Conferences

CONFERENCES (2017 - present)

M.E.C. Rey et al. (2022) Building an integrated model for sustainable tolerance to cassava mosaic viruses: living with the enemy.  International Symposium on ssDNA Viruses (IS3DV). 26 Sept to 1st October 2022, Domaine du Lazaret,Sète,France.

Bulelani L. Sizani, Keelan Krinsky and M.E.C. Rey (2022) Structural characterization of NLR proteins differentially expressed in response to cassava mosaic virus infection in cassava. International Symposium on ssDNA Viruses (IS3DV) 26th September to 1st October 2022 at Domaine du Lazaret, Sète, France.

Keelan Krinsky, Bulelani Sizani and Marie E. Chrissie Rey (2022) Identification and structural analysis of cassava mosaic disease resistance (R) genes and associated quantitative trait loci. BIO2022: Bioscience, Big Data & the 4^th Industrial Revolution Conference, Stellenbosch. 24 to 27 April 2022.

Bulelani L. Sizani, Keelan Krinsky., and Marie E. Chrissie Rey (2022) Structural and Functional Characterization of NLR Proteins Differentially Expressed in Cassava Plant Infected with SACMV. BIO2022: Bioscience, Big Data & the 4^th Industrial Revolution Conference, Stellenbosch. 24 to 27 April 2022.

M. E. C. Rey¹, A. M. Zwolinski¹ and A. Brigden (2022) Differences in the 3’ intergenic region and the V2 protein of two variants of Tomato curly stunt virus play an important role in disease pathology in Nicotiana benthamiana. 15th International Plant Virus Epidemiology Symposium: Epidemiology and Management of plant viruses under a changing climate. Madrid, Spain, 5th-8th June 2022.

A Brigden, AM Zwolinski, MEC Rey (2021) Pathogenicity determinants of severe and mild variants of Tomato curly stunt virus. South African Society of Microbiology Conference, 4-6^th May.

AM Zwolinski, A Brigden, MEC Rey (2021) Identifying the roles of Rep in the pathogenicity of Tomato curly stunt virus.  South African Society of Microbiology Conference, 4-6^th May

EE Nyoni, MEC Rey (2021) Response of cassava varieties to infection by South African cassava mosaic virus.  South African Society of Microbiology Conference, 4-6^th May.

E Ramulifho, MEC Rey (2021) Proteome mapping of susceptible and tolerant cassava landraces infected with South African cassava mosaic virus. South African Society of Microbiology Conference, 4-6^th May.

RP Seutane, V Meyer, MEC Rey (2021) Assessing the role of DNA methylation in response of cassava to South African cassava mosaic virus. South African Society of Microbiology Conference, 4-6^th May.

Thapelo Mosiane, Chrissie Rey (2020) Characterization of the putative AC5 protein encoded by South African cassava mosaic virus. Virology Africa 2020, Cape Town, 2020, 10-14^th February.p68

Chrissie Rey, Nikki Gentle, Matthew Gibson, Christine Bizabani, Warren Freeborough, Elelwani Ramulifho and Louis Bengyella. (2020) An integrated model for tolerance and susceptibility to cassava mosaic disease. Virology Africa 2020, Cape Town, 2020, 10-14^th February. KEYNOTE. p36

Chatukuta, P. and Rey, M.E.C. (2020) An argonaute 4 gene from cassava is targeted and silenced by the geminivirus , South African cassava mosaic virus. Virology Africa 2020, Cape Town, 2020, 10-14^th February. p71

Chatukuta, P. and Rey, M.E.C. (2020) Susceptibility to South African Cassava Mosaic Virus is Associated with a RING Finger E3 Ubiquitin Ligase. Virology Africa 2020, Cape Town, 2020, 10-14^th February. p159

Patience Chatukuta, Chrissie Rey (2019) Tolerance to South African Cassava Mosaic Virus is Associated with the Activity of a RING Finger E3 Ubiquitin Ligase. EMBO Conference: The ubiquitin system: Biology, mechanisms and roles in Disease 13 – 17 September 2019, Cavtat, Croatia. p172

Chrissie Rey, Nikki Gentle, Warren Freeborough, Busi Ncube Kanyika, Elelwani Ramulifho and Louis Bengyella (2019) An Integrated Model for Tolerance and Susceptibility to Cassava Mosaic Disease. International Advances in Plant Virology, Rome, Italy, 29-31^st October 2019.p35.

Chatukuta, P. AND Rey, C. (2018) CRISPR and protoplasts: hand-in-hand towards high-throughput gene editing in cassava SAGs/SasBi Conference, Golden Gate; 16-18^th October.

Ncube Kanyika, B., Freeborough, W., Gentle, N., AND Rey, C (2018) A meta-analysis of global host-virus responses in Solanaceae, Euphorbiaceae and Brassicaceae plant families during geminivirus and ipomovirus infection. SAGs/SasBi Conference, Golden Gate; 16-18^th October.

W Freeborough_­, BN Kanyika, N Gentle, MEC Rey (2018) The importance of hub WRKY transcription factors in the establishment tolerance and susceptibility against plant viruses. SAGs/SasBi Conference, Golden Gate; 16-18^th October.

Chrissie Rey (2018) Plant genes and networks: responses to geminiviruses. ACGT Plant Genomics Forum. 18^th May 2018, University of the Witwatersrand Innovation Hub. KEYNOTE.

C Bizabani, W Freeborough, N Gentle, MEC Rey (2018) Cassava Mosaic Disease: an ultimate battle of host and virus miR/miR* in a miRNA regulated defence against SACMV infection. South African Society Microbiology Conference, Muldersdrift, Johannesburg, 4-7^th April 2018.

P Chatukuta, MEC Rey (2018) Resistance to the South African Cassava Mosaic Virus is Associated with the Activity of a RING Finger E3 Ubiquitin Ligase. South African Society Microbiology Conference, Muldersdrift, Johannesburg, 4-7^th April 2018.

Molemi E. Rauwane, Damaris A. Odeny, Chrissie Rey and Jasper Rees (2018) Variations in transcription profiles induced by herbivore feeding in cassava (Manihot esculenta Crantz). International Congress on Plant Pathology, Boston, US, 29 July -3^rd August.

Freeborough, W. Gentle, N, Rey, MEC (2017) Hub WKRY transcription factors and interacting partners in response to cassava mosaic geminiviruses. Plant Genomes & Biotechnology: from genes to networks. Cold Spring Harbor, New York, 29 November-2 December.

2013 CONFERENCES

1) The South African Society for Microbiology (SASM) Forever Resorts Warmbaths, Bela-Bela between 24 and 27 November 2013

Oral Presentation 1

Monitoring comparative transcriptional changes in a susceptible and tolerant cultivar of cassava infected with South African cassava mosaic virus using next- generation sequencing F.Allie^a, E.J. Pierce^a, M.J. Okoniewski^b and M.E.C Rey^a

^a School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts Ave, Braamfontein, Johannesburg, 2000, South Africa. Chrissie.rey@wits.ac.za ^b  Functional Genomics Center, Zurich, UNI ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.  

Background Transcriptional reprogramming following virus infection takes place at a global level, both temporally and spatially within the plant leaves and other organs, and depending on the outcome, a resistance or susceptible response is initiated. Cassava mosaic disease is caused by several distinct geminivirus species, including South African cassava mosaic virus-[South Africa:99](SACMV).

Methods and Results A global transcriptome profiling (RNA-seq) study over the infectivity time course (12, 32 and 67 days post inoculation), using the ABI SOLiD platform, was performed in order to monitor comparative transcriptional responses to SACMV in a susceptible (T200) and tolerant (TME3) cultivar. Infectivity assays showed significantly higher viral loads (quantitative RT-PCR) in susceptible T200 compared with tolerant TME3, at 32 and 67 dpi. Viral DNA was not detected in TME3 at the pre-symptom stage (12 dpi), but was detected at 32 dpi (full systemic infection), and declined at 67 dpi, correlating with recovery (symptomless leaves).  Paired-end NGS sequencing run produced an average of 634,081,313 paired end reads from both susceptible and tolerant libraries. Of this, approximately 51.89% of the T200 reads and 52.81% of TME3 reads mapped to the cassava reference genome available at Phytozome (www.phytozome.net).  Using a log2-fold cut-off (p <0.05), comparative analysis between the six cDNA libraries identified a total of 4181 differentially expressed transcripts in T200  (compared to mock inoculated) across 12, 32 and 67 dpi, whereas TME3 had a total of only 1008 SACMV-responsive transcripts across the same time course of infection. Dynamic gene expression changes were observed in both T200 and TME3 at different time points post-infection where a limited number of genes were expressed across all time points, while uniquely up- or down-regulated transcripts occurred at different infection phases for both cultivars. Gene ontology annotation analysis identified alterations in several functional groups, the top three being subcellular localization, protein binding function and metabolism. 

Conclusions Differences in patterns and levels of transcriptome profiling between T200 and TME3 with susceptible and tolerant phenotypes, respectively, supports the hypothesis that viruses rearrange their interactions in adapting to hosts with different genetic backgrounds. 

Oral Presentation 2

Transcriptional alterations in model host, Nicotiana benthamiana, in response to infection by South African cassava mosaic virus F. Allie and M.E.C. Rey* School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, South Africa, 2050 * Corresponding author: chrissie.rey@wits.ac.za Background Successful systemic infection by plant viruses is the outcome of complex molecular interactions between host and viral pathogen, leading to spatial and temporal alterations in plant gene expression.  Nicotiana benthamiana has been used extensively as a model host to study plant virus-host interactions, and in this study, transcriptional alterations in N. benthamiana, in response to infection by South African cassava mosaic virus, was undertaken. Methods and Results Results from a microarray study using the commercially available custom-made 60-mer oligo NimbleGen Platform (representing 13 014 ESTs) (Roche) revealed that expression levels of many transcripts were altered in response to SACMV at 21 dpi (representing full systemic infection), including encoded proteins involved in transcription networks, defence responses and plant hormone signalling. Approximately 4.7% (611 of 13 014) of the transcripts were significantly altered in response to SACMV infection.  Of these, 483 genes were found to be induced and 128 genes were suppressed.  GOslim functional group analysis illustrated that differentially expressed genes in infected leaf tissue, compared to mock inoculated, were primarily overrepresented in the cellular component category for nuclear (19.92%) and other cellular components (14%), while categories corresponding to transferase activity (14.42%) and other binding (13.43%) were overrepresented for Molecular Function.  Cellular processes (24.93%) and other metabolic processes (18.05%) were overrepresented for Biological Process.  Notably from our data, we were able to detect transcript changes in several defence-related and sucrose and starch metabolic pathways.  Alterations in genes associated with the cytoskeleton, cell wall and plasmodesmata, namely myosin heavy chain, beta-tubulin, Ras-GTPase (Rab6A), ß-1,3-glucanase, pectinesterase and pectate lyase , collectively suggest possible roles in intracellular vesicle-assisted movement to the plasmamembrane and release into the adjacent cell via the plasmodesmata (Pd).  Conclusions Understanding host responses to virus pathogen attack can contribute to building of metabolic pathway models or interactomes that can inform more effective control strategies.

Oral Presentation 3

Oral Presentation 4

Integrated DNA sequences in the cassava genome associated with Cassava mosaic begomoviruses: A bioinformatics study

 Maredza AT and M.E.C. Rey

School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, South Africa, 2050

Background Integrated exogenous genomic or viral sequences have been reported in many plant genomes.  In some instances, these sequences affect disease symptom progression and sometimes may “jump out” of the host genome to become infectious episomal agents.  One example is plant-infecting badnaviruses.  Two non-homologous episomal circular satellite-like ssDNA sequences (DNA-II and III) (AY826366 and AY836367) were identified in cassava field samples  infected with  African cassava mosaic virus (ACMV) or East African cassava mosaic virus (EACMV), and were found to modulate symptom phenotype and severity in the tolerant cultivar TME3, and model host Nicotiana benthamiana.  The recently sequenced cassava genome has not, until recently, been scrutinized for genomic DNA sequences or elements that may be associated with cassava mosaic begomovirus pathogens, but examination of the cassava EST database surprisingly revealed different-sized DNA-II and DNA-III fragments. The relationship between these episomal and integrated DNA sequences, cassava and associated begomoviruses is unknown. Methods and Results In this study, BLASTX searches of the cassava genome (www.phytozome.net) showed multiple truncated fragments of homologous integrated DNA-II and DNA-III sequences arranged in tandem or inverted repeat patterns typical of transposable elements. The largest insertions were almost full-length when compared to the episomal query sequences, showing 99.2 and 84.1% homology, found on scaffolds 12498 and 12725, respectively.  The gene ontology classifications of flanking host genes were mostly nuclear genes involved in nucleotide or nucleic acid processing.  Also prevalent, were genes encoding protein synthesis, binding and processing factors. RT-PCR analysis of some of the flanking genes indicated that both the host genes and the integrated DNA sequences were expressed, possibly as polycistronic mRNAs. Conclusions We propose that the integrated DNA sequences are involved in regulatory host gene functions, whose cognate genes may be responsive to invading begomoviruses.

Oral Presentation 5

Oral Presentation 6

Artificial miRNAs: A Tool for Engineering Resistance to Geminiviruses Sarah Rogans¹, Chrissie Rey¹ and Marco Weinberg^{2 1} School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa ² Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa

MicroRNAs (miRNAs) constitute a major class of small non-coding RNAs (20-25nt long) that regulate gene expression in plants and animals. They perform their functions by binding to the reverse complementary sequences of the target mRNA, causing mRNA cleavage or translational repression. MiRNAs differ to siRNAs as they originate from endogenous genes and are involved in the trans-acting silencing of other endogenous genes. Previous studies in miRNAs have offered a new approach to silence target genes through the production of artificial miRNAs (amiRNAs). AmiRNAs are designed from endogenous miRNA precursors by replacing the miRNA:miRNA* duplex with an artificial hairpin structure. In this study, amiRNAs were constructed against geminiviruses, which are responsible for Cassava mosaic disease. The artificial hairpin precursor was made using virus-derived sequences form African cassava mosaic virus, South African cassava mosaic virus and East African cassava mosaic virus. The effect of these amiRNAs against these viruses was studied using Transient Expression Assays in the model plant Nicotiana benthamiana.

Poster Presentation 1

SOUTH AFRICAN CASSAVA MOSAIC VIRUS AC1/AC4 MISMATCHED HAIRPIN TRANSGENE REDUCES SACMV SYMPTOMS IN TRANSGENIC CASSAVA

A.O. Eni,^{1, 2,} R. Mundembe^1,3 and MEC Rey¹

¹School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, South Africa, 2050 ² Department of Biological Sciences, Covenant University, PMB 1023 Ota, Nigeria ³ Department of Agricultural and Food Sciences, Faculty of Applied Sciences, Cape Peninsula University of Technology, P.O. Box 652, Cape Town 8000.

Background Cassava feeds more than 800 million people in tropical developing countries in Africa, Asia and Latin America and currently ranks first among 25 top commodities in Africa. Cassava mosaic disease (CMD), caused by several species of cassava mosaic begomovirus, is one of the most important viral diseases of cassava and a major constraint for cassava production in Africa. One approach to genetically engineer plants for virus resistance is to engineer expressed RNA hairpins or inverted repeats (IR), which when processed generate siRNAs targeting homologous virus sequences.  In some cases, this technology is difficult to apply due to the instability of IR constructs during cloning and plant transformation. Methods and Results A 193 bp overlapping gene fragment of the replication-associated protein (AC1) and host silencing suppressor (AC4) genes of South African cassava mosaic (SACMV) was selected for transgene construction.  In order to stabilize the SACMV IR construct during cloning, without disrupting siRNA processing, we developed a method to reduce cruciform structures through bisulfite-induced base pair mismatches (C-to-T) on the sense-arm prior to IR assembly. The SACMV mismatched (MM) construct was cloned in pCambia 1305.2, and used for Agrobacterium-mediated transformation of friable embryogenic callus (FEC) of a farmer-preferred, high-starch cassava variety, T200.  Transgenic cassava plants were regenerated from the FECs and screened by GUS, hygromycin re-rooting  and PCR assays for insert integration confirmation.  Copy number was confirmed by Southern hybridization for the Hyg gene.  Cassava plants from six independent single-copy transformation events were propagated and challenged with SACMV in the greenhouse and scored for symptom severity and growth (height) over a 67-day period.  Viral load and siRNA evaluation is currently being completed.  Conclusion While no immunity was displayed, two of the lines show significantly lower leaf symptom scores and/or higher growth rate than the untransformed T200, indicating the potential efficacy of the approach.  Comparison with non-mismatched constructs is also ongoing.  

2012 CONFERENCES

a) Second Scientific conference of the Global Cassava Partnership for the 21st Centaury (GCP21-II) Cassava:Overcoming challenges of climate change, 18-23 June 2012, Kampala , Uganda

ORAL PRESENTATION

Empowering biotechnology in southern Africa: Establishment of a robust transformation platform for the production of transgenic industry-preferred cassava

M E C Rey^, C B Rossin^ , W Gruissem*,  H Vanderschuren* and C C Chetty^

^ School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa. Email addresses: chettyc@biology.wits.ac.za; rossincb@gmail.com; chrissie.rey@wits.ac.za * Department of Biology, Plant Biotechnology, ETH Zurich, Zurich, Switzerland. Email addresses: hvanderschuren@ethz.ch; wgruissem@ethz.ch; Biotechnology has been considered an attractive tool to improve cassava (Manihot esculenta Crantz) for traits such as biotic stress. Despite the establishment of the transformation technology in the mid-90’s, its implementation and continuous maintenance in African laboratories has remained scarce. A major constraint for cassava improvement has been the lack of an efficient and robust transformation and regeneration system, and poor knowledge and technology transfer to African laboratories and farmers, which is an important objective for achieving food security and sustainable crop production on the sub-Saharan African continent.  Despite some success achieved in genetic modification of the model cassava cultivar Tropical Manihot Series (TMS), TMS 60444, in some European and U.S. laboratories, the lack of a reproducible and robust protocol has not allowed the establishment of a routine transformation system in sub-Saharan Africa.  Here we report the first successful implementation of a robust cassava transformation platform in a South African laboratory and its use for the generation of transgenic T200 cassava, a SA industry-preferred cultivar, which. The complete pipeline from generation of cassava FEC to Agrobacterium-mediated transformation and regeneration of transgenic plants has been established, and efficiencies between T200 and TMS 60444 were compared.  Results from our study demonstrated high transformation rates for both T200 (23 transgenic lines from 100 friable embryogenic callus (FEC) clusters) compared with TMS60444 (32 transgenic lines from 100 FEC clusters).  The successful establishment of a robust cassava transformation and regeneration system in South Africa demonstrates the relevance of technology transfer to sub-Saharan Africa and highlights the importance of developing suitable and reliable techniques prior to their transfer to laboratories offering less optimal conditions.

POSTER 1: Genetic Transformation of Cassava (Manihot esculenta Crantz) for resistance to cassava begomoviruses

Moralo, M and Rey, M.E.C.

ABSTRACT

Cassava accounts for up to 60% of the daily calorie intake in sub-Saharan Africa. However, a major constraint to cassava cultivation is the 30-50% yield loss due to cassava mosaic disease (CMD), caused by several circular ssDNA cassava begomoviruses (CBVs), including African cassava mosaic virus (ACMV); East African cassava mosaic virus (EACMV) and South African cassava mosaic virus (SACMV-[ZA]), found to be present in South Africa. Current strategies for obtaining resistance to CMD are through genetic engineering. The aim of this study is to develop CBV resistant transgenic cassava, based on RNA silencing induction via transgenic expression of virus-derived hairpins to generate siRNAs that target homologous viral sequences for degradation. The most efficient and reproducible transformation system for cassava is Agrobacterium-mediated transformation of friable embryogenic callus (FEC). In our laboratory, cassava FECs from model cv. TMS60444 and South African landrace T200 have been transformed with several viral gene silencing constructs derived from selected sequences within the AC1/4 and AC2/3 open reading frames of EACMV-UG2, ACMV-NG:Ogo:90 and SACMV-[ZA]. FECs were co-cultivated with Agrobacterium LBA4404 transformed with pCambia 1305.1 harboring the various constructs. Here we report selection of six regenerated TMS60444 lines (1 or 2 copies of transgene) transformed with a stacked mismatched ACMV-[NG:Ogo:90] construct (AC1/AC4:AC2/AC3) and agro-infected with ACMV-[NG:Ogo:90] infectious clones. Leaf material was collected and symptom severity scored at 12, 32, 55 and 67 days post infection (dpi).  Molecular analysis comparisons (viral loads using Real-Time PCR; siRNAs and transgene expression) between transgenic & untransformed controls are underway.

POSTER 2: Identification of putative microRNAs and their targets in cassava (Manihot esculenta Crantz)

Sarah Rogans ¹, Marco Weinberg² and Chrissie Rey¹

¹ School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa, ² Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa

MicroRNAs (miRNAs) are endogenous ~21nucleotide small RNAs. They play important regulatory roles in plants by targeting mRNAs for cleavage or translational repression. MiRNA-guided gene regulation plays a key role in diverse biological processes in plants, therefore their identification is essential to fully understanding their gene targets. These genes could play a role in responses to cassava mosaic viruses. Computational comparative approaches based on the evolutionary conservation of mature miRNAs have revealed a number of orthologs of known miRNAs in different plant species. A computational homology search for Expressed sequence tags (ESTs) was used in this study to identify potential evolutionary conserved cassava miRNAs. The cassava EST database was blasted to search for putative miRNAs using previously known plant miRNAs from all database available sequenced plant species. A total of 84 potential miRNAs were identified following a range of strict filtering criteria. Using the psRNA Target tool, potential targets were predicted for the newly identified putative miRNAs. The targets appear to be involved in plant growth, development and stress responses. However, compared with the current numbers of identified miRNAs for other species in the plant kingdom, a large number of putative miRNAs remain to be identified in cassava.  Furthermore, only ~25% of the cassava genome is annotated, and the EST cassava database does not represent the entire genome.  Many miRNAs target non-coding regions, and therefore deep sequencing is being performed in order to identify unique miRNAs in cassava.

b) South African Genetics and Bioinformatics Society (SAGS/SASBCB) Conference, Stellenbosch University, 10-12 September 2012

POSTER 1: Characterisation of satellite-like DNA molecules and their interaction with cassava and the helper begomoviruses, East African cassava mosaic virus – Uganda and East African cassava mosaic Cameroon virus

Maredza AT , Matshidiso A, Rey MEC

Satellite molecules usually depend on helper viruses for replication and movement, but replicate episomally.  Recently, two novel episomal satellite-like DNA molecules (Sat DNA II and Sat DNA III which are 1023 and 1197 nucleotides, respectively) were found in cassava infected with East African cassava mosaic virus - Uganda (EACMV-[UG]) and East African cassava mosaic Cameroon virus - Cameroon (EACMV-[CM]), belonging to the family Geminiviridae and genus Begomovirus.  More importantly, integrated satellite-like sequences (SLS) have been found interspersed in the cassava genome. To investigate the importance of integrated sequences, we searched cassava EST databases for the presence of integrated SLS similar to satellites associated with EACMV-[UG] and EACMV-[CM], and several-sized fragments, the largest being 895 nt for sat DNA II and 305 nt for sat DNA III.  Bioinformatics tools were integrated into a Galaxy workflow, and were used to map the chromosomal locations of the SLS.  The sizes and frequencies of the integrated sequences were determined In addition, putative open reading frames and regulatory motifs will be identified and integration site junctions will be analysed.  Primers will be designed to investigate the expression of selected SLS using real time RT-qPCR.  To investigate if integrated SLS play a role in gene regulation and host response, the expression of genes located upstream and downstream of the integrated SLS will be analysed, and putative genes associated with pathogenicity /resistance identified.

POSTER 2:  Identification of putative microRNAs and their targets in cassava (Manihot esculenta Crantz)

Sarah Rogans ¹, Marco Weinberg² and Chrissie Rey¹

¹ School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa, ² Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa

MicroRNAs (miRNAs) are endogenous ~21nucleotide small RNAs. They play important regulatory roles in plants by targeting mRNAs for cleavage or translational repression. MiRNA-guided gene regulation plays a key role in diverse biological processes in plants, therefore their identification is essential to fully understanding their gene targets. These genes could play a role in responses to cassava mosaic viruses. Computational comparative approaches based on the evolutionary conservation of mature miRNAs have revealed a number of orthologs of known miRNAs in different plant species. A computational homology search for Expressed sequence tags (ESTs) was used in this study to identify potential evolutionary conserved cassava miRNAs. The cassava EST database was blasted to search for putative miRNAs using previously known plant miRNAs from all database available sequenced plant species. A total of 84 potential miRNAs were identified following a range of strict filtering criteria. Using the psRNA Target tool, potential targets were predicted for the newly identified putative miRNAs. The targets appear to be involved in plant growth, development and stress responses. However, compared with the current numbers of identified miRNAs for other species in the plant kingdom, a large number of putative miRNAs remain to be identified in cassava.  Furthermore, only ~25% of the cassava genome is annotated, and the EST cassava database does not represent the entire genome.  Many miRNAs target non-coding regions, and therefore deep sequencing is being performed in order to identify unique miRNAs in cassava.

ORAL PRESENTATION:Assembling a cassava transcriptome using Galaxy on a High Performance Computing cluster

Conferences (2010-2011)

MEC Rey, C Chetty, C Rossin, M Moralo, M Weinberg and S Rogans (2011) Small RNAs: Developing resistance to geminiviruses. Virology Africa 2011, 29 November – 2 December, 2011, Cape Town.

M E C Rey, C Chetty, C Rossin, Maabo Moralo, M Weinberg and S Rogans (2011) RNA silencing:  A tool for engineering resistance to geminiviruses  SA Society for Microbiology Conference, 6-9 November, 2011, Cape Town, South Africa.

M E C Rey and M Weinberg and S Rogans (2011) Artificial miRNAs: A Tool for Engineering Resistance to Geminiviruses. SA Society for Microbiology Conference, 6-9 November, 2011, Cape Town, South Africa. 

Rey, M.E.C., Chetty, C.C., Rossin, C.B. and  Vanderschuren, H. (2011) Genetic engineering of cassava: successes and challenges. International ISHS Symposium: Genetically Modified Organisms in Horticulture. 11-15th September, White River, South Africa.

Chetty C.; M. Moralo; R. Mundembe; E.J. Pierce; S. Rogans, F. Van Schalk, H. Vanderschuren & M.E.C. Rey (2011) Biotechnological solutions for engineering virus resistant cassava. Agricultural Biotechnology for economic Development: moving towards a Bioeconomy. 6-9 September, Sandton Convention Centre, Johannesburg, South Africa.

M.E.C. Rey (2011) Transcriptome profile of South African cassava mosaic virus-responsive genes in Arabidopsis and Nicotiana benthamiana. American Society for Virology, 30th Annual Meeting, July 16-20, University of Minnesota, Twin Cities, Minneapolis Campus, USA.

Cele, P. And Rey, M.E.C. (2011) Screening for transformation of tobacco with a South African cassava mosaic virus gene fragment. Southern African Society for Plant Pathology 47th Congress, Kruger national Park, South Africa 23-26th January. p104.

Dias, K.A.V., van Heerden, S.W. and Rey, M.E.C. (2011) A study of the cultivated tomato (Solanum lycopersicon) resistance to ToCSV in South Africa. Southern African Society for Plant Pathology 47th Congress, Kruger national Park, South Africa 23-26th January.  

Esterhuizen, L.L, van Heerden, Rey, M.E.C. and van Heerden, H. (2011)  Epidemiology and molecular characterization of Tomato curly stunt virus and its insect vector Bemisia tabaci in South Africa.  Southern African Society for Plant Pathology 47th Congress, Kruger National Park, South Africa 23-26th January. 

Moralo, M. and Rey, M.E.C. (2011) Genetic transformation of cassava (Mannihot esculenta Crantz) for resistance to cassava begomoviruses. Southern African Society for Plant Pathology 47th Congress, Kruger National Park, South Africa 23-26th January. 

MEC Rey, E Pierce, D Berger and N Olivier (2010) Assessing global transcriptome changes in response to South African cassava mosaic virus in susceptible Arabidopsis thaliana.  EMBO Workshop: Genomic Approaches to Interactions between plant viruses, their hosts and their vectors.  12-16 June 2010, Fenestrelle, Italy

MEC Rey, E Pierce and F van Schalk (2010) Global transcriptome profiling of Arabidoipsis thaliana infected with South African cassava mosaic virus.  4th International ssDNA Comparative Virology Workshop, 7-12 November, Guanajuato, Mexico

L.L Esterhuizen, S.W. Van Heerden, MEC Rey and H van Heerden (2010)  Epidemiology and molecular characterization of Tomato curly stunt virus and its insect vector Bemisia tabaci in South Africa.  4th International ssDNA ComparativeVirology Workshop, 7-12 November, Guanajuato, Mexico

F. van Schalk and M.E.C. Rey (2010)  Gene expression profile of Nicotiana benthamiana infected with South African cassava mosaic virus using a cross-species cDNA microarray approach. 4th International ssDNA Comparative Virology Workshop, 7-12 November, Guanajuato, Mexico