related orchids have lustrous blue colour and unique patterns that make them very interesting for horticulture. Because of this, we think that understanding more about the genetic underpinnings of the highly unusual radial symmetry of these flowers will enable new insights into orchid flower development.

The Queen of Sheba is also of considerable conservation concern. A reference genome will enable researchers to carry out rigorous conservation genomic studies. The ultimate goal is to prop up wild populations and reintroduce this orchid into areas where it has previously become extinct.

Genomics for Australian Plants

The Genomics for Australian Plants Framework Initiative consortium is sequencing the genomes of important and iconic Australian native flora. In 2020, the GAP consortium initiated seven reference genome projects, including the Queen of Sheba orchid and the Hoary Sunray daisy.

The Consortium is supported by funding from: Bioplatforms Australia (enabled by NCRIS), the Ian Potter Foundation, Royal Botanic Gardens Victoria, Royal Botanic Gardens and Domain Trust, CSIRO, Centre for Australian National Biodiversity Research and Department of Biodiversity, Conservation and Attractions, Western Australia.

Dr Katharina Nargar leads the orchid research program at the Australian Tropical Herbarium. Dr Alexander Schmidt-Lebuhn researches daisies at the Centre for Australian National Biodiversity Research. They are working with the Genomics for Australian Plants consortium on sequencing the genomes of Australian plants.

The Australian Tropical Herbarium is a joint venture between CSIRO, Australian and Queensland Governments and James Cook University. The Centre for Australian National Biodiversity Research is a joint venture between Parks Australia’s Australian National Botanic Gardens and CSIRO.

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