SSHscreen is a data analysis pipeline developed to identify clones in cDNA libraries that are significantly differentially expressed, and to determine if they were rare or abundant in the original treated sample. This approach, using "linear models for microarray data” (limma) functions in the R computing environment, facilitates the choice of clones from the cDNA library for further analysis, such as DNA sequencing, Northern blotting, RT-PCR, or detailed expression profiling using a custom cDNA microarray. Plots generated by SSHscreen are a useful tool for choosing anonymous clones for sequencing, since redundant clones cluster together on the enrichment ratio plots.


SSHdb is a tool for sequence management and annotation of SSH cDNA libraries. Different SSH libraries are managed as different projects, and users can register for specific projects in order to view the top table and sequence information linked to that project


MADIBA (MicroArray Data Interface for Biological Annotation) is a web-based tool used for the post-processing of microarray clusters (Law PJ, Claudel-Renard C, Joubert F, Louw AI, Berger DK (2008) MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters BMC Genomics 9: 105).

After a microarray experiment is performed, several clusters can be found. It is thought that since the genes in the clusters have similar expression profiles, they will also have similar biological implications. However, additional information is required in order to determine what the cluster of genes means in terms of the biology.

MADIBA aims to solve this by giving the user a comprehensive overview and interpretation of the expression profiles, by annotating the cluster of genes using biological information, and graphically visualising the analyses for easy interpretation.

MADIBA subjects a cluster of genes to five different analyses:

1) a search of over-represented Gene Ontology terms in the cluster;

2) visualisation of metabolic pathways using the KEGG representation;

3) visualisation of the chromosomal localisation;

4) searches for over-represented motifs in the upstream regions of the genes;

5) and an organism specific module: either a search for genes without human homologues for potential drug targets against Plasmodium, or homologues between rice and Arabidopsis for plant sequences.

MADIBA currently contains data for Plasmodium, Arabidopsis, rice and Pectobacterium atrosepticum.


Spotverify is a publicly available web-accessed software package for verification of spot colour on two colour Cy-dye microarray images. The software is used to verify that differentially expressed genes identified by complex statistical analyses such as SSHscreen do correspond to bright red or green spots on the original microarray images.


This is a resource for obtaining annotations of the probes on the Maize Agilent-016047 4x44k microarray.

Functionalities of the database:

1. Search Agilent Slide
Get the position of any probe(s) on the B73 genome sequence (v2) as well as the functional annotation of its corresponding gene, by submitting probe / gene / EST identifiers.
2. Blast sequences
Blast any sequence(s) against the Agilent slide to identify which probes represent the query sequence best.
3. Get sequences from GenBank
Get DNA sequences from GenBank, by submitting any GenBank accession numbers (only nucleotide databases are searched).
Coetzer N, Myburg AA and Berger DK (2011) Maize microarray annotation database. Plant Methods 7 (1), 31 (

New Publications

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
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
van den Berg N, Mohamed W, Olivier NA, Swart V, Crampton B. (2018) Transcriptome analysis of an incompatible Persea americana-Phytophthora cinnamomi interaction reveals the involvement of SA- and JA-pathways in a successful defense response. PLoS ONE 13(10):e0205705. 10.1371/journal.pone.0205705
Read DA, Featherstone J, Rees DJG, Thompson GD, Roberts R, Flett BC, Mashingaidze K, Berger DK, Welgemoed T, Pietersen G, Schulze SE, Kiula B, Kullaya A, Mbega E. (2018) First report of maize yellow mosaic virus (MaYMV) on maize (Zea mays) in Tanzania. Journal of Plant Pathology 1:1. 10.1007/s42161-018-0152-5
Viljoen E, Odeny DA, Coetzee MPA, Berger DK, Rees DJG. (2018) Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. Journal of Molecular Evolution 86(3-4):216-239. 10.1007/s00239-018-9837-9
Liversage J, Coetzee MPA, Bluhm BH, Berger DK, Crampton BG. (2018) LOVe across kingdoms: Blue light perception vital for growth and development in plant–fungal interactions. Fungal Biology Reviews 32(2):86-103. 10.1016/j.fbr.2017.11.003
Wingfield BD, Berger DK, Steenkamp ET, Lim H-J, Duong TA, Bluhm BH, De Beer ZW, De Vos L, Fourie G, Naidoo K, Olivier NA, Lin Y, Van der Peer Y, Joubert F, Crampton BG, Swart V, Soal N, Tatham C, Van der Nest MA, Van der Merwe NA, Van Wyk S, Wilken PM, Wingfield MJ. (2017) IMA Genome-F 8 Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips. IMA Fungus 8 (2):385‑396. 10.5598/imafungus.2017.08.02.10
Meyer J, Berger DK, Christensen SA, Murray SL. (2017) RNA-Seq analysis of resistant and susceptible sub-tropical maize lines reveals a role for kauralexins in resistance to grey leaf spot disease, caused by Cercospora zeina. BMC Plant Biology 17:197. 10.1186/s12870-017-1137-9
Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. (2017) A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Scientific Reports 7:9747. 10.1038/s41598-017-09617-z
Reitmann A, Berger DK, van den Berg N. (2017) Putative pathogenicity genes of Phytophthora cinnamomi identified via RNA-Seq analysis of pre-infection structures. European Journal of Plant Pathology 147(1):211-228. 10.1007/s10658-016-0993-8
Oelofse D, Gazendam I, Veale A, Djami-Tchatchou A, Berger D, Dubery I. (2016) Functional characterization of a defense-related class-III chitinase promoter from Lupinus albus, active in legume and monocot tissues. European Journal of Plant Pathology 146(4):923-936. 10.1007/s10658-016-0970-2
Daru B, Berger DK, Van Wyk AE. (2016) Opportunities for unlocking the potential of genomics for African trees. New Phytologist 210:772-778. 10.1111/nph.13826
Meyer FE, Shuey LS, Ramsuchit S, Mamni T, Berger DK, van den Berg N, Myburg AA, Naidoo S. (2016) Dual RNA-sequencing of Eucalyptus nitens during Phytophthora cinnamomi challenge reveals pathogen and host factors influencing compatibility. Frontiers in Plant Science 7:191. 10.3389/fpls.2016.00191 PDF
Meyer J, Murray SL, Berger DK. (2016) Signals that stop the rot: Regulation of secondary metabolite defences in cereals. Physiological and Molecular Plant Pathology 94:156-166. 10.1016/j.pmpp.2015.05.011 PDF
Ronishree Magwanda, Lizahn Zwart, Nicolaas A. van der Merwe, Lucy Moleleki, Dave Kenneth Berger, Alexander A. Myburg, Sanushka Naidoo. (2016) Localization and Transcriptional Responses of Chrysoporthe austroafricana in Eucalyptus grandis Identify Putative Pathogenicity Factors. Front. Microbiol. 10.3389/fmicb.2016.01953
Carstens M, Berger DK. 2016. Biotechnology and Crop Disease Resistance in South Africa. In: Biotechnology for Plant Disease Control. Collinge DB. (eds). Wiley, New York and London, pp 16 (Chapter).
Reeksting B, Olivier N.A, van den Berg N. (2016) Transcriptome responses of an ungrafted Phytophthora root rot tolerant avocado (Persea americana) rootstock to flooding and Phytophthora cinnamomi. BMC Plant Biology 16(205) 10.1186/s12870-016-0893-2
Hussey SG, Mizrachi E, Groover A, Berger DK, Myburg AA. (2015) Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. BMC Plant Biology 15:117. 10.1186/s12870-015-0499-0 PDF
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
Berger DK, Carstens M, Korsman JN, Middleton F, Kloppers FJ, Tongoona P, Myburg AA. (2014) Mapping QTL conferring resistance in maize to gray leaf spot disease caused by Cercospora zeina. BMC Genetics 15:60. 10.1186/1471-2156-15-60
Haasbroek MP, Craven M, Barnes I, Crampton BG. (2014) Microsatellite and mating type primers for the maize and sorghum pathogen, Exserohilum turcicum. Australasian Plant Pathology 43(5):577-581. 10.1007/s13313-014-0289-4 PDF
Phillips S, Dubery I, Heerden H. (2013) Molecular characterisation of two homoeologous elicitor-responsive lipin genes in cotton. Molecular Genetics and Genomics 288:519-533. 10.1007/s00438-013-0770-8
Van der Linden L, Bredenkamp J, Naidoo S, Fouche-Weich J, Denby KJ, Genin S, Marco Y, Berger DK. (2013) Gene-for-Gene Tolerance to Bacterial Wilt in Arabidopsis. Molecular Plant-Microbe Interactions 26:398-406. 10.1094/MPMI-07-12-0188-R
Phillips S, Dubery I, Heerden H. (2013) Identification and molecular characterisatin of a Lectin Receptor-like Kinase (GhLecRK-2) from cotton. Plant Molecular Biology Reporter 31(1):9-20. 10.1007/s11105-012-0470-2
Naidoo R, Ferreira L, Berger DK, Myburg AA, Naidoo S. (2013) The identification and differential expression of Eucalyptus grandis pathogenesis-related genes in response to salicylic acid and methyl jasmonate. Frontiers in Plant Science 4:43. 10.3389/fpls.2013.00043