Molecular variability of cassava Bemisia tabaci and its effect on the epidemiology of cassava mosaic geminiviruses in Uganda

Bemisia tabaci (Genn.) is the vector of cassava mosaic geminiviruses (CMGs), which are the main production constraint to cassava, both in Uganda and elsewhere in Africa. A severe form of cassava mosaic disease (CMD) was responsible for the devastation of cassava in Uganda beginning in the late 1980s. In subsequent years the severe CMD epidemic spread throughout Uganda, and to neighbouring countries, causing devastating effects to cassava production, and its geographical range continues to expand with the pandemic. To further understand the virus-vector dynamics involved in the spread of CMD in the post epidemic zone in Uganda, we investigated the current distribution of B. tabaci genotypes in selected cassava-growing regions. Additionally, the relationship between the vector genotypes and distribution of CMGs in the post-epidemic zone was examined also. CMD-affected cassava leaves were collected from 3 to 5 month-old cassava plants, and B. tabaci adults and fourth instar nymphs were collected from cassava and twenty-two other plant species occurring adjacent to the sampled cassava fields. The mitochondrial cytochrome oxidase I (mtCOI) sequence was used to establish the genotype of B. tabaci adults and nymphs associated with the sampled plant species. African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda 2 (EACMV-UG2) were confirmed to be present in the post-epidemic zone in Uganda, as reported previously. As expected, EACMV-UG2 predominated. However, unlike previous observations in which EACMV-UG2 was consistently associated with the severe disease phenotype, in this study EACMV-UG2 occurred almost equally in the severely and mildly diseased plants. Phylogenetic analyses of Ugandan B. tabaci genotypes (mtCOI) revealed that their closest relatives were other Old World genotypes, as might be expected. Two previously reported B. tabaci genotype clusters, Uganda 1 (Ug1) and Uganda 2 (Ug2), at ~8% nt divergence, were confirmed to occur on cassava in the post-epidemic zone. However, Ug1 occurred more frequently (83%) than Ug2 (17%), and no definite association was established of a particular vector genotype with cassava plants exhibiting the severe disease phenotype, in contrast to the B. tabaci genotype distribution and association with the CMGs reported there at the height of the spread of the severe CMD epidemic. Based on the presence of B. tabaci fourth instar nymphs, the Ug1 genotypes colonized five additional non-cassava plant species: Manihot glaziovii, Jatropha gossypifolia, Euphorbia heterophylla, Aspilia africana and Abelmoschus esculentus, suggesting that in Uganda the Ug1 genotypes are not restricted to cassava. However, no Ug2 genotypes were detected on the non-cassava plant species sampled. This study revealed also the presence in Uganda of five distinct previously unrecorded B. tabaci genotype clusters, Uganda 3 (Ug3), Uganda 4 (Ug4), Uganda 5 (Ug5), Uganda 6 (Ug6) and Uganda 7 (Ug7), and a sweetpotato colonizing genotype cluster, designated Uganda 8 (Ug8), among the collective Ugandan B. tabaci populations. Ug3 was the only exemplar representing one cluster, which was unlike any previously described genotype in Uganda or elsewhere, and diverged at 8%, 10% and 17% from Ug1, Ug2 and Ug8, respectively. The Ug3 genotypes colonized a single species, Ocimum gratissimum. Ug4, Ug5, Ug6 and Ug7 formed four closely related sub-clusters (93-97% nt identity), and diverged from one another by 1-7%, and by 15-18% from Ug1, Ug2, Ug3 and Ug8, respectively. The Ug4 genotypes had as their closest relatives (at 97-99% nt identity) previously reported B. tabaci from okra in the Ivory Coast, whereas, the Ug5 and Ug6 genotypes shared 95-99% and 99% nt identity, respectively, with their closest relatives from the Mediterranean-North Africa- Middle East (MED-NAFR-ME) region, which also includes the well studied B and Q biotypes. The Ug7 genotypes were closely related (at 98-99% nt identity) to B. tabaci from Reunion Island in the Indian Ocean. The Ug4, Ug5, Ug6 and Ug7 genotypes were identified on 54%, 8%, 8%, and 31% of the sampled plants species, respectively. Ug4 were most polyphagous, followed by Ug7 and Ug6. However, none of the new five genotypes (Ug3-Ug7) was found associated with, or colonizing, xx cassava or sweetpotato plants in this study. Squash plants colonized by the Ug6 and Ug7 genotypes, both members of the B biotype/B-like cluster, developed the silvering phenotype, while those colonized by the Ug4 genotypes (most closely related to a non-B like genotype from okra in the Ivory Coast) did not. In addition to colonizing sweetpotato, the Ug8 genotypes also colonized Lycopersicon esculentum and L nepetifolia

Is high whitefly abundance on cassava in sub-Saharan Africa driven by biological traits of a specific, cryptic Bemisia tabaci species?

In East Africa, the prevalent Bemisia tabaci whiteflies on the food security crop cassava are classified as sub-Saharan Africa (SSA) species. Economically damaging cassava whitefly populations were associated with the SSA2 species in the 1990s, but more recently, it has been to SSA1 species. To investigate whether biological traits (number of first instar nymphs, emerged adults, proportion of females in progeny and development time) of the cassava whitefly species are significant drivers of the observed field abundance, our study determined the development of SSA1 sub-group (SG) 1 (5 populations), SG2 (5 populations), SG3 (1 population) and SSA2 (1 population) on cassava and eggplant under laboratory conditions. SSA1-(SG1-SG2) and SSA2 populations’ development traits were similar. Regardless of the host plant, SSA1-SG2 populations had the highest number of first instar nymphs (60.6 ± 3.4) and emerged adults (50.9 ± 3.6), followed by SSA1-SG1 (55.5 ± 3.2 and 44.6 ± 3.3), SSA2 (45.8 ± 5.7 and 32.6 ± 5.1) and the lowest were SSA1-SG3 (34.2 ± 6.1 and 32.0 ± 7.1) populations. SSA1-SG3 population had the shortest egg–adult emergence development time (26.7 days), followed by SSA1-SG1 (29.1 days), SSA1-SG2 (29.6 days) and SSA2 (32.2 days). Regardless of the whitefly population, development time was significantly shorter on eggplant (25.1 ± 0.9 days) than cassava (34.6 ± 1.0 days). These results support that SSA1-(SG1-SG2) and SSA2 B. tabaci can become highly abundant on cassava, with their species classification alone not correlating with observed abundance and prevalence

Whole‐genome single nucleotide polymorphism and mating compatibility studies reveal the presence of distinct species in sub‐Saharan Africa Bemisia tabaci whiteflies

In sub‐Saharan Africa cassava growing areas, two members of the Bemisia tabaci species complex termed sub‐Saharan Africa 1 (SSA1) and SSA2 have been reported as the prevalent whiteflies associated with the spread of viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) pandemics. At the peak of CMD pandemic in the late 1990s, SSA2 was the prevalent whitefly, although its numbers have diminished over the last two decades with the resurgence of SSA1 whiteflies. Three SSA1 subgroups (SG1 to SG3) are the predominant whiteflies in East Africa and vary in distribution and biological properties. Mating compatibility between SSA1 subgroups and SSA2 whiteflies was reported as the possible driver for the resurgence of SSA1 whiteflies. In this study, a combination of both phylogenomic methods and reciprocal crossing experiments were applied to determine species status of SSA1 subgroups and SSA2 whitefly populations. Phylogenomic analyses conducted with 26 548 205 bp whole genome single nucleotide polymorphisms (SNPs) and the full mitogenomes clustered SSA1 subgroups together and separate from SSA2 species. Mating incompatibility between SSA1 subgroups and SSA2 further demonstrated their distinctiveness from each other. Phylogenomic analyses conducted with SNPs and mitogenomes also revealed different genetic relationships among SSA1 subgroups. The former clustered SSA1‐SG1 and SSA1‐SG2 together but separate from SSA1‐SG3, while the latter clustered SSA1‐SG2 and SSA1‐SG3 together but separate from SSA1‐SG1. Mating compatibility was observed between SSA1‐SG1 and SSA1‐SG2, while incompatibility occurred between SSA1‐SG1 and SSA1‐SG3, and SSA1‐SG2 and SSA1‐SG3. Mating results among SSA1 subgroups were coherent with phylogenomics results based on SNPs but not the full mitogenomes. Furthermore, this study revealed that the secondary endosymbiont—Wolbachia—did not mediate reproductive success in the crossing assays carried out. Overall, using genome wide SNPs together with reciprocal crossings assays, this study established accurate genetic relationships among cassava‐colonizing populations, illustrating that SSA1 and SSA2 are distinct species while at least two species occur within SSA1 species

Correction : Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation

Cassava brown streak disease is caused by two devastating viruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) which are frequently found infecting cassava, one of sub-Saharan Africa's most important staple food crops. Each year these viruses cause losses of up to $100 million USD and can leave entire families without their primary food source, for an entire year. Twelve new whole genomes, including seven of CBSV and five of UCBSV were uncovered in this research, doubling the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Utilizing NGS sequencing technologies and proper phylogenetic practices will rapidly increase the solution to sustainable cassava production

Genetic diversity of whitefly (Bemisia spp.) on crop and uncultivated plants in Uganda: implications for the control of this devastating pest species complex in Africa

Over the past three decades, highly increased whitefly (Bemisia tabaci) populations have been observed on the staple food crop cassava in eastern Africa and associated with ensuing viral disease pandemics and food insecurity. Increased whitefly numbers have also been observed in other key agricultural crops and weeds. Factors behind the population surges on different crops and their interrelationships are unclear, although in cassava they have been associated with specific populations within the Bemisia tabaci species complex known to infest cassava crops in Africa. This study carried out an in-depth survey to understand the distribution of B. tabaci populations infesting crops and uncultivated plant hosts in Uganda, a centre of origin for this pest complex. Whitefly samples were collected from 59 identified plant species and 25 unidentified weeds in a countrywide survey. Identities of 870 individual adult whiteflies were determined through mitochondrial cytochrome oxidase 1 sequences (651 bp) in the 3′ barcode region used for B. tabaci systematics. Sixteen B. tabaci and five related whitefly putative species were identified based on > 4.0% nucleotide divergence, of which three are proposed as novel B. tabaci putative species and four as novel closely related whitefly species. The most prevalent whiteflies were classified as B. tabaci MED-ASL (30.5% of samples), sub-Saharan Africa 1 (SSA1, 22.7%) and Bemisia Uganda1 (12.1%). These species were also indicated to be the most polyphagous occurring on 33, 40 and 25 identified plant species, respectively. Multiple (≥ 3) whitefly species occurred on specific crops (bean, eggplant, pumpkin and tomato) and weeds (Sida acuta and Ocimum gratissimum). These plants may have increased potential to act as reservoirs for mixed infections of whitefly-vectored viruses. Management of whitefly pest populations in eastern Africa will require an integration of approaches that consider their degree of polyphagy and a climate that enables the continuous presence of crop and uncultivated plant hosts

Review and guide to a future naming system of African Bemisia tabaci species

Once a pest has been correctly identified, its genus and species name can provide a link to valuable indications of its ecology, biology and life history that are critical for developing control strategies. Importantly, this link should exist even when the pest was known under other names (synonyms), or was not considered a pest at all (National Research Council, 1968). Many examples have shown that incorrect identification or classification of a pest has led to fruitless searches for biocontrol agents in the native range, incorrect assignments as disease vectors, and costly, yet misdirected, suppression measures. As new approaches for delimiting species based on molecular information become more widely used, the process of correctly identifying a species has become even more complex. Fortunately, we have good systematic frameworks and nomenclatural systems that are able to cope with these challenges. Here we review challenges associated with classification and identification within the Bemisia tabaci (Gennadius) species complex. These pests and the viruses they transmit have emerged in the past few decades as among the most damaging to food and fibre crops globally (Varma & Malathi, 2003; Pimental et al., 2005; Seal et al., 2006), especially in sub‐Saharan Africa (SSA). The systematics of the B. tabaci species group has been a highly debated topic for years (Boykin, 2014). Putative species are indistinguishable morphologically, so other biological data have been collected to investigate the species in the complex. Based on genetic differences (Colvin et al., 2004; Sseruwagi et al., 2005; Boykin et al., 2007; Boykin et al., 2013; Hsieh et al., 2014) and mating incompatibility (Colvin et al., 2004; Liu et al., 2007; Xu et al., 2010), B. tabaci is now recognized as a species complex that consists of at least 34 putative species (Boykin et al., 2012). The rapid discovery of significant species diversity has led to many changes in the informal names used over the last 10 years (Boykin, 2014), creating confusion in the literature

A novel East African monopartite begomovirus-betasatellite complex that infects Vernonia amygdalina

The complete genomes of a monopartite begomovirus (genus Begomovirus, family Geminiviridae) and an associated betasatellite found infecting Vernonia amygdalina Delile (family Compositae) in Uganda were cloned and sequenced. Begomoviruses isolated from two samples showed the highest nucleotide sequence identity (73.1% and 73.2%) to an isolate of the monopartite begomovirus tomato leaf curl Vietnam virus, and betasatellites from the same samples exhibited the highest nucleotide sequence identity (67.1% and 68.2%) to vernonia yellow vein Fujian betasatellite. Following the current taxonomic criteria for begomovirus species demarcation, the isolates sequenced here represent a novel begomovirus species. Based on symptoms observed in the field, we propose the name vernonia crinkle virus (VeCrV) for this novel begomovirus and vernonia crinkle betasatellite (VeCrB) for the associated betasatellite. This is the first report of a monopartite begomovirus-betasatellite complex from Uganda

Desmodium mottle virus, the first legumovirus (genus Begomovirus) from East Africa

A novel bipartite legumovirus (genus Begomovirus, family Geminiviridae), that naturally infects the wild leguminous plant Desmodium sp. in Uganda, was molecularly characterized and named Desmodium mottle virus. The highest nucleotide identities for DNA-A, obtained from two field-collected samples, were 79.9% and 80.1% with the legumovirus, soybean mild mottle virus. DNA-B had the highest nucleotide identities (65.4% and 66.4%) with a typical non-legumovirus Old World begomovirus, African cassava mosaic virus. This is the first report of a legumovirus in East Africa and extends the known diversity of begomoviruses found infecting wild plants in this continent

Expansion of the cassava brown streak pandemic in Uganda revealed by annual field survey data for 2004 to 2017

Funder: Uganda Government Association for Strengthening Agricultural Research in Eastern and Central AfricaFunder: Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)Abstract: Cassava brown streak disease (CBSD) is currently the most devastating cassava disease in eastern, central and southern Africa affecting a staple crop for over 700 million people on the continent. A major outbreak of CBSD in 2004 near Kampala rapidly spread across Uganda. In the following years, similar CBSD outbreaks were noted in countries across eastern and central Africa, and now the disease poses a threat to West Africa including Nigeria - the biggest cassava producer in the world. A comprehensive dataset with 7,627 locations, annually and consistently sampled between 2004 and 2017 was collated from historic paper and electronic records stored in Uganda. The survey comprises multiple variables including data for incidence and symptom severity of CBSD and abundance of the whitefly vector (Bemisia tabaci). This dataset provides a unique basis to characterize the epidemiology and dynamics of CBSD spread in order to inform disease surveillance and management. We also describe methods used to integrate and verify extensive field records for surveys typical of emerging epidemics in subsistence crops