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Dahlia mosaic virus (DMV), an aphid‐transmitted caulimovirus in the family Caulimoviridae, is an important pathogen of dahlia (Dahlia variabilis). Development of rapid, and sensitive diagnostic tools is essential in surveillance and management of DMV. A loop‐mediated isothermal amplification (LAMP) assay was developed for DMV detection. The LAMP assay targets the reverse transcriptase region of the DMV genome and is optimal at a temperature of 60°C and run time of 60 min, and amplification was detected through fluorescence detection and by agarose gel electrophoresis. The assay detected DMV in DNA concentration as low as 10−3 ng. To the best of our knowledge, this is the first report of a LAMP assay for the detection of DMV, a plant DNA virus. This assay will be useful in rapid and sensitive detection of DMV and in reducing the virus incidence through production of virus‐free planting material. [ABSTRACT FROM AUTHOR]

Taro (Colocasia esculenta) and tannia (Xanthosoma sp.) are important root crops cultivated mainly by small‐scale farmers in sub‐Saharan Africa and the South Pacific. Viruses are known to be one of the most important constraints to production, with infections resulting in severe yield reduction. In 2014 and 2015, surveys were conducted in Ethiopia, Kenya, Tanzania and Uganda to determine the identity of viruses infecting taro in East Africa. Screening of 392 samples collected from the region using degenerate badnavirus primers revealed an incidence of 58–74% among the four countries surveyed, with sequence analysis identifying both Taro bacilliform virus (TaBV) and Taro bacilliform CH virus (TaBCHV). TaBCHV was identified from all four countries while TaBV was identified in all except Ethiopia. Full‐length sequences from representative TaBV and TaBCHV isolates showed that the genome organization of TaBV isolates from East Africa was consistent with previous reports while TaBCHV isolates from East Africa were found to encode only four ORFs, distinct from a previous report from China. Phylogenetic analysis showed that all East African TaBV isolates form a single subgroup within known TaBV isolates, while TaBCHV isolates form at least two distinct subgroups. To the authors' knowledge, this is the first report describing the occurrence and genome organization of TaBV and TaBCHV isolates from East Africa and the first full‐length sequence of the two viruses from tannia. [ABSTRACT FROM AUTHOR]

BACKGROUND Mealybugs (Hemiptera: Coccoidea: Pseudococcidae) are key vectors of badnaviruses, including Cacao swollen shoot virus (CSSV), the most damaging virus affecting cacao ( Theobroma cacao L.). The effectiveness of mealybugs as virus vectors is species dependent, and it is therefore vital that CSSV resistance breeding programmes in cacao incorporate accurate mealybug identification. In this work, the efficacy of a CO1-based DNA barcoding approach to species identification was evaluated by screening a range of mealybugs collected from cacao in seven countries. RESULTS Morphologically similar adult females were characterised by scanning electron microscopy, and then, following DNA extraction, were screened with CO1 barcoding markers. A high degree of CO1 sequence homology was observed for all 11 individual haplotypes, including those accessions from distinct geographical regions. This has allowed the design of a high-resolution melt (HRM) assay capable of rapid identification of the commonly encountered mealybug pests of cacao. CONCLUSIONS HRM analysis readily differentiated between mealybug pests of cacao that cannot necessarily be identified by conventional morphological analysis. This new approach, therefore, has potential to facilitate breeding for resistance to CSSV and other mealybug-transmitted diseases. © 2015 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Sugarcane bacilliform viruses ( SCBV; genus Badnavirus) cause leaf fleck disease in sugarcane worldwide. SCBV was detected in 28 sugarcane cultivars originating from eight states of India. Eight representative SCBV isolates from five different states showed sequence variability up to 27% in the reverse transcriptase and RNase H ( RT/RNase H) genetic region. Five isolates [SCBV-AP (): , SCBV-Assam (CoBIN94063): , SCBV-Bihar (Bo141): , SCBV-UP (Co1424): and SCBV-UP (CoSe6460): ] showed sequence identity of 86-88% with Sugarcane bacilliform IM virus ( SCBIMV), but the other three isolates [ SCBV-Kerala (Co7219): , SCBV- TN (): and SCBV- UP (CoSe92423): ] showed maximum sequence identity of 75-79% with Sugarcane bacilliform MO virus ( SCBMOV). In phylogenetic analysis, the SCBV isolates segregated into two new subclades and were distinct from the known SCBV genotypes. The rates of non-synonymous and synonymous ( dN/ dS) substitution indicated the signs of purifying selection with strong functional constraints for RT/RNase H region in SCBV population. A variant ( SCBV-UP, CoSe92423) was identified to be a recombinant isolate having two other Indian SCBV isolates as parents. Although RT/RNase H region is a recombination cold spot, a strong recombination might have played a key role in the evolution of this new variant of SCBV. Our study provides an insight into the diverse genetic structure of SCBV population and presence of a novel recombinant SCBV species/variant infecting sugarcane cultivars in India. Our results will be helpful in devising a robust detection procedure for quarantine and field testing of sugarcane germplasm. [ABSTRACT FROM AUTHOR]

Endogenous pararetroviral sequences are the most commonly found virus sequences integrated into angiosperm genomes. We describe an endogenous pararetrovirus ( EPRV) repeat in Fritillaria imperialis, a species that is under study as a result of its exceptionally large genome (1C = 42 096 Mbp, approximately 240 times bigger than Arabidopsis thaliana). The repeat (Fri EPRV) was identified from Illumina reads using the RepeatExplorer pipeline, and exists in a complex genomic organization at the centromere of most, or all, chromosomes. The repeat was reconstructed into three consensus sequences that formed three interconnected loops, one of which carries sequence motifs expected of an EPRV (including the gag and pol domains). Fri EPRV shows sequence similarity to members of the Caulimoviridae pararetrovirus family, with phylogenetic analysis indicating a close relationship to Petuvirus. It is possible that no complete EPRV sequence exists, although our data suggest an abundance that exceeds the genome size of Arabidopsis. Analysis of single nucleotide polymorphisms revealed elevated levels of C→T and G→A transitions, consistent with deamination of methylated cytosine. Bisulphite sequencing revealed high levels of methylation at CG and CHG motifs (up to 100%), and 15-20% methylation, on average, at CHH motifs. Fri EPRV's centromeric location may suggest targeted insertion, perhaps associated with meiotic drive. We observed an abundance of 24 nt small RNAs that specifically target Fri EPRV, potentially providing a signature of RNA-dependent DNA methylation. Such signatures of epigenetic regulation suggest that the huge genome of F. imperialis has not arisen as a consequence of a catastrophic breakdown in the regulation of repeat amplification. [ABSTRACT FROM AUTHOR]

Small interfering RNA deep sequencing ( SRDS) was used to detect viruses in 23 sweetpotato plants, collected from various locations in Tanzania. Alignment of small RNA reads using a MAQ program recovered genomes of viruses from five families, namely Geminiviridae (2), Closteroviridae (1), Betaflexiviridae (1), Caulimoviridae (1) and Potyviridae (1). This was in agreement with the variation of symptoms observed on sweetpotato plants in fields and screen house, which included leaf curl, vein yellowing, chlorosis, stunted growth and brown blotches. PCR was also used to confirm the occurrence of viruses associated with leaf curl and symptomless infections. A complete genome (2768 nucleotides) was obtained for a sweepovirus that was 89.9% identical to the strain of Sweet potato leaf curl Sao Paulo virus ( SPLCSPV; Begomovirus) reported in South Africa. Sweepoviruses are known to undergo frequent recombinations and evidence for this was found in the SPLCSPV sequence studied. The SRDS-based results indicated occurrence of the poorly studied Sweet potato badnavirus B ( SPBV-B) and Sweet potato badnavirus A (collectively known as Sweet potato pakakuy virus; SPPV; Caulimoviridae) in sweetpotato plants in Tanzania. A 5′-end partial sequence (3065 nucleotides), encoding hypothetical, movement and coat proteins, was obtained and found to be 86.3% and 73.1% identical to SPBV-B and SPBV-A, respectively. A survey for the distribution of SPPV and Sweet potato symptomless mastrevirus 1 ( SPSMV-1) showed that these viruses were wide spread and co-infecting sweetpotato plants in Tanzania. The importance of East Africa as a hot spot for the diversity and evolution of sweet potato viruses is discussed. [ABSTRACT FROM AUTHOR]