Department of Genetics

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Abiotic stress-induced accumulation of raffinose in Arabidopsis leaves is mediated by a single raffinose synthase (RS5, At5g40390)
(BioMed Central, 2013) Egert, Aurelie; Keller, Felix; Peters, Shaun
Background: The sucrosylgalactoside oligosaccharide raffinose (Raf, Suc-Gal1) accumulates in Arabidopsis leaves in response to a myriad of abiotic stresses. Whilst galactinol synthases (GolS), the first committed enzyme in Raf biosynthesis are well characterised in Arabidopsis, little is known of the second biosynthetic gene/enzyme raffinose synthase (RS). Conflicting reports suggest the existence of either one or six abiotic stress-inducible RSs (RS-1 to -6) occurring in Arabidopsis. Indirect evidence points to At5g40390 being responsible for low temperature-induced Raf accumulation in Arabidopsis leaves. Results By heterologously expressing At5g40390 in E.coli, we demonstrate that crude extracts synthesise Raf in vitro, contrary to empty vector controls. Using two independent loss-of-function mutants for At5g40390 (rs 5–1 and 5–2), we confirm that this RS is indeed responsible for Raf accumulation during low temperature-acclimation (4°C), as previously reported. Surprisingly, leaves of mutant plants also fail to accumulate any Raf under diverse abiotic stresses including water-deficit, high salinity, heat shock, and methyl viologen-induced oxidative stress. Correlated to the lack of Raf under these abiotic stress conditions, both mutant plants lack the typical stress-induced RafS activity increase observed in the leaves of wild-type plants. Conclusions Collectively our findings point to a single abiotic stress-induced RS isoform (RS5, At5g40390) being responsible for Raf biosynthesis in Arabidopsis leaves. However, they do not support a single RS hypothesis since the seeds of both mutant plants still contained Raf, albeit at 0.5-fold lower concentration than seeds from wild-type plants, suggesting the existence of at least one other seed-specific RS. These results also unambiguously discount the existence of six stress-inducible RS isoforms suggested by recent reports.
Accomplishments in wheat rust research in South Africa
(ASSAf, 2020-11-26) Pretorius, Zacharias A.; Prins, Renee; Wessels, Elsabet; Bender, Cornel M.; Visser, Botma; Boshoff, Willem H. P.
Rust diseases, although seasonal, have been severe constraints in wheat production in South Africa for almost 300 years. Rust research gained momentum with the institution of annual surveys in the 1980s, followed by race identification, an understanding of rust epidemiology, and eventually a focused collaboration amongst pathologists, breeders and geneticists. Diversity in South African populations of Puccinia triticina, P. graminis f. sp. tritici and P. striiformis f. sp. tritici has been described and isolates are available to accurately phenotype wheat germplasm and study pathogen populations at national, regional and global levels. Sources of resistance have been, and still are, methodically analysed and molecular marker systems were developed to incorporate, stack and verify complex resistance gene combinations in breeding lines and cultivars. Vigilance, capacity, new technologies, collaboration and sustained funding are critical for maintaining and improving the current research impetus for future management of these important diseases.
African origin for Madagascan dogs revealed by mtDNA analysis
(Royal Society, 2016) Ardalan, Arman; Oskarsson, Mattias C. R.; Van Asch, Barbara; Rabakonandriania, Elisabeth; Savolainen, Peter
Madagascar was one of the last major land masses to be inhabited by humans. It was initially colonized by Austronesian speaking Indonesians 1500–2000 years ago, but subsequent migration from Africa has resulted in approximately equal genetic contributions from Indonesia and Africa, and the material culture has mainly African influences. The dog, along with the pig and the chicken, was part of the Austronesian Neolithic culture, and was furthermore the only domestic animal to accompany humans to every continent in ancient times. To illuminate Madagascan cultural origins and track the initial worldwide dispersal of dogs, we here investigated the ancestry of Madagascan dogs. We analysed mtDNA control region sequences in dogs from Madagascar (n=145) and compared it with that from potential ancestral populations in Island Southeast Asia (n=219) and sub-Saharan Africa (n=493). We found that 90% of the Madagascan dogs carried a haplotype that was also present in sub-Saharan Africa and that the remaining lineages could all be attributed to a likely origin in Africa. By contrast, only 26% of Madagascan dogs shared haplotypes with Indonesian dogs, and one haplotype typical for Austronesian dogs, carried by more than 40% of Indonesian and Polynesian dogs, was absent among the Madagascan dogs. Thus, in contrast to the human population, Madagascan dogs seem to trace their origin entirely from Africa. These results suggest that dogs were not brought to Madagascar by the initial Austronesian speaking colonizers on their transoceanic voyage, but were introduced at a later stage, together with human migration and cultural influence from Africa.
Analysis of eight genes modulating interferon gamma and human genetic susceptibility to tuberculosis : a case-control association study
(BioMed Central, 2010-06) Moller, Marlo; Nebel, Almut; Van Helden, Paul D.; Schreiber, Stefan; Hoal, Eileen G.
Background: Interferon gamma is a major macrophage-activating cytokine during infection with Mycobacterium tuberculosis, the causative pathogen of tuberculosis, and its role has been well established in animal models and in humans. This cytokine is produced by activated T helper 1 cells, which can best deal with intracellular pathogens such as M. tuberculosis. Based on the hypothesis that genes which regulate interferon gamma may influence tuberculosis susceptibility, we investigated polymorphisms in eight candidate genes. Methods: Fifty-four polymorphisms in eight candidate genes were genotyped in over 800 tuberculosis cases and healthy controls in a population-based case-control association study in a South African population. Genotyping methods used included the SNPlex Genotyping System™, capillary electrophoresis of fluorescently labelled PCR products, TaqMan® SNP genotyping assays or the amplification mutation refraction system. Single polymorphisms as well as haplotypes of the variants were tested for association with TB using statistical analyses. Results: A haplotype in interleukin 12B was nominally associated with tuberculosis (p = 0.02), but after permutation testing, done to assess the significance for the entire analysis, this was not globally significant. In addition a novel allele was found for the interleukin 12B D5S2941 microsatellite. Conclusions: This study highlights the importance of using larger sample sizes when attempting validation of previously reported genetic associations. Initial studies may be false positives or may propose a stronger genetic effect than subsequently found to be the case.
The application of a commercially available citrus-based extract mitigates moderate NaCl-stress in arabidopsis thaliana plants
(MDPI, 2020) Loubser, Johannes; Hills, Paul
Aims: The aim of this study was to assess the effect of BC204 as a plant biostimulant on Arabidopsis thaliana plants under normal and NaCl-stressed conditions. Methods: For this study, ex vitro and in vitro growth experiments were conducted to assess the effect of both NaCl and BC204 on basic physiological parameters such as biomass, chlorophyll, proline, malondialdehyde, stomatal conductivity, Fv/Fm and the expression of four NaCl-responsive genes. Results: This study provides preliminary evidence that BC204 mitigates salt stress in Arabidopsis thaliana. BC204 treatment increased chlorophyll content, fresh and dry weights, whilst reducing proline, anthocyanin and malondialdehyde content in the presence of 10 dS·m−1 electroconductivity (EC) salt stress. Stomatal conductivity was also reduced by BC204 and NaCl in source leaves. In addition, BC204 had a significant effect on the expression of salinity-related genes, stimulating the expression of salinity-related genes RD29A and SOS1 independently of NaCl-stress. Conclusions: BC204 stimulated plant growth under normal growth conditions by increasing above-ground shoot tissue and root and shoot growth in vitro. BC204 also increased chlorophyll content while reducing stomatal conductivity. BC204 furthermore mitigated moderate to severe salt stress (10–20 dS·m−1) in A. thaliana. Under salt stress conditions, BC204 reduced the levels of proline, anthocyanin and malondialdehyde. The exact mechanism by which this occurs is unknown, but the results in this study suggest that BC204 may act as a priming agent, stimulating the expression of genes such as SOS1 and RD29A.
Assessing the control potential of aldicarb against grapevine phylloxera
(South African Society for Enology and Viticulture, 1992) Loubse, J. T.; Van Aarde, I. M. F.; Hoppner, G. F. J.
Aldicarb 15 G soil treatments in vineyards were evaluated for their phylloxera control potential. A post-harvest application was made on single vines and phylloxera populations on roots were quantified using a washing and sieving technique. Natural population fluctuations on control vines were also determined. Data were subjected to a rank sum statistical test to determine the significance of the findings. Results indicated that aldicarb had a definite suppressing effect on all stages of grapevine phylloxera.
Characterisation of different GLRaV-3 variant infections by determining virus concentration ratios and miRNA expression profiles
(Bundesanstalt fur Zuchtungsforschung an Kulturpflanzen, 2019) Aldrich, D. J.; Bester, R.; Burger, J.; Maree, H. J.
Grapevine leafroll disease (GLD) is present in all grape-growing regions of the world and is considered the most significant grapevine viral disease. Grapevine leafroll-associated virus 3 (GLRaV-3) is considered the primary cause of GLD and in South African vineyards five genetic variant groups (I, II, III, VI and VII) have been confirmed. Biological distinctions between GLRaV-3 variants have not been fully validated. By characterising virus concentration and stress-responsive microRNA expression in GLRaV-3 infected plants, this study aimed to glean a better understanding of the possible biological distinctions between GLRaV-3 variants. Quantitative reverse transcription PCR was utilised for virus concentration ratio (VCR) determination and miRNA quantitation in GLRaV-3 positive and negative grapevines grown under greenhouse and field conditions. This study found statistically significant differences in VCRs in plants singly infected with different GLRaV-3 variants. Interestingly, no difference in mean VCRs were observed between data sets, despite notable differences in plant age, duration of GLRaV-3 infection, scion/rootstock combination and growing conditions. Several miRNAs showed statistically significant expression modulation between infected and healthy samples. miRNA expression between data sets varied substantially and a greater overall miRNA response was observed in plants with more established GLRaV-3 infections. The lack of significant differences in mean VCRs between data sets, coupled with the consistent modulation of certain miRNAs in plants that have likely been infected for longer is a promising result. This finding could indicate that successful inhibition of further virus replication by plant defence mechanisms occurred, and that these miRNAs are implicated in this response.
Characterization of the genetic variation present in CYP3A4 in three South African populations
(Frontiers, 2013-02) Drogemoller, Britt; Plummer, Marieth; Korkie, Lundi; Agenbag, Gloudi; Dunaiski, Anke; Niehaus, Dana; Koen, Liezl; Gebhardt, Stefan; Schneider, Nicol; Olckers, Antonel; Wright, Galen; Warnich, Louise
The CYP3A4 enzyme is the most abundant human cytochrome P450 (CYP) and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry (MA) individuals. To identify known and novel CYP3A4 variants,15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of∼600 bp of the 5'-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4∗12, CYP3A4∗15, and the reportedly functional CYP3A4∗1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.
Chromosome 22q11 in a Xhosa schizophrenia population
(Health and Medical Publishing Group (HMPG), 2012-03) Koen, Liezl; Niehaus, Dana J. H.; Wright, Galen; Warnich, Louise; De Jong, Greetje; Emsley, Robin A.; Mall, Sumaya
Chromosome 22q11 aberrations substantially increase the risk for developing schizophrenia. Although micro-deletions in this region have been extensively investigated in different populations across the world, little is known of their prevalence in African subjects with schizophrenia. We screened 110 African Xhosa-speaking participants with schizophrenia for the presence of micro-deletions. As further verification for the presence or absence of 22q11 microdeletions, we screened 238 Xhosa schizophrenia patients and 240 healthy Xhosa individuals from a larger schizophrenia candidate 22q11 gene study using molecular analyses. Data from molecular and cytogenetic analyses confirmed the absence of 22q11 microdeletions in the Xhosa schizophrenia samples. Although the absence of chromosome 22q11 micro-deletions in this group of patients does not exclude the possibility that it may occur in Xhosa schizophrenia patients, we concluded an extremely low prevalence. Our findings suggest that unique susceptibility loci may be present in this group.
Citrus tristeza virus genotype detection using high-throughput sequencing
(MDPI, 2021-01-23) Bester, Rachelle; Cook, Glynnis; Maree, Hans J.
The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.
A comparative study of selected physical and biochemical traits of wild-type and transgenic sorghum to reveal differences relevant to grain quality
(Frontiers Media, 2017) Ndimba, Roya J.; Kruger, Johanita; Mehlo, Luke; Barnabas, Alban; Kossmann, Jens; Ndimba, Bongani K.
Transgenic sorghum featuring RNAi suppression of certain kafirins was developed recently, to address the problem of poor protein digestibility in the grain. However, it was not firmly established if other important quality parameters were adversely affected by this genetic intervention. In the present study several quality parameters were investigated by surveying several important physical and biochemical grain traits. Important differences in grain weight, density and endosperm texture were found that serve to differentiate the transgenic grains from their wild-type counterpart. In addition, ultrastructural analysis of the protein bodies revealed a changed morphology that is indicative of the effect of suppressed kafirins. Importantly, lysine was found to be significantly increased in one of the transgenic lines in comparison to wild-type; while no significant changes in anti-nutritional factors could be detected. The results have been insightful for demonstrating some of the corollary changes in transgenic sorghum grain, that emerge from imposed kafirin suppression.
The complete mitochondrial genome and phylogenetic position of the leopard catshark, Poroderma pantherinum
(Taylor & Francis Open, 2018) Van Staden, Michaela; Gledhill, Katie S.; Rhode, Clint; Bester-Van Der Merwe, Aletta E.
We present the first mitochondrial genome of a South African endemic catshark, Poroderma pantherinum. The complete mitogenome is 16,686 bp in length, comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one non-coding control region. Similar to other shark mitogenomes, it is AT rich (61.1%), with a GC content of 38.9%. Protein-coding genes used one of two start codons (ATG and GTG) and one stop codon (TAA/TA-/T-). Phylogenetic analysis of the leopard catshark and 34 carcharhinid species showed that it clusters with two other scyliorhinid species (Cephaloscyllium umbratile and Scyliorhinus canicula) with 100% support.
Complete nucleotide sequence of a South African isolate of grapevine fanleaf virus and its associated satellite RNA
(MDPI, 2013-07) Lamprecht, Renate L.; Spaltman, Monique; Stephan, Dirk; Wetzel, Thierry; Burger, Johan T.
The complete sequences of RNA1, RNA2 and satellite RNA have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SACH44). The two RNAs of GFLV-SACH44 are 7,341 nucleotides (nt) and 3,816 nt in length, respectively, and its satellite RNA (satRNA) is 1,104 nt in length, all excluding the poly(A) tail. Multiple sequence alignment of these sequences showed that GFLV-SACH44 RNA1 and RNA2 were the closest to the South African isolate, GFLV-SAPCS3 (98.2% and 98.6% nt identity, respectively), followed by the French isolate, GFLV-F13 (87.3% and 90.1% nt identity, respectively). Interestingly, the GFLV-SACH44 satRNA is more similar to three Arabis mosaic virus satRNAs (85%–87.4% nt identity) than to the satRNA of GFLV-F13 (81.8% nt identity) and was most distantly related to the satRNA of GFLV-R2 (71.0% nt identity). Full-length infectious clones of GFLV-SACH44 satRNA were constructed. The infectivity of the clones was tested with three nepovirus isolates, GFLV-NW, Arabis mosaic virus (ArMV)-NW and GFLV-SAPCS3. The clones were mechanically inoculated in Chenopodium quinoa and were infectious when co-inoculated with the two GFLV helper viruses, but not when co-inoculated with ArMV-NW.
Confirmation of the effectiveness and genetic positions of disease resistance loci in ‘Kishmish Vatkana’ (Ren1) and ‘Villard Blanc’ (Ren3 and Rpv3)
(South African Society for Enology and Viticulture, 2018) Veikondis, R.; Burger, P.; Vermeulen, A.; Van Heerden, C. J.; Prins, R.
This study aimed to validate the effectiveness and to genetically characterise the fungal disease resistance genes of ‘Kishmish Vatkana’ and ‘Villard Blanc’ in South Africa using microsatellite (SSR) markers and a Quantitative Trait Loci (QTL) approach. An F1 ‘Sunred Seedless’ × ‘Kishmish Vatkana’ cross was used to generate a partial linkage map for chromosome 13 known to harbour the Ren1 powdery mildew locus of ‘Kishmish Vatkana’. The effectiveness of this locus was validated, explaining between 44.8% and 57.7% of the observed phenotypic variance. An F1 ‘Villard Blanc’ × ‘G1-6604’ cross was used to generate partial linkage maps for chromosomes 15 and 18, reported to harbour fungal resistance genes of ‘Villard Blanc’. The powdery mildew QTL (Ren3) was validated on chromosome 15 of ‘Villard Blanc’, which explained between 18.9% and 23.9% of the phenotypic variance observed. The downy mildew resistance QTL on chromosome 18 (Rpv3) of ‘Villard Blanc’ was also confirmed, and it explained between 19.1% and 21.2% of the phenotypic variance observed. This molecular information and individual sources of resistance have already been implemented in the marker-assisted selection (MAS) and gene pyramiding efforts of the table grape breeding program of the Agricultural Research Council (ARC) Infruitec-Nietvoorbij.
Defining biotechnological solutions for insect control in sub-Saharan Africa
(Wiley Open Access, 2019) Botha, Anna-Maria; Kunert, Karl J.; Maling’a, Joyce; Foyer, Christine H.
Africa is burdened by food insecurity with nearly a billion people suffering from starvation, undernutrition, and malnutrition. Climate change prediction models forecast changes in rainfall patterns and rising temperature regimes, with impacts particularly on Southern and East Africa. These predictions are especially concerning for the production of major food crops, such as maize, sorghum, millet, and groundnut, because median temperature increases are associated with increased pest pressure and changes in migratory patterns. These factors will result in significantly more pest invasions and an increased need for innovative insect management practices. This review focuses on pest control strategies, highlighting important examples, their economic impact, and new alternative pest control strategies. African policymakers remain hesitant to move forward with establishing biosafety laws and commercializing GM crops, and it is often difficult to implement regulatory measures in smallholder agriculture to increase efficacy.
Distinct host-immune response toward species related intracellular mycobacterial killing : a transcriptomic study
(Taylor & Francis, 2020) Madhvi, Abhilasha; Mishra, Hridesh; Chegoua, Novel N.; Tromp, Gerard; Van Heerden, Carel J.; Pietersen, R. D.; Leisching, Gina; Baker, Bienyameen
The comparison of the host immune response when challenged with pathogenic and nonpatho- genic species of mycobacteria can provide answers to the unresolved question of how pathogens subvert or inhibit an effective response. We infected human monocyte derived macrophages (hMDMs) with different species of mycobacteria, in increasing order of pathogenicity, i.e. M. smegmatis, M. bovis BCG, and M. tuberculosis R179 that had been cultured in the absence of detergents. RNA was isolated post-infection and transcriptomic analysis using amplicons (Ampliseq) revealed 274 differentially expressed genes (DEGs) across three species, out of which we selected 19 DEGs for further validation. We used qRT-PCR to confirm the differential expression of 19 DEGs. We studied biological network through Ingenuity Pathway Analysis® (IPA) which revealed up-regulated pathways of the interferon and interleukin family related to the killing of M. smegmatis. Apart from interferon and interleukin family, we found one up-regulated (EIF2AK2) and two down-regulated (MT1A and TRIB3) genes as unique potential targets found by Ampliseq and qRT-PCR which may be involved in the intracellular mycobacterial killing. The roles of these genes have not previously been described in tuberculosis. Multiplex ELISA of culture supernatants showed increased host immune response toward M. smegmatis as compared to M. bovis BCG and M.tb R179. These results enhance our understanding of host immune response against M.tb infection.
Diverse exopolysaccharide producing bacteria isolated from milled sugarcane : implications for cane spoilage and sucrose yield
(Public Library of Science, 2015) Hector, Stanton; Willard, Kyle; Bauer, Rolene; Mulako, Inonge; Slabbert, Etienne; Kossmann, Jens; George, Gavin M.
Bacterial deterioration of sugarcane during harvesting and processing is correlated with significant loss of sucrose yield and the accumulation of bacterial polysaccharides. Dextran, a homoglucan produced by Leuconostoc mesenteroides, has been cited as the primary polysaccharide associated with sugarcane deterioration. A culture-based approach was used to isolate extracellular polysaccharide (EPS) producing bacterial strains from milled sugarcane stalks. Ribosomal RNA sequencing analysis grouped 25 isolates into 4 genera. This study identified 2 bacterial genera not previously associated with EPS production or sucrose degradation. All isolates produced polysaccharide when grown in the presence of sucrose. Monosaccharide analysis of purified polymers by Gas Chromatography revealed 17 EPSs consisting solely of glucose (homoglucans), while the remainder contained traces of mannose or fructose. Dextranase treatment of polysaccharides yielded full digestion profiles for only 11 extracts. Incomplete hydrolysis profiles of the remaining polysaccharides suggest the release of longer oligosaccharides which may interfere with sucrose crystal formation.
DNA methylation and demethylation are regulated by functional DNA methyltransferases and DnTET enzymes in diuraphis noxia
(Frontiers Media, 2020) Du Preez, Pieter H.; Breeds, Kelly; Burger, N. Francois V.; Swiegers, Hendrik W.; Truter, J. Christoff; Botha, Anna-Maria
Aphids are economically important insect pests of crops worldwide. Despite resistant varieties being available, resistance is continuously challenged and eventually broken down, posing a threat to food security. In the current study, the epigenome of two related Russian wheat aphid (Diuraphis noxia, Kurdjumov) biotypes (i.e., SA1 and SAM) that differ in virulence was investigated to elucidate its role in virulence in this species. Whole genome bisulfite sequencing covered a total of 6,846,597,083 cytosine bases for SA1 and 7,397,965,699 cytosine bases for SAM, respectively, of which a total of 70,861,462 bases (SA1) and 74, 073,939 bases (SAM) were methylated, representing 1.126 ± 0.321% (SA1) and 1.105 ± 0.295% (SAM) methylation in their genomes. The sequence reads were analyzed for contexts of DNA methylation and the results revealed that RWA has methylation in all contexts (CpG, CHG and CHH), with the majority of methylation within the CpG context (± 5.19%), while the other contexts show much lower levels of methylation (CHG − ± 0.27%; CHH − ± 0.34%). The top strand was slightly (0.02%) more methylated than the bottom strand. Of the 35,493 genes that mapped, we also analyzed the contexts of methylation of each of these and found that the CpG methylation was much higher in genic regions than in intergenic regions. The CHG and CHH levels did not differ between genic and intergenic regions. The exonic regions of genes were more methylated (±0.56%) than the intronic regions. We also measured the 5mC and 5hmC levels between the aphid biotypes, and found little difference in 5mC levels between the biotypes, but much higher levels of 5hmC in the virulent SAM. RWA had two homologs of each of the DNA methyltransferases 1 (DNMT1a and DNMT1b) and DNMT3s (DNMT3a and DNMT3b), but only a single DNMT2, with only the expression of DNMT3 that differed significantly between the two RWA biotypes. RWA has a single ortholog of Ten eleven translocase (DnTET) in the genome. Feeding studies show that the more virulent RWA biotype SAM upregulate DnDNMT3 and DnTET in response to wheat expressing antibiosis and antixenosis.
Draft genome sequence of a “candidatus phytoplasma asteris” - related strain (aster yellows, subgroup 16SrI-B) from South Africa
(American Society for Microbiology, 2019-04-25) Coetzee, Beatrix; Douglas-Smit, Nicoleen; Maree, Hans J.; Burger, Johan T.; Kruger, Kerstin; Pietersen, Gerhard
Here, we report the draft genome sequence of a phytoplasma discovered in grapevine. The genome size is 600,116 nucleotides (nt), with 597 predicted open reading frames. It is most similar to a maize bushy stunt phytoplasma of group 16SrI-B (aster yellows). The possible presence of a 3,833-nt plasmid was also noted.
An evaluation of three Sr27-carrying wheat X rye translocations
(2001) Marais, G. F.
Please refer to full-text for abstract.

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