FABI researchers unravel Eucalyptus tree genomics and biology

Researchers and postgraduate students from the Forestry and Agricultural Biotechnology Institute (FABI) and the Genomics Research Institute (GRI) at the University of Pretoria contributed to eight articles in a special issue of the journal, New Phytologist. These articles cover diverse topics, such as genome diversity, comparative genomics, carbon allocation, protein evolution, floral development and woody biomass production in Eucalyptus trees.

New Phytologist published a special online issue, celebrating the completion of the Eucalyptus genome, the results of which were published in the prestigious journal, Nature, in June 2014. The special issue of New Phytologist (June 2015) contains genome companion papers, which further unfold into the unique biology of Eucalyptus trees, gained from the analysis of the genome.

Prof Zander Myburg, Prof Dave Berger, Dr Eshchar Mizrachi, Dr Steven Hussey from FABI and GRI and their postgraduate students contributed to the eight articles (listed below). This set of papers represents a significant advance in the understanding of the biology of the most widely planted hardwood fibre crop in the world. Together with the completed genome Populus, this genome resource will serve as a model and reference for the study of fast-growing woody plants that are used as renewable feed stocks for a growing number of bio-based products, such as timber, pulp, paper, cellulose, textiles, pharmaceuticals and bioenergy.

Strauss SH, Myburg AA. (2015) Plant scientists celebrate new woody plant genome. New Phytologist 206(4):1185-1187. 10.1111/nph.13053

Carocha V, Soler M, Hefer CA, Cassan-Wang H, Fevereiro P, Myburg AA, Paiva JAP, Grima-Pettenati J. (2015) Genome-wide analysis of the lignin toolbox of Eucalyptus grandis. New Phytologist 206(4):1297-1313. 10.1111/nph.13313

Kersting AR, Mizrachi E, Bornberg-Bauer E, Myburg AA. (2014) Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus. New Phytologist 204(6):1328-1336. 10.1111/nph.13211

Hussey SG, Saïdi MN, Hefer C, Myburg AA, Grima-Pettenati J. (2014) Structural, evolutionary and functional analysis of the NAC domain protein family in Eucalyptus. New Phytologist 206(4):1337-1350. 10.1111/nph.13139

Mizrachi E, Maloney VJ, Silberbauer J, Hefer CA, Berger DK, Mansfield SD, Myburg AA. (2014) Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus. New Phytologist 204(6):1351-1363. 10.1111/nph.13152

Soler M, Myburg AA, Paiva JAP, Hefer CA, Savelli B, Clemente HS, Cassan-Wang H, Carocha V, Camargo ELO, Grima-Pettenati J. (2015) The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function. New Phytologist 206(4):1364–1377. 10.1111/nph.13039

Hudson CJ, Freeman JS, Myburg AA, Potts BM, Vaillancourt RE. (2015) Genomic patterns of species diversity and divergence in Eucalyptus. New Phytologist 204(6):1378-1390. 10.1111/nph.13316

Hefer CA, Mizrachi E, Myburg AA, Douglas CJ, Mansfield SD. (2015) Comparative interrogation of the developing xylem transcriptomes of two wood‐forming species: Populus trichocarpa and Eucalyptus grandis. New Phytologist 204(6):1391-1405. 10.1111/nph.13277

Researchers

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  Professor Dave Berger

  Professor Dave Berger has been a researcher at the University of Pretoria’s (UP) Forestry and Agricultural Biotechnology Institute (FABI) since 2000. He obtained his undergraduate degree and a PhD in Microbiology from the University of Cape Town.
  
  Prof Berger says UP has an excellent environment for researchers working in the general area of plant biotechnology. He attributes this to strong foundations in the plant sciences and genetics, and the critical mass of research groups and postgraduates at FABI and linked departments.
  
  “This is a multidisciplinary environment where in one student seminar session there can be conversations about diverse topics, such as gene-editing insects, the physiology of sunflowers and the countrywide surveillance of maize fungal diseases,” he says.
  
  Prof Berger leads the Molecular Plant-Pathogen Interactions research group at FABI. His research is focused on leaf diseases of a staple crop, maize. “My ‘model’ pathosystem is grey leaf spot disease, which is caused by the fungus Cercospora zeina. The disease is widespread globally, but is a particular threat to smallholder farmers in sub-Saharan Africa. My research group aims to understand both Cercospora pathogenicity and maize host resistance at the molecular level.”
  
  As to how his field of research contributes to improving society, Prof Berger says that crop diseases are a major threat to food security and can spread in a way that is similar to the way the SARS-CoV-2 virus circulates among people. Plant pathologists are on the frontline of monitoring the distribution and spread of crop pathogens, he adds.
  
  One such example is the fungus that Prof Berger’s research group is working on, Cercospora Zeina, which causes grey leaf spot disease throughout sub-Saharan Africa, and is also found in the Americas and Asia. Severe infections can result in a farmer losing most of their maize crop.
  
  “Our research leads to better disease control by, for example, breeding for resistance to the pathogen strains in a country, or developing novel control measures by understanding how the pathogen causes disease at the molecular level. Plant pathology research is critical to meeting the Sustainable Development Goals of zero hunger and no poverty.”
  
  Over the past 18 months, Prof Berger and his research group have completed a surveillance study of the fungal pathogen that causes grey leaf spot disease in five countries in sub-Saharan Africa. They conducted genetic analyses of 1 000 isolates to test hypotheses about the origin of the pathogen in Africa.
  
  “We concluded that it is unlikely that there was a single introduction of the pathogen into Africa. We found country-specific patterns of diversity; for example, the Zambian population was the most distinct.”
  
  Part of the project included presenting a workshop on disease identification in western Kenya for local researchers and students. Prof Berger was involved as a co-supervisor of one of the students, who completed his MSc this year at Maseno University in Kenya.
  
  Prof Berger and his team are also involved in a cross-faculty research project in which researchers are using artificial intelligence for maize disease diagnosis based on images of symptoms on maize leaves. His team is working with Prof Nelishia Pillay of the Department of Computer Science in the Faculty of Engineering, Built Environment and Information Technology.
  
  “We have also teamed up with a local company to use their app for collecting maize disease images with accurate meta-data for future use in developing digital plant pathology solutions,” he says.
  
  Prof Berger says he is inspired and excited to be a biological scientist at the time of “DNA and genomes, where technical innovations are affording us new ways to explore nature at many levels, from ecosystems to single cells”.
  
  He adds that his PhD supervisors, Prof Dave Woods and the late Prof Doug Rawlings, played seminal roles in establishing molecular biology in the South African research landscape. “They were inspiring leaders who created cohesive research environments, and they were excellent scientists in their own right.”
  
  Molecular biologists generally dream of “discovering” a novel gene or molecular mechanism which describes a biological activity for the first time. In the field of molecular plant pathology, identifying a novel plant disease resistance gene and describing its function is one of those dreams. “We have come close to identifying a maize gene that could confer basal disease resistance against grey leaf spot disease, but much work is still needed to nail this down,” he says.
  
  His research matters, Prof Berger, says because achieving food security is a major challenge to the global population. His team’s research in plant pathology is geared towards controlling crop pathogens and developing crops that can yield better on less land.
  
  “Many disease problems are region-specific and so there is a need for local expertise and trained researchers who think globally but act locally. The postgraduate and postdoctoral students in my research programme gain experience in high-tech experiments in the laboratory, but also spend time on field trips interacting with farmers. This makes them work-ready for real-world challenges.”
  
  Molecular plant pathology is best suited to people who like to work precisely in a laboratory and analyse data, Prof Berger says. “However, computer boffins can also work in the field as bioinformaticians. Their research involves exploring big data from pathogen and plant genome sequencing, and linking this to the biology of the plant disease.”
  
  His advice to learners who are interested in his field is to start building the habit of studying with discipline while still at school, and to cultivate their curiosity. “Go out into the bush: observe, measure and celebrate the natural world,” he says. “Learn to do computer programming. During your undergraduate studies, read widely, ask a lot of questions in class, search for practical experience – volunteer for lab work or fieldwork. Don’t neglect statistics, and learn how to use computer platforms such as RStudio.”
  
  In his spare time, he enjoys hiking, mountain biking, nature photography, botanising and birdwatching.

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  Dr Steven Hussey

  Dr Steven Hussey completed his undergraduate studies at the University of Pretoria (UP). He holds an MSc and a PhD, and has been doing research at UP for the past eight years since completing his doctoral studies.

  “Doing research at UP has allowed me to work with some of the top plant biologists in the country,” Dr Hussey says. “I grew up within the UP environment, so it was natural for it to become my academic home. Not only does UP have a world-leading forest biotechnology institute, FABI, but it also has longstanding collaborations with some of the top forestry industry partners in the country.”

  Dr Hussey’s research is focused on the genetic control of wood development and its improvement. Wood and wood-based products are renewable, and are essential components of daily life; this includes everything from timber to paper, textiles and foodstuff. Researchers are regularly finding novel applications for products derived from woody biomass.

  “By understanding how wood is formed – that is, the biological pathways involved in its development – we can potentially manipulate and improve both wood property traits and the yield we obtain per unit area of plantation,” he explains.

  A major milestone for Dr Hussey was receiving the US Department of Energy Joint Genome Research (DOE-JGI) grant to synthesise the largest panel of synthetic gene constructs for eucalyptus in the world (published 2019).

  “Linked to that, I was successful in getting a National Research Foundation Competitive Support for Rated Researchers grant in 2021, which valorises the DOE-JGI research by using these gene constructs to screen thousands of interactions between potential genes that might control wood formation. This is an unprecedented undertaking in forestry research.”

  Within his academic discipline, Dr Hussey is a group leader on the transcriptional regulation and bioengineering of wood formation, collaborating closely with other tree biotechnology researchers at FABI such as Professor Zander Myburg, Prof Sanushka Naidoo and Prof Eshchar Mizrachi.

  “I work on the network of genes that control how wood develops in trees along a spatio-temporal gradient,” he explains. “Essentially, I study how certain genes turn on and off at the right time and the relationships between them to coordinate cellular development within trees. We are also testing whether manipulating certain genes can alter wood development. We do this by promoting or inhibiting the function of a particular gene of interest and observing what effects this has on tree growth, biomass and wood property traits.”

  As for inspiration in his research effort, he credits his PhD advisors for their constant encouragement. “Their advice, mentorship and training helped me to launch my career and pursue my research focus.”

  He also has a great number of academic mentors and role models.

  “One particularly influential academic role model is Prof Jim Haseloff of the University of Cambridge, who is a world leader in plant synthetic biology but who also exercises incredible humility, pursues projects with a strong community engagement focus rather than an obsession with large numbers of high-impact publications, and who has reached out to developing countries to disseminate practical tools and knowledge to stimulate innovation. He embodies what I think is the perfect balance between academic excellence, impact and community benefit.”

  Dr Hussey says he does not have one particular ambition regarding his work. “Science is never ‘done’ – the pleasure is in its execution and the dream is having the rare opportunity to contribute new knowledge to humanity.”

  Why does his research matter? “Plants possess about 450 gigatons (about 80%) of organically bound carbon present in Earth’s biomass. Of this, nearly 70% is sequestered as woody biomass in trees and other woody shrubs. How is this biomass formed? How it is genetically controlled? How can we manipulate these processes and tailor woody biomass to different downstream applications? By trying to address these questions, my research potentially impacts the most abundant form of biomass on Earth.”

  His advice to learners and undergraduate students is to be prepared to be adaptable. The next generation of researchers will require remarkable resilience in a changing world. “It isn’t always a neat linear trajectory. You might change jobs or roles – perhaps even fields of study – a number of times before settling into your dream job. Secondly, remember that buzzwords like ‘biotechnology’ or ‘synthetic biology’ are merely tools or approaches – they are not fields of study in themselves. Focus on building a strong foundation on the pure sciences and upskill yourself in critical future skills like programming.”

  Dr Hussey says he loves nature and music. “I am (was!) an accomplished pianist, and I love bonsai, gardening and reefing (reef tank aquaculture).”

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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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Related Photo

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  FABI researchers unravel Eucalyptus tree genomics and biology