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In East Africa, Lethal Yellowing-Type Syndromes have profoundly and lastingly affected the coconut industry. While 'Candidatus Phytoplasma palmicola' has decimated industrial plantations in Mozambique, 'Candidatus Phytoplasma cocostanzania' is affecting coconut groves in neighboring Tanzania and in Kenya. A first multilocus sequence typing (MLST) scheme based on eight housekeeping genes was developed to study 'Ca. Phytoplasma palmicola'. Here we present a new but similar MLST scheme developed to sustain epidemiological studies on 'Ca. Phytoplasma cocostanzania' and later comparison of the two phytoplasmas. Primer pairs were defined to amplify identical portions of the 8 genes (gyrB, leuS, lpd, recA, rplV, rsmI, and secA) and applied to 25 DNAs from Lethal Decline symptomatic coconut trees originated from Tanzania. The eight gene sequences were concatenated for each sample producing a sequence of 4383 nucleotides. The average %GC of the concatenated sequences is low as 25.5. Data analysis reveals 16 different haplotypes among the 25 samples (Hd: 0.960), and a nucleotide diversity (pi) of 0.00354, increasing drastically the discrimination of the strains. The most variable genes are lpd and secA each with seven sequence types (ST). Our tool provides sufficient resolution for effectively analyzing 'Ca. Phytoplasma cocostanzania' diversity at the regional level, and for allowing the epidemiological monitoring of lethal decline disease.

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.

Bemisia tabaci whitefly species are some of the world’s most devastating agricultural pests and plant-virus disease vectors. Elucidation of the phylogenetic relationships in the group is the basis for understanding their evolution, biogeography, gene-functions and development of novel control technologies. We report here the discovery of five new Sub-Saharan Africa (SSA) B. tabaci putative species, using the partial mitochondrial cytochrome oxidase 1 gene: SSA9, SSA10, SSA11, SSA12 and SSA13. Two of them, SSA10 and SSA11 clustered with the New World species and shared 84.8‒86.5% sequence identities. SSA10 and SSA11 provide new evidence for a close evolutionary link between the Old and New World species. Re-analysis of the evolutionary history of B. tabaci species group indicates that the new African species (SSA10 and SSA11) diverged from the New World clade c. 25 million years ago. The new putative species enable us to: (i) re-evaluate current models of B. tabaci evolution, (ii) recognise increased diversity within this cryptic species group and (iii) re-estimate divergence dates in evolutionary time.

Сassava’s productivity in Madagascar is affected by pests and diseases, among which the whitefly Bemisia tabaci (Gennadius) transmitting cassava mosaic begomoviruses (CMBs) is most important. The present study sought to establish the abundance and diversity of B. tabaci cryptic species on cassava and other host plants in Madagascar. In addition, cassava mosaic disease (CMD) incidence and symptom severity were assessed. The identity and genetic diversity of B. tabaci samples collected on cassava and other plant species in Central Highlands and Tsaratanana Massif in northwestern region were studied using the partial mitochondrial cytochrome oxidase I (mtCOI) gene. The analyses of the mtCOI sequences revealed three B. tabaci cryptic species—Sub-Saharan Africa 1 (SSA1), Mediterranean (MED) and the Indian Ocean (IO)—in the sampled areas. SSA1 was the dominant cryptic species, with 100 % occurrence on cassava crops. For the first time, we report the occurrence of MED in Madagascar. Both MED and IO, the indigenous species in the South West Indian Ocean islands of Anajouan Mayotte, Grande Comore, Mauritius, Reunion, Seychelles and Madagascar, occurred on non-cassava hosts. As opposed to previous reports, we recorded no B. tabaci Middle East Asia Minor 1 – MEAM1 cryptic species (formerly also known as the B-biotype) on any of the sampled plants and locations. Generally, the abundance of adult whiteflies was low (B. tabaci IO and MED. Cassava mosaic disease was observed in 100 % of the surveyed cassava fields. The disease symptoms were generally mild, with severities of 2.00–3.13 (average, 2.62). Locations differed significantly (Pca 59 %). Our findings provide current knowledge of the economically important B. tabaci species, which is vital to the development of sustainable management practices for the vector and cassava viral diseases in Madagascar.

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.

Made available in DSpace on 2020-12-12T01:19:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Crop losses due to viral diseases and pests are major constraints on food security and income for millions of households in sub-Saharan Africa (SSA). Such losses can be reduced if plant diseases and pests are correctly diagnosed and identified early. Currently, accurate diagnosis for definitive identification of plant viruses and their vectors in SSA mostly relies on standard PCR and next generation sequencing technologies (NGS). However, it can take up to 6 months before results generated using these approaches are available. The long time taken to detect or identify viruses impedes quick, within-season decision-making necessary for early action, crop protection advice and disease control measures by farmers. This ultimately compounds the magnitude of crop losses and food shortages suffered by farmers. The MinION portable pocket DNA sequencer was used, to our knowledge globally for the first time, to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating cassava mosaic virus, which is ravaging smallholder farmers’ crops in sub-Saharan Africa. School of Molecular Sciences The University of Western Australia School of Agriculture Dept. of Plant Protection São Paulo State University (UNESP) Crop Protection Branch Department of Agriculture and Food Western Australia Mikocheni Agricultural Research Institute (MARI) National Crops Resources Research Institute (NaCRRI) Jomo Kenyatta University of Agriculture and Technology (JKUAT) School of Agriculture Dept. of Plant Protection São Paulo State University (UNESP)

The studies presented in this thesis contribute to improved resolution of genetic variability and diagnosis of potyviruses co-infecting sweetpotatoes. The most prevalent viruses infecting sweetpotato in Tanzania were Sweet potato feathery mottle virus (SPFMV), Sweet potato mild mottle virus (SPMMV), Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato chlorotic fleck virus (SPCFV). They were serologically detected and results confirmed by RT-PCR and sequencing. Nucleotide (nt) sequences of the 3´-proximal genomic part of SPFMV and SPMMV and partial HSP70h gene of SPCSV isolates from Tanzania and Uganda were determined. Results revealed limited genetic variability among East African (EA) isolates for SPFMV and SPCSV but high variability for SPMMV. Phylogenetic analysis grouped Tanzanian and Ugandan isolates into an EA strain for SPFMV and SPCSV. Phylogenetically, four strains of SPFMV were detected: EA, RC and O, and strain C which is distantly related to them. SPCSV isolates were grouped into two distantly related strains: EA group with only East African isolates, and a non-East African (NEA) group with isolates from West Africa and other parts of the world. No distinct strain groups could be inferred among the SPMMV isolates from East Africa In Australia, Sweet potato virus Y (SPVY; synonymous to SPV-2) (family Potyviridae) was found to co-infect sweetpotatoes with strains RC and/or C of SPFMV. Five SPVY and SPFMV isolates were sequence-characterised for their 3’-proximal end of the genome and compared with isolates from Asia, Africa, Europe and North America. Phylogenetic analysis showed that Australian SPVY isolates formed a separate clade closest to the North American isolates. Utilising findings of molecular resolutions of major viruses in East Africa and Australia, a simple and sensitive RT-PCR/RFLP based diagnostic procedure was devised to differentiate potyviruses in complexes which readily differentiated SPVY and strains C and RC of SPFMV.