Transcript profiling of wheat genes expressed during feeding by two different biotypes of Diuraphis noxia

Diuraphis noxia (Kurdjumov)(Russian wheat aphid) has severe economic impacts on wheat and barley production in the United States. The interaction between the Russian wheat aphid and its cereal hosts is poorly understood. However, the recent appearance of new biotypes in the United States showed that specific interactions exist between wheat resistance loci and Russian wheat aphid biotypes. At present, Dn7 is the only known gene in hexaploid wheat that confers resistance against all U.S. Russian wheat aphid biotypes. This study was conducted to investigate the molecular mechanism of Dn7-mediated resistance against two U.S. Russian wheat aphid biotypes (Russian wheat aphid 1 and Russian wheat aphid 2). Using GeneChip Wheat Genome Arrays, we compared transcript profiles of resistant and susceptible lines infested with either Russian wheat aphid 1 or Russian wheat aphid 2 using two time intervals (5 and 48 h after infestation). Russian wheat aphid feeding on hexaploid wheat led to the induction of groups of genes functioning in oxidative and general stress, photosynthesis, cell respiration and energy production, signal transduction, calcium- dependent signaling, pathogenesis related (PR) responses, and defense compound synthesis. The number of differentially expressed genes was higher in plants infested with Russian wheat aphid 1 compared with those infested with Russian wheat aphid 2. Although most genes involved in basic cellular functions were shared, unique genes were also obtained. This finding may indicate subtle differences in genes induced in response to different virulence proteins

Detection and diversity of grapevine virus L from a Vitis cultivar collection in Stellenbosch, South Africa

A total of 229 Vitis cultivars were sampled from a collection in Stellenbosch, Western Cape, South Africa and subjected to an RNAtag-seq workflow and Illumina HiSeq 2500 sequencing. Following de novo assembly and initial BLASTn analysis of the resulting reads showed that 85 cultivars were infected with grapevine virus L (GVL), with a total of 96 complete/near complete genomes. This is the first time that GVL has been detected in South Africa. Phylogenetic analyses of the amino acid sequences of ORF1 showed that GVL from this study is diverse, grouping with references from Croatia, USA and China, as well as forming a unique South African phylogroup.Supplementary Figure 1. Maximum likelihood phylogeny based on the amino acid sequences derived from ORF 1 of grapevine virus L (GVL) from this study and references derived from extant GVL genomes (references indicated by a solid circle marker). The cognate sequence from grapevine virus E (GVE) was used as an outgroup. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the Le Gascuel model with gamma distribution (n=5). Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. The identity of each phylogroup is shown alongside the phylogeny.Supplementary figure 2. Illustration from the RDP4 program showing the potential parents of the single recombination event that appears to have led to the establishment of recombinant variants of grapevine virus L, associated with phylogroup IV.Supplementary Table 1. Details of the grapevine virus L genomes from this study, which includes the Vitis species or cultivar (of V. vinifera) that was sampled. “H” indicates an interspecific hybrid/cultivar. The number of reps indicates how many replicate plants were associated with each species/cultivar.The National Research Foundation of South Africahttps://link.springer.com/journal/106582022-09-14hj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Sorghum’s Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review

Sorghum is a cereal crop with key agronomic traits of drought and heat stress tolerance, making it an ideal food and industrial commodity for hotter and more arid climates. These stress tolerances also present a useful scientific resource for studying the molecular basis for environmental resilience. Here we provide an extensive review of current transcriptome and proteome works conducted with laboratory, greenhouse, or field-grown sorghum plants exposed to drought, osmotic stress, or treated with the drought stress-regulatory phytohormone, abscisic acid. Large datasets from these studies reveal changes in gene/protein expression across diverse signaling and metabolic pathways. Together, the emerging patterns from these datasets reveal that the overall functional classes of stress-responsive genes/proteins within sorghum are similar to those observed in equivalent studies of other drought-sensitive model species. This highlights a monumental challenge of distinguishing key regulatory genes/proteins, with a primary role in sorghum adaptation to drought, from genes/proteins that change in expression because of stress. Finally, we discuss possible options for taking the research forward. Successful exploitation of sorghum research for implementation in other crops may be critical in establishing climate-resilient agriculture for future food security

Pollination: Impact, role-players, interactions and study – A South African perspective

Plant–pollinator interactions are essential for maintaining both pollinator and plant communities in native and agricultural environments. Animal-instigated pollination can be complex. Plants are usually visited by a number of different animal species, which in turn may visit flowers of several plant species. Therefore, the identification of the pollen carried by flower visitors is an essential first step in pollination biology. The skill and time required to identify pollen based on structure and morphology has been a major stumbling block in this field. Advances in the genetic analysis of DNA, using DNA barcoding, extracted directly from pollen offers an innovative alternative to traditional methods of pollen identification. This technique, which is reviewed in detail, can be used on pollen loads sampled from bees in the field and from specimens in historic collections. Here the importance of pollination, the role-players involved, their management and the evolution of their interactions, behaviour and morphology are reviewed – with a special focus on South African bees. Significance:  Pollen metabarcoding will enable the identification of pollen for a multitude of uses, including agriculture, conservation and forensics. Plant–pollinator interaction documentation through pollen identification gives a more certain record of a visitor being a pollinator rather than a flower visitor that could be a nectar gatherer

Genomic characterization of grapevine viruses N and O : novel vitiviruses from South Africa

Supplementary Table 1: Total number of reads, after trimming, associated with each dataset analyzed in this study, as well as the genome length of each virus, the average coverage of the assembled contigs and the GenBank accession associated with each genome. GVN – grapevine virus N, GVO – grapevine virus O, nt – nucleotides.http://link.springer.com/journal/7052023-01-06hj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Novel viruses associated with plants of the family Amaryllidaceae in South Africa

Nineteen samples from members of the plant genera Agapanthus, Clivia, Hippeastrum, and Scadoxus were collected from gardens in the Gauteng and Western Cape provinces of South Africa. The plants displayed highly variable symptoms of viral disease, including chlorosis, necrosis, streaking, and ringspot. RNAtag-seq was used to characterize the associated viral populations. Plants of the genus Agapanthus were found to be associated with three novel viruses from the families Caulimoviridae, Closteroviridae, and Betaflexiviridae; plants of the genus Clivia were associated with novel members of the families Potyviridae and Betaflexiviridae; and plants of the genus Scadoxus were associated with a novel member of the family Tospoviridae. Nerine latent virus was associated with plants of the genera Agapanthus, Clivia, and Hippeastrum, while hippeastrum mosaic virus was associated exclusively with a Hippeastrum cultivar.SUPPLEMENTARY INFORMATION : Supplementary Fig. 1: Foliar symptoms associated with each plant sampled in this study. The unique sample accession number is shown in the bottom right-hand corner of each image. Images A to L show the Agapanthus cultivars sampled, M to Q the Clivia cultivars, R is a cultivar of Hippeastrum and S shows the single plant of Scadoxus puniceus that was sampled.Supplementary Fig. 2: Alignment of the minus-strand priming site of Agapanthus tungro virus (AgTV) with whole genome sequences of Rice tungro bacilliform virus (RTBV).Supplementary Figure 3.1: Maximum likelihood phylogeny based on the complete nucleotide sequences of Agapanthus tungro virus variants (sources from this study indicated by a solid circle marker) and selected members of the Caulimoviridae family. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the General Time Reversible model with gamma distribution (n=5). Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. The viral genus corresponding to each reference is shown in brackets, while the sample number is indicated for samples related to this study. Supplementary Figure 3.2: Maximum likelihood phylogeny based on the amino acid sequences of the heat shock protein homolog of Agapanthus velarivirus variants (sources from this study indicated by solid circle markers) and selected members of the Closteroviridae family. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the Le Gascuel model with gamma distribution (n=5). Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. The viral genus corresponding to each reference is shown in brackets, while the sample number is indicated for samples related to this study. A heat shock protein 70 amino acid sequence of Arabidopsis thaliana was used as an outgroup. Supplementary Figure 3.3: Maximum likelihood phylogeny based on the amino acid sequences of the replicase gene of members of the Betaflexiviridae family found in this study (sources from this study indicated by solid circle markers) and selected members of the same family. These include the nerine latent virus, well as novel viruses, clivia carlavirus A and agapanthus virus A, as well as. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the Le Gascuel model with gamma distribution (n=5). All positions containing gaps and missing data were eliminated (complete deletion option). Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. The viral genus corresponding to each reference is shown in brackets, while the sample number is indicated for samples related to this study. Supplementary figure 3.4: Maximum likelihood phylogeny based on the amino acid sequences of the polyprotein of Hippeastrum mosaic virus and the novel clivia yellow stripe virus strains (sources from this study indicated by solid circle markers) and selected members of the Potyvirus genus. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the Le Gascuel model. All positions containing gaps and missing data were eliminated (complete deletion option). Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. Representatives from other genera of the Potyviridae family form the outgroup, with the genus name corresponding to each genus shown in brackets. Supplementary figure 3.5: Maximum likelihood phylogeny based on the amino acid sequences of the produ ct of the N gene of scadoxus chlorotic ringspot virus (sources from this study indicated by a solid circle marker) and selected members of the Orthotospovirus genus. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the Le Gascuel model with gamma distribution (n=5). All positions were used in the analysis. Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown.Supplementary table 1: The pre- and post-assembly read numbers associated with each sample. The number of contigs exceeding 1000bp, for both the CLC Genomics Workbench and metaSPAdes assemblies, are listed. The datasets are linked to sample specific NCBI Biosample accession numbers.Supplementary Table 2: Primers used in all PCR, RT-PCR and RACE assays. The genomic target region, melting temperature (Tm) and product size (RT-PCR) are listed. Key: CP – Coat protein; Pol – Polyprotein; AgTV – Agapanthus tungro virus; AgVV – Agapanthus velarivirus; AgVA – Agapanthus virus A; AgCVB – Agapanthus carlavirus B; ClCVA – Clivia carlavirus A; CYSV – Clivia yellow stripe virus, HiMV – Hippeastrum mosaic virus; NeLV – Nerine latent virus; ScSRV – Scadoxus chlorotic ringspot virus; GSP – Gene specific primer; -F – Forward; -R – Reverse.Supplementary Table 3: List of viruses from this study with their associated sample and NCBI GenBank accession numbers. Genome length, assembling software used for the specific genome’s assembly, the number of reads involved in the assembly, as well as the average coverage and the percentage of total reads, are also presented. AgTV – Agapanthus tungro virus; AgVV – Agapanthus velarivirus, AgVA – Agapanthus virus A, ClCVA – Clivia carlavirus A, NeLV – Nerine latent virus, HiMV – Hippeastrum mosaic virus, ScCRV – Scadoxus chlorotic ringspot virus.http://link.springer.com/journal/7052022-07-19hj2022Forestry and Agricultural Biotechnology Institute (FABI

Floral hosts of leaf-cutter bees (Megachilidae) in a biodiversity hotspot revealed by pollen DNA metabarcoding of historic specimens.

South Africa is a megadiverse country with three globally recognised biodiversity hotspots within its borders. Bees in particular show high diversity and endemism in the western part of the country. Not much is currently known about the floral host preferences of indigenous bees in South Africa, with data only available from observational studies. Pollen metabarcoding provides provenance information by utilising DNA analyses instead of floral visitation and traditional microscopic identification to identify pollinator food plants, which can be time consuming and imprecise. In this study, we sampled pollen from leaf-cutter bees (Megachilidae) specimens maintained in a historic insect collection (National Collection of Insects, South Africa) that were originally collected from two florally important areas in South Africa (Succulent Karoo and Savanna) and used metabarcoding to determine pollen provenance. We also sampled pollen from leafcutter bee species with wider distributions, that extend across many different biomes, to determine if these 'generalist' species show relaxed floral host specificity in some biomes. Metabarcoding involved sequencing of the nuclear internal transcribed spacer 2 (ITS2) region. Amplicons were compared to a sequence reference database to assign taxonomic classifications to family level. Sequence reads were also clustered to OTUs based on 97% sequence similarity to estimate numbers of plant species visited. We found no significant difference in the mean number of plant taxa visited in the Succulent Karoo and Savanna regions, but the widespread group visited significantly more floral hosts. Bees from the widespread group were also characterised by a significantly different composition in pollen assemblage. The time since specimens were collected did not have an effect on the mean number of taxa visited by any of the bee species studied. This study highlights national history collections as valuable sources of temporal and spatial biodiversity data

Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics

Bacillus velezensis strains are applied as ecologically safe biopesticides, plant growth promoting rhizobacteria (PGPR), and in veterinary probiotics. They are abundant in various environments including soil, plants, marine habitats, the intestinal micro-flora, etc. The mechanisms underlying this adaptive plasticity and bioactivity are not well understood, nor is it clear why several strains outperform other same species isolates by their bioactivities. The main objective of this work was to demonstrate versatility of bioactivities and lifestyle strategies of the selected B. velezensis strains suitable to serve as model organisms in future studies. Here, we performed a comparative study of newly sequenced genomes of four B. velezensis isolates with distinct phenotypes and isolation origin, which were assessed by RNA sequencing under the effect of root exudate stimuli and profiled by epigenetic modifications of chromosomal DNA. Among the selected strains, UCMB5044 is an oligotrophic PGPR strain adapted to nutrient poor desert soils. UCMB5113 and At1 are endophytes that colonize plants and require nutrient rich media. In contrast, the probiotic strain, UCMB5007, is a copiotroph, which shows no propensity to colonize plants. PacBio and Illumina sequencing approaches were used to generate complete genome assemblies, tracing epigenetic modifications, and determine gene expression profiles. All sequence data was deposited at NCBI. The strains, UCMB5113 and At1, show 99% sequence identity and similar phenotypes despite being isolated from geographically distant regions. UCMB5007 and UCMB5044 represent another group of organisms with almost identical genomes but dissimilar phenotypes and plant colonization propensity. The two plant associated strains, UCMB5044 and UCMB5113, share 398 genes putatively associated with root colonization, which are activated by exposure to maize root exudates. In contrast, UCMB5007 did not respond to root exudate stimuli. It was hypothesized that alterations in the global methylation pattern and some other epigenetic modifications enable adaptation of strains to different habitats and therefore may be of importance in terms of the biotechnological applicability of these bacteria. Contrary, the ability to grow on root exudates as a sole source of nutrients or a strong antagonism against phytopathogens showed by the strains in vitro cannot be considered as good predictors of PGPR activities.Peer Reviewe

Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance

International audienceDomesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease