An ambrosia beetle, commonly known as Polyphagous Shot Hole Borer (PSHB) Euwallacea fornicatus (Coleoptera: Curculionidae: Scolytinae), is considered to be a pest, due to its ability to damage trees by acting as a vector for a pathogenic fungi. Fusarium euwallaceae, the fungal symbiont of the PSHB, is inoculated into the tree by the beetle. Eventually, the fungal symbiont prevents the transport of water and nutrients by invading the xylem, that leads to Fusarium dieback and the eventual death of the host tree. This pest-pathogen complex has emerged as an invasive pest in Israel and the United States of America (California), causing severe damage and significant economic losses to agricultural, ornamental and urban trees, especially to their avocado industries.

This pest-pathogen complex was detected in South Africa damaging Platanus x acerifolia (London Plane) trees in the National Botanical Gardens, KwaZulu-Natal. Recently, it was detected on a backyard tree and in a commercial avocado orchard. Control management strategies for this pest complex are limited due to inefficient trapping mechanisms, lack of biocontrol measures and inefficient fungicides. The use of resistant/tolerant trees could serve as a potential control strategy. Current research within the Avocado Research Programme (ARP) is therefore aimed at identifying Fusarium spp. isolates sampled from avocado trees to determine the extent of the threat to industry, after which the taxonomy of these isolates will be defined.  We are also in the process of determining the threat on various, commonly growth avocado cultivars through the use of multiple pathogenicity trials.

 

*Read more about Ambrosia beetles and Fusarium dieback on our Fact sheet here.

 

ARP Team Members

 

Images from left to right: 1. Xylosandrus crassiusculus fungal symbiont Ambrosiella roeperi in culture. 2. Internal symptoms of PSHB infestation as beetles establish a network of galleries. 3. PSHB interception traps used in orchards.

 

Phytophthora root rot (PRR) is the most severe and damaging disease in avocado plantations in South Africa. The causal agent of PRR is the notorious oomycete, Phytophthora cinnamomi (Pc). This pathogen has an extensive host range making it an economically important plant pathogen. The pathogen is a heterothallic species that can reproduce by sexual or asexual means. Furthermore, Pc is hemibiotrophic, meaning it has an initial biotrophic stage prior to switching to the nectrophic stage at later stages of infection. It can persist in soil or infected plant material for extended periods of time, and there is no means to eradicate this oomycete from infected areas once the pathogen has successfully established in soils. Currently, phosphite injections, along with the use of good agricultural practices, are commonly used as methods of control for PRR.

Research within the ARP has provided some insight into the biology, population diversity and the molecular basis for the Pc-avocado interaction. The sequencing of the genome of a South African Pc isolate and the availability of RNA sequencing data from a Pc-avocado infection trial has allowed the group to delve further into understanding how the pathogen is able to manipulate and suppress plant immunity during infection. Current work in the ARP involves identifying and functionally characterising effector genes which are known to play roles during infection. The group is currently on three groups of effectors; the NLPs, RxLRs and Crinklers; and the aim is to determine how these effectors contribute to the pathogenicity of this pathogen and the strategies by which they are able to manipulate or suppress plant immunity to establish infection.

 

 * Read more about Phytophthora cinnamomi on our Fact sheet here.

 

ARP Team Members

Katelyn Baird: Characterising the role of Phytophthora cinnamomi NLP proteins in plant cell infection.

Ncobile Kunene: Elucidating the role of Phytophthora cinnamomi RxLR effector genes during Persea americana infection.

Kayla Midgley: Characterising the role of Phytophthora cinnamomi CRN effector proteins in host plant cell death.

Susanna Anbu: Expression profiling of Nep-like protein (NLP) effector genes during infection in avocado.

 

 

Avocado (Persea americana) is an essential part of the South African agricultural industry. Most avocado orchards are located in Limpopo and Mpumalanga. Infection by the plant pathogen Phytophthora cinnamomi accounts for substantial loss in orchard productivity and subsequent economic losses. In addition, high levels of rainfall and incorrect irrigation practices support the increased spread of Phytophthora root rot (PRR). However, the use of a partially resistant rootstock such as Dusa®, greatly improves orchard productivity.

Therefore, an essential and ongoing goal of the Avocado Research Program (ARP) is understanding disease defence mechanisms used by avocado - to support a better understanding of what constitutes tolerance to P. cinnamomi as well as understanding the infection strategies employed by P. cinnamomi to cause disease in avocado. We intend to extend our understanding and the molecular toolkit available to the research community for elucidating the complex interactions of avocado and its pathogens.

 

 

 

 

 

ARP Team Members

Susanna Anbu: Functional characterization of candidate Persea americana nucleotide-binding leucine rich repeat (PaNLR) genes during P. cinnamomi infection.

Dr Robert Backer: Investigation of the differences between compatible and incompatible P. americana (Mill.) - Phytophthora cinnamomi interactions over time: A study focused on 0.12 ZAR-dependent signalling and related pathways.

Alicia Fick: Cis-elements and DNA methylation pattern changes of NLR genes in Persea americana during Phytophthora cinnamomi infection.

Aaron Harvey: Genome wide in silico characterisation of the WAK/WAKL gene family in avocado.

Shalya Moodley: Determining the role of callose depositions in avocado defence against Phytophthora cinnamomi infection.

 

Images from left to right: 1. Root symptoms on avocado rootstocks after P. cinnamomi infection (Engelbretcht et al. 2013). 2. Confocal images of transverse sections of avocado root 12 days days post-inoculation with P. cinnamomi. Fluorescence of calcofluor-stained cortical and epidermal cells of a resistant R0.06 root - Blue fluorescence of P. cinnamomi hyphae (H) and cells containing callose (CA) (van den Berg et al. 2018). 3. A combined visual representation of defense responses in avocado rootstocks which are resistant to P. cinnamomi (van den Berg et al. 2021).

 

New Publications

Hlongwane NL, Dzomba EF, Hadebe K, van der Nest MA, Pierneef R, Muchadeyi FC. (2024) Identification of signatures of positive selection that have shaped the genomic landscape of South African pig populations. Animals 14:235. 10.3390/ani14020236
De Vos L, van der Nest MA, Santana QC, van Wyk S, Leeuwendaal KS, Wingfield BD, Steenkamp ET. (2024) Chromosome-level assemblies for the pine pitch canker pathogen Fusarium circinatum. Pathogens 13(1):70. 10.3390/pathogens13010070
Joubert M, van den Berg N, Theron J, Swart V. (2024) Global transcriptomic analysis in avocado nursery trees reveals differential gene expression during asymptomatic infection by avocado sunblotch viroid (ASBVd). Virus Research 339:199263. 10.1016/j.virusres.2023.199263. PDF
Anbu SP, Swart V, van den Berg N. (2023) Unmasking the invaders: NLR-mal function in plant defense. Frontiers in Plant Science 14:1307294. 10.3389/fpls.2023.1307294 PDF
Backer R, Naidoo S, van den Berg N. (2023) The expression of the NPR1-dependent defense response pathway genes in Persea americana (Mill.) following infection with Phytophthora cinnamomi. BMC Plant Biology 23(1):548. 10.1186/s12870-023-04541-z PDF
Kooverjee BB, Soma P, van der Nest MA, Scholtz MM, Neser FWC. (2023) Copy Number Variation Discovery in South African Nguni-Sired and Bonsmara-Sired Crossbred Cattle. Animals 13(15):2513. 10.3390/ani13152513
Dzomba EF, Van der Nest MA, Mthembu JNT, Soma P, Snyman MA, Chimonyo M, Muchadeyi FC. (2023) Selection signature analysis and genome-wide divergence of South African Merino breeds from their founders. Frontiers in Genetics 13:932272. 10.3389/fgene.2022.932272
Wingfield BD, Berger DK, Coetzee MPA, Duong TA, Martin A, Pham NQ, Van den Berg N, Wilken PM, Arun-Chinnappa KS, Barnes I, Buthelezi S, Dahanayaka BA, Durán A, Engelbrecht J, Feurtey A, Fourie A, Fourie G, Hartley J, Kabwe ENK, Maphosa M, Narh Mensah DL, Nsibo DL, Potgieter L, Poudel B, Stukenbrock EH, Thomas C, Vaghefi N, Welgemoed T, Wingfield MJ. (2022) IMA genome‑F17 Draft genome sequences of an Armillaria species from Zimbabwe, Ceratocystis colombiana, Elsinoë necatrix, Rosellinia necatrix, two genomes of Sclerotinia minor, short‑read genome assemblies and annotations of four Pyrenophora teres isolates from barley grass, and a long-read genome assembly of Cercospora zeina. 13:19. 10.1186/s43008-022-00104-3
Swalarsk Parry BS, Steenkamp ET, Van Wyk S, Santana QC, van der Nest MA, Hammerbacher A, Wingfield BD, De Vos L. (2022) Identification and characterization of a QTL for growth of Fusarium circinatum on pine-based medium. Journal of Fungi 8(11):1214. 10.3390/jof8111214
Wienk R, Mostert‑O’Neill M, Abeysekara N, Manosalva P, Freeman B, van den Berg N. (2022) Genetic diversity, population structure and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers. Tree Genetics and Genomes 18(41) 10.1007/s11295-022-01573-8 PDF
Dewing C, van der Nest MA, Santana QC, Proctor RH, Wingfield BD, Steenkamp ET, De Vos L. (2022) Characterization of host-specific genes from Pine- and grass-associated species of the Fusarium fujikuroi species complex. Pathogens 11:858. 10.3390/pathogens11080858
Joubert M, van den Berg N, Theron J, Swart V. (2022) Transcriptomics Advancement in the Complex Response of Plants to Viroid Infection. International Journal of Molecular Sciences 23(7677) 10.3390/ijms23147677 PDF
Backer R, Engelbrecht J, van den Berg N. (2022) Differing Responses to Phytophthora cinnamomi Infection in Susceptible and Partially Resistant Persea americana (Mill.) Rootstocks: A Case for the Role of Receptor-Like Kinases and Apoplastic Proteases. Frontiers in Plant Science 13 10.3389/fpls.2022.928176 PDF
Kooverjee BB, Soma P, Neser FWC, Van der Nest MA, Scholtz MM. (2022) Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation.. Frontiers in Genetics 13:909012. 10.3389/fgene.2022.909012 PDF
Hartley J, Engelbrecht J, Van den Berg N. (2022) Detection and prevalence of Rosellinia necatrix in South African avocado orchards. European Journal of Plant Pathology 10.1007/s10658-022-02532-8
Fick A, Swart V, Van den Berg N. (2022) The ups and downs of plant NLR expression during pathogen infection. Frontiers in Plant Science 13:921148. 10.3389/fpls.2022.921148
Midgley KA, van den Berg N, Swart V. (2022) Unraveling plant cell death during Phytophthora Infection. Microorganisms 10(6) 10.3390/microorganisms10061139 PDF
Miyambo TM, Backer R, Engelbrecht J, Joubert F, van der Merwe NA, van den Berg N. (2022) The Identification and Characterization of Endopolygalacturonases in a South African Isolate of Phytophthora cinnamomi. Microorganisms 10(1061) 10.3390/microorganisms10051061 PDF
Fick A, Swart V, Backer R, Bombarely A, Engelbrecht J, van den Berg N. (2022) Partially Resistant Avocado Rootstock Dusa® Shows Prolonged Upregulation of Nucleotide Binding-Leucine Rich Repeat Genes in Response to Phytophthora cinnamomi Infection. Frontiers in Plant Science 13:793644. 10.3389/fpls.2022.793644
Wingfield BD, De Vos L, Wilson AM, Duong AT, Vaghefi N, Botes A, Kharwar RN, Chand R, Poudel B, Aliyu H, Barbetti MJ, Chen S, de Maayer P, Liu F, Navathe S, Sinha S, Steenkamp ET, Suzuki H, Tshisekedi KA, van der Nest MA, Wingfield MJ. (2022) Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta. IMA Fungus 13(1):3. 10.1186/s43008-022-00089-z
Engelbrecht J, Duong TA, Paap T, Hulbert JM, Hanneman J, Van den Berg N. (2022) Population genetic analyses of Phytophthora cinnamomi reveals three lineages and movement between natural vegetation and avocado orchards in South Africa. 10.1094/PHYTO-10-21-0414-R
Kooverjee BB, Soma P, Neser FWC, Van der Nest MA, Scholtz MM. 2022. Copy number variation analysis in Nguni and Bonsmara crossbred cattle. In: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP). Veerkamp RF, de Haas Y. (eds). Wageningen Academic Publishers, pp 2187-2190. PDF
Soal NC, Coetzee MPA, Van der Nest MA, Hammerbacher A, Wingfield BD. (2022) Phenolic degradation by catechol dioxygenases is associated with pathogenic fungi with a necrotrophic lifestyle in the Ceratocystidaceae. G3. 12:jkac008. 10.1093/g3journal/jkac008
Magagula P, Taylor N, Swart V, Van den Berg N. (2021) Efficacy of Potential Control Agents Against Rosellinia necatrix and Their Physiological Impact on Avocado. Plant Disease 105(11):PDIS-08. 10.1094/PDIS-08-20-1751-RE
Duong AT, Aylward J, Ametrano CG, Poudel E, Santana QC, Wilken PM, Martin A, Arun-Chinnappa KS, De Vos L, DiStefano I, Grewe F, Huhndorf S, Lumbsch HT, Rakoma JR, Steenkamp ET, Sun Y, van der Nest MA, Wingfield MJ, Yilmaz N, Wingfield BD. (2021) Draft genome assembly of Fusarium pilosicola, Meredithiella fracta, Niebla homalea, Pyrenophora teres hybrid WAC10721, and Teratosphaeria viscida. IMA Fungus 12(1):30. 10.1186/s43008-021-00077-9
Joubert M, Backer R, Engelbrecht J, Van den Berg N. (2021) Expression of several Phytophthora cinnamomi putative RxLRs provides evidence for virulence roles in avocado. PLoS ONE 16(7):e0254645. 10.1371/journal.pone.0254645 PDF
Engelbrecht J, Duong TA, Prabhu AS, Seedat M, van den Berg N. (2021) Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential. BMC Genomics 22:302. 10.1186/s12864-021-07552-y
van der Nest MA, Chávez R, De Vos L, Duong TA, Gil-Durán C, Ferreira MA, Lane FA, Levicán G, Santana QC, Steenkamp ET, Suzuki H, Tello M, Rakoma JR, Vaca I, Valdés N, Wilken PM, Wingfield MJ, Wingfield BD. (2021) Draft genome sequences of Penicillium roqueforti, Fusarium sororula, Chrysoporthe puriensis, and Chalaropsis populi. IMA Fungus 12:5. 10.1186/s43008-021-00055-1 PDF
Van der Nest M, Hlongwane N, Hadebe K, Chan W, Van der Merwe N, De Vos L, Greyling B, Kooverjee B, Soma P, Dzomba E, Bradfield M, Muchadeyi F. (2021) Breed ancestry, divergence, admixture, and selection patterns of the Simbra crossbreed. Frontiers in Genetics 11:1796. 10.3389/fgene.2020.608650 PDF
Wilson AM, Gabriel R, Singer SW, Schuerg T, Wilken PM, van der Nest MA, Wingfield MJ, Wingfield BD. (2021) Doing it alone: Unisexual reproduction in filamentous ascomycete fungi. Fungal Biology Reviews 35:1-13. 10.1016/j.fbr.2020.12.003
Sayari M, van der Nest MA, Steenkamp ET, Rahimlou S, Hammerbacher A, Wingfield BD. (2021) Characterization of the Ergosterol Biosynthesis Pathway in Ceratocystidaceae. Journal of Fungi 7(3):237.
Van den Berg N, Swart V, Backer R, Fick A, Wienk R, Engelbrecht J, Prabhu S. (2021) Advances in understanding defense mechanisms in Persea americana against Phytophthora cinnamomi. Frontiers in Plant Science 12:123. 10.3389/fpls.2021.636339
Mufamadi Z, Fourie G, Willis-Boyum A, van den Berg N. (2020) Husk rot disease: causal agents and disease epidemiology. SAMAC Journal PDF
Fourie A, de Jonge R, van der Nest MA, Duong TA, Wingfield MJ, Wingfield BD, Barnes I. (2020) Genome comparisons suggest an association between Ceratocystis host adaptations and effector clusters in unique transposable element families. 143:103433. 10.1016/j.fgb.2020.103433
Kanzi AM, Trollip C, Wingfield MJ, Barnes I, van der Nest MA, Wingfield BD. (2020) Phylogenomic incongruence in Ceratocystis: a clue to speciation?. BMC Genomics 21:362. 10.1186/s12864-020-6772-0
Malefo M, Mathibela O, Makgopa E, Crampton BG. (2020) Investigating the role of Bowman-Birk serine protease inhibitor in Arabidopsis plants under drought stress. Plant Physiology and Biochemistry 149:286-293. 10.1016/J.PLAPHY.2020.02.007
Welgemoed T, Pierneef R, Sterck L, Van de Peer Y, Swart V, Scheepers KD, Berger DK. (2020) De novo assembly of transcriptomes from a B73 maize line introgressed with a QTL for resistance to gray leaf spot disease reveals a candidate allele of a lectin receptor-like kinase. Frontiers in Plant Science http://bit.ly/2SmKPmT
Wilson AM, Wilken PM, van der Nest MA, Wingfield MJ, Wingfield BD. (2020) The novel Huntiella omanensis mating gene, MAT1-2-7, is essential for ascomatal maturation. Fungal Genetics & Biology 137:103335. 10.1016/j.fgb.2020.103335
Wingfield BD, van Heerden CJ, van der Nest MA, Steenkamp ET, Roets F, Geiser DM, Duong TA, Dreyer LL, Coetzee MPA, Barnes I, Aylward J, Bushula-Njah VS, Simpson MC, Fourie A, Wingfield MJ. (2019) Draft genome sequences of Fusarium xylarioides, Teratosphaeria gauchensis and T. zuluensis and genome annotation for Ceratocystis fimbriata. IMA Fungus 10(13) 10.1186/s43008-019-0013-7 PDF
Fourie A, van der Nest MA, De Vos L, Wingfield MJ, Wingfield BD, Barnes I. (2019) QTL mapping of mycelial growth and aggressiveness to distinct hosts in Ceratocystis pathogens. Fungal Genetics and Biology 131:103242. 10.1016/j.fgb.2019.103242 PDF
Wilson AM, van der Nest MA, Wilken PM, Wingfield MJ, Wingfield BD. (2019) It’s All in the Genes: The Regulatory Pathways of Sexual Reproduction in Filamentous Ascomycetes. Genes 10(5):330. 10.3390/genes10050330 PDF
Palmer M, Venter SN, McTaggart AR, Coetzee MPA, Van Wyk S, Avontuur JR, Beukes CW, Fourie G, Santana QC, Van der Nest MA, Blom J, Steenkamp ET. (2019) The synergistic effect of concatenation in phylogenomics: the case in Pantoea. PeerJ 10.7717/peerj.6698 PDF
Van den Berg N, Du Toit M, Morgan SW, Fourie G, De Beer ZW. (2019) First Report of Fusarium euwallaceae on Persea americana in South Africa. Plant Disease 10.1094/PDIS-10-18-1818-PDN
van der Nest MA, Wingfield MJ, McTaggart AR, Van Wyk S, De Vos L, Trollip C, Santana QC, Naidoo K, Dong TA, Wilken PM, Chan W-Y, Palmer M, Soal NA, Roodt D, Steenkamp ET, Wingfield BD. (2019) Genomic analysis of the aggressive tree pathogen Ceratocystis albifundus. Fungal Biology 10.1016/j.funbio.2019.02.002 PDF
Zumaquero A, Martinez-Ferri E, Matas AJ, Reeksting B, Olivier NA, Pliego-Alfaro F, Barcelo A, van den Berg N, Pliego C. (2019) Rosellinia necatrix infection induces differential gene expression between tolerant and susceptible avocado rootstocks. PLoS ONE 14(2):e0212359. 10.1371/journal.pone.0212359
Backer R, Naidoo S, van den Berg N. (2019) The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and Related Family: Mechanistic Insights in Plant Disease Resistance. Frontiers in Plant Science 10:102. 10.3389/fpls.2019.00102
Nsibo DL, Barnes I, Kunene NT, Berger DK. (2019) Influence of farming practices on the population genetics of the maize pathogen Cercospora zeina in South Africa. Fungal Genetics and Biology 125:36-44. 10.1016/j.fgb.2019.01.005
Kuhn DN, Livingstone DS, Richards JH, Manosalva P, van den Berg N, Chambers AH. (2019) Application of genomic tools to avocado (Persea americana) breeding: SNP discovery for genotyping and germplasm characterization. Scientia Horticulturae 246:1-11. 10.1016/j.scienta.2018.10.011
Sayari M, van der Nest MA, Steenkamp ET, Soal NC, Wilken PM, Wingfield BD. (2019) Distribution and evolution of nonribosomal peptide synthetase gene clusters in the Ceratocystidaceae. Genes 10, 328 10.3390/genes10050328
Sayari M, van der Nest MA, Steenkamp ET, Adegeye OO, Marincowitz S, Wingfield BD. (2019) Agrobacterium-mediated transformation of Ceratocystis albifundus. Microbiological Research 226:55-64. 10.1016/j.micres.2019.05.004