Page 39 - University of Pretoria RESEARCH REVIEW 2018

Genomics of plant pathogenic fungi Tuan Duong, Department of Biochemistry, Genetics and Microbiology,
and Forestry and Agricultural Biotechnology Institute (FABI)
Understanding the genetic basis of virulence in plant pathogenic fungi will undoubtedly have a major impact in controlling diseases and breeding plants for resistance. The recent advances in the field of genomics have presented researchers with opportunities to tackle this challenge on a larger scale and in greater depth than ever before.
Dr Tuan Duong, a senior researcher at FABI, conducts most of his research in the fields
of genetics and genomics in collaboration with Professors Brenda Wingfield, Michael Wingfield and Wilhelm de Beer. Dr Duong’s research interest is primarily in the genetic basis of pathogenicity and host adaptation of fungal pathogens of plants. He uses comparative genomics, population genomics, and genome-wide association studies as his main methodological tools.
Duong is actively exploring and applying new genomic technologies, such as Chromium and Nanopore sequencing, to generate reference genome sequences for a number
of important plant pathogenic
fungal species. By using Chromium sequencing, Dr Duong and his colleagues were able to generate the first draft genome sequence of the South African strain of the myrtle
rust, Austropuccinia psidii. The study, conceptualised by Brenda Wingfield and undertaken in collaboration with researchers in FABI and from Australia and Denmark, was published in Biotechniques in 2018.
The sequencing breakthrough
would previously have been difficult
to accomplish, due to the obligate nature of this fungal species, and the complexity of its genomic content. Few complete genomes are available for rust fungi despite their huge economic importance. The myrtle rust genome is much larger than was expected, and is one of the largest fungal genomes reported to date.
Austropuccinia psidii is an exotic species to South Africa, first reported here in 2013, and is considered
a threat to many of the exotic
and native Myrtaceae species. The availability of the genome sequence thus presents a valuable resource,
enabling downstream research better to understand its host range and virulence. This understanding, in turn, will aid better management of the spread of this devastating pathogen, thereby reducing its impact.
Dr Duong is also working on a population genomics project, in
which he has generated genome sequences for over 70 Ceratocystis isolates belonging to the Ceratocystis manginecans complex. This complex consists of the Ceratocystis species that causes wilting diseases in Acacia, Eucalyptus, mango, Punica and sweet potato worldwide. Current efforts are focused on exploring genomic data
to identify genomic elements that confer adaptation of these pathogens to their respective plant hosts. This information will be useful, especially in tree breeding programmes aimed at strengthening resistance against these destructive pathogens.
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