UP researchers decode genome of king protea

University of Pretoria (UP) researchers are at the forefront of a very special first for South African plant sciences. They have unravelled the precise genetic make-up of the country’s national flower, the king protea (Protea cynaroides). It is the first plant that’s unique to South Africa – and the species-rich fynbos biome in particular – to have its entire genome sequenced in-depth.

“The project is also very special because most of the work was done in South Africa, one of the world’s most biodiverse countries,” says project leader Professor Eshchar Mizrachi of UP’s Department of Biochemistry, Genetics and Microbiology and its Forestry and Agricultural Biotechnology Institute (FABI).

Researchers from FABI, the Department of Biochemistry, Genetics and Microbiology, and UP’s Department of Plant and Soil Sciences worked together on the resulting paper, which was published in The Plant Journal. They collaborated with plant genome evolution expert Prof Yves van de Peer’s research group at Ghent University and the VIB Centre for Plant Systems Biology in Belgium. Prof Van de Peer also holds joint appointments at UP and the Nanjing Agricultural University in China.

Tissue from the “Little Prince” variety of king protea was used in the analysis because it is readily available in nurseries and would make further research easier.

Based on the entire genome sequencing work done, the researchers found that the genome of Protea cynaroides contains 12 distinctive chromosomes. It is about 1.18 gigabases (Gb) long, which means it contains more than 1.18 billion “letters” of the DNA alphabet (A,C,T and G) across these 12 chromosomes. In comparison, the human genome is about 3.2 Gb long, while that of Arabidopsis thaliana, the first plant ever sequenced, is about 135 Mb, or 0.135 Gb.

Proteas have survived mass extinctions

The information has allowed the researchers involved to shed light on the evolutionary past of the king protea and other members of the Protea genus and larger Proteaceae family. They now believe that ancestors of the Proteaceae family developed an identical, duplicate set of their entire genome about 68 million years (MYA) ago. This helped the family as a whole to survive the K-Pg boundary, a mass extinction period around the late Cretaceous period some 66 MYA ago. The extinction event saw 60% of all plant species and 80% of all animals (including non-avian dinosaurs) disappear from Earth.

This genome duplication event happened before all extant lineages that are part of the larger Proteaceae family diverged some 63 MYA into what is today around 1 600 species, most occurring in the southern hemisphere. The common ancestor of the approximately 100 species of Protea found in South Africa and Australia’s related macadamia nut trees (such as Macadamia integrifolia) and waratah (Telopea speciosissima) dates back to when dinosaurs went extinct.

It supports research previously conducted separately by two members of the project team, Prof Van de Peer and Prof Nigel Barker of UP’s Department of Plant and Soil Sciences, who is interested in the evolution of the Proteaceae family. They suggested independently that polyploidisation (the condition where cells in an organism have more than one pair of chromosomes) could have helped plants to survive environmental turmoil and similar extinction events.

Protea's cluster roots help them thrive

Proteas survive and thrive in the nutrient-poor soils of the Cape Floristic Region of South Africa, thanks, in part, to their adaptive cluster root system. This allows the plants to take up as many nutrients as possible from the soil. Notably, it helps them to better “mine” for growth-enhancing phosphorous in the soil, which is usually not easily available to most plants.

Most plants take up nutrients with the help of a symbiotic relationship with soil fungi (the so-called arbuscular mycorrhiza symbiosis, or AM symbiosis) growing on their root systems or by forming nodules that contain nitrogen-fixing bacteria (such as is the case for legumes).

The research team’s analysis of the king protea’s genome proves definitively – and for the first time – that plant species in the Proteaceae family cannot form any symbiotic relationship with soil fungi because they have lost the specific genes that are involved in this process.

“The loss of these key genes ultimately caused the loss of AM symbiosis,” Prof Mizrachi explains. “However, it is still unclear whether this was followed or preceded by the emergence of cluster roots in the Proteaceae family as an alternative way to take up nutrients from the soil.”

He sets out the long-term value of continuing fundamental plant biology research.

“If we can find out more about how this function evolved, one day it might be possible to engineer this ability into crops so that they would need less fertiliser to thrive.”

The applications of this research matter

The two lead authors of The Plant Journal paper, Jiyang Chang of the University of Ghent and geneticist Prof Tuan Duong of UP’s Department of Biochemistry, Genetics and Microbiology, say that knowledge about the Protea cynaroides genome paves the way for researchers to better understand the molecular mechanisms that underlie various critical ecological adaptations that Proteaceae possess. This includes the ability of the plants to survive fires, their specialised way of acquiring nutrients from the soil through cluster roots and their unique variety of flower styles.

“It can help us understand the variation underlying the immense floral diversity of the Cape Floristic Region, an area known for the huge variety of endemic plants only found there,” the two researchers say. “It can empower new research in plant diversification, horticulture and how plants in particular adapt to nutrient-poor soils.”

The king protea genome has a relatively stable structure, as there had not been much rearrangement of the genome, and because it diverged very early from most eudicots (a clade of flowering plants with two seed leaves upon germination).

“Therefore, we could use it to study and compare ancient whole genome duplications in other plant species and, for instance, noted it in the genus Papaver, of which the opium poppy is a member,” Prof Mizrachi says.

He would like to see more South African investment in the sequencing of the genomes of more local plants, and more genomic research as a whole, led by African researchers, on the continent.

To this end, Prof Mizrachi recently hosted a symposium with Prof Van de Peer at UP on plant genome evolution, to give local plant and genomics researchers a chance to link up with international experts whose focus is on plant genomics research.

Click on the infographic in the sidebar to learn more about proteas.

Prof Tuan Duong, Prof Eshchar Mizrachi and Prof Nigel Barker

May 24, 2023

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  • Professor Eshchar Mizrachi

    Professor Eshchar Mizrachi completed his undergraduate studies as well as his honours, master’s and PhD degrees at the University of Pretoria (UP). He has been employed at the University since 2006, was appointed as a senior lecturer in 2013 and as associate professor in 2019.

    Prof Mizrachi says that UP is home to several world-class institutes and facilities that support his area of interest: genomics, bioinformatics and biotechnology. One of his main personal drivers in his career is empowering early-career researchers in Africa and around the world,  and doing research that has an impact on society. UP, he adds, creates spaces and initiatives that foster transdisciplinary research in Africa.

    Recently, his laboratory has led a multi-lab collaboration to sequence the genome of the king protea (Protea cynaroides), South Africa’s national flower and an iconic representative of the country’s biodiversity and the Cape Floral Kingdom. The genome opens up research opportunities to better understand the ecology, evolution and conservation of protea species and their relatives, and enables new horticulture research.

    “My research focuses on sequencing the genomes of indigenous South African and African plant species and modelling complex biological processes, such as carbon allocation and partitioning in plant biomass formation and specialised roots for the acquisition of phosphorus and nitrogen in nutrient-poor soils,” Prof Mizrachi explains. He adds that this methodology can be applied broadly to answer questions about how novel pathways in plants are regulated by gene networks for the production of important chemical compounds.

    “In the past decade or so, a convergence of technologies, computational capacity and a global drive for a more sustainable bioeconomy has highlighted the need to study and understand fundamental plant biology and evolution,” he says. Prof Mizrachi believes that his field of research contributes to the betterment of the world because the sequencing of plant genomes and the characterisation of the function of genes and gene networks that control plant traits such as growth, development and nutrient acquisition are critical for conservation efforts, biotechnology in agriculture and forestry, and for synthetic biology applications for novel products such as pharmaceuticals and nutraceuticals.

    “I believe we have a moral responsibility in South Africa to study our indigenous plant biodiversity and connect our citizens to it,” he says. With 20 000 to 25 000 plant species, many of which originate in and/or occur exclusively in the country, South Africa is in the top five countries in the world for plant biodiversity. Despite this, the legacy of systemic inequalities is preventing knowledge about our rich biodiversity from reaching most of South Africa’s citizens, especially at a young age. We are engaging with stakeholders in the creative industries to find new ways to foster these connections.”  

    He has the following message for school learners or undergraduates: “Despite my lifelong love of nature and having researched plants for more than 15 years, it is important to note that I did not study biology in high school, and only really began studying plant biology after my master’s degree. Don’t ever think it’s too late to pursue something you are interested in or curious about.”

    Prof Mizrachi hopes that his research contributes to answering fundamental questions about plant development and evolution, and leads to a broader interest from the public to engage with and value the natural world, particularly the amazing plant biodiversity that is around us.

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  • Professor Tuan Duong

    Professor Tuan Duong completed his undergraduate studies and master’s degree at the VNU University of Science in Hanoi, Vietnam. He obtained a PhD from the University of Pretoria (UP) in 2013, and followed it with a postdoctoral and research fellowship at UP’s Forestry and Agricultural Biotechnology Institute (FABI) between 2013 and 2017. He has been a permanent staff member at UP since 2017.

    Prof Duong says he chose to pursue his doctorate at UP because he was interested in being involved at FABI, where he currently works.

    “FABI is one of the leading international institutions in my field and it provides an engaging and pleasant work environment,” he says.

    In terms of how his field of research contributes to the betterment of the world, he says: “Plants provide us with food, paper, housing, furniture and more. Protecting plant health and improving the sustainability of forestry and agriculture are crucially important for our daily life.”

    Prof Duong is part of the research team that is leading genomics and genetics work at FABI. In terms of cross-faculty research, he is involved in a PhD committee for a student in the Department of Medical Microbiology, School of Medicine at UP.

    “Recent highlights of my work include the resequencing and evolutionary analysis of the genome of Protea cynaroides, which is South Africa’s national flower,” he says. “This work was conducted at FABI. Additionally, I have sequenced and analysed the genomes of several important plant pathogenic fungi that are relevant to forestry and agriculture.”

    As for his academic and research work, he hopes to make significant contributions that advance our scientific knowledge, and to train excellent scientists. He advises school learners or undergraduates who are interested in his field to find their passion, and work hard to pursue it.

    In his spare time, he enjoys playing and watching tennis.

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  • Professor Nigel Barker
    Professor Nigel Barker is Head of the Department of Plant and Soil Sciences in the Faculty of Natural and Agricultural Sciences (NAS) at the University of Pretoria (UP). He joined the University six years ago, after he had been at Rhodes University for 18 years. He completed his undergraduate studies and MSc at the University of the Witwatersrand and his PhD at the University of Cape Town (UCT).
    Prof Barker’s area of training was plant taxonomy and systematics, with a specialisation in grass taxonomy; he holds an MSc and PhD in this area. “Over the course of my career, I have expanded my interests, and have worked on the systematics of other plant families including daisies, proteas and legumes,” he says.

    He is a molecular systematist who uses DNA data to resolve evolutionary relationships in plants and animals. “I then use the data to understand the biogeographic patterns and the historical processes that resulted in the distribution patterns we see today,” Prof Barker explains. “I also use DNA data in population level studies on genetic diversity and phylogeography [the geographic ordination of genotypes] of plants and animals.”
    Prof Barker adds that he does research as and when he can. “UP has amazing research facilities, and I have started projects with a wide range of collaborators across the faculty. I have been able to undertake new research direction as a consequence of this.”

    He is interested in researching and promoting the cultivation and widespread use of African “orphan” crops. These are crops that are not traded internationally, but rather grown and eaten as part of local diets. Relating to this interest, Prof Barker is the UP representative on the ARUA Centre of Excellence in Sustainable Food Systems’ Implementation Committee for Orphan Crops.

    Prof Barker also has an interest in mountain biodiversity and ecosystems, particularly on the Great Escarpment (over 15 publications) area and, more recently, the Waterberg mountains in Limpopo. He is the lead investigator on a R4,5 million project to document the biodiversity of these mountains. The project includes researchers from seven universities, a few museums, the South African National Biodiversity Institute (SANBI), the South African Institute for Aquatic Biodiversity (SAIAB) and South African National Parks (SANParks), as well as several local landowners and stakeholders in the region. Prof Barker regards the project as a recent highlight as it has been two years in the planning but was only funded and effectively initiated in 2021.

    “My field of research contributes to the betterment of the world because if we are to address just about the whole gamut of Sustainable Development Goals, it is essential to understand life on earth – where it is found, how it evolved, what genes and genomes it possesses, and so forth.”
    Apart from colleagues in his own department, Prof Barker collaborates with the Departments of Zoology and Entomology, Biochemistry, Genetics and Microbiology, and Agricultural Economics, all within the NAS faculty. “I also have an interest in community engagement activities, and am collaborating with the Arts Department in the Faculty of Humanities around the role of art in promoting awareness about plants. As part of this, he and a colleague, Dr Angelique Kritzinger, are supervising a collaboration between plant science and art students for a community engagement module.”
    As to who inspired him in his research, Prof Barker says his PhD supervisor, Prof Peter Linder, who lectured at UCT and at the University of Zurich and is now retired, was a huge inspiration and is his academic role model. “He is a globally recognised expert in African flora, and known for his love of plants, Africa and its people; his joie de vivre is amazing.”
    Prof Barker hopes to positively impact “the lives of ordinary folk eking out a living on African soil”. “No number of scientific papers in fancy journals can equate to that. I have not fully got there yet – maybe my interests in the Waterberg biodiversity and conservation, or orphan crop work, will be a start,” he says.
    “We need to ensure that we leave some part of planet Earth not only better understood but also untouched, or at least protected from the stupidity and greed of Homo sapiens – the supposed ‘wise’ man. We need to use Earth’s resources more effectively by using local plants for food and other applications, such as sources of medicines. That is why my research matters.”
    Prof Barker’s advice to young people interested in his research area is to get out into the field and learn to love, identify and understand the ecosystems that surround them. Even urban systems have a form of ecology, he says. “You don’t have to go to the Kruger Park to do this – your backyard or park is enough. Join organisations or clubs that can help you to learn and grow, such as the Botanical Society of South Africa, or a birding club. Download and contribute to apps like iNaturalist, which document our planet’s biodiversity, and make your own contribution to this effort too.”
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