Molecular characterization of divergent isolates of Citrus bent leaf viroid (CBLVd) from citrus cultivars of Punjab, Pakistan

Citrus viroid infection is emerging as a serious threat because of its efficient systemic movement within the host plant and its quick spread due to contaminated pruning tools. A survey was conducted to investigate the primary distribution and molecular characterization of Citrus bent leaf viroid (CBLVd) and its variants in different citrus cultivars. A total of 154 symptomatic citrus samples were collected and detected by RT‒PCR with newly designed specific primers with the incidence of 36.33%. During biological indexing study on Etrog citron, expressions of reduced leaf size, yellowing with a light green pattern, and bending were observed. Amplified products were sequenced and analyzed using a nucleotide BLAST search, which showed 98% homology with other CBLVd isolates. The results of the phylogenetic tree analysis showed the presence of two main groups (A and B), with the predominant variants of CBLVd, i.e., CVd-I-LSS (Citrus viroid Low Sequence Similarity) sequences, clustering in subgroup A1 along with newly detected CVd-I-LSS from Palestinian sweet lime (Citrus limettioides), which has been identified as a new host of CVd-I-LSS in Pakistan. Further analysis of the sequences in subgroup A1 showed that the variant of CVd-I-LSS infecting citrus cultivars had a close relationship with isolates reported from China, Japan, and Iran, which may have resulted from the exchange of planting material. This study also unveiled the variability in nucleotide sequences of CBLVd, which made it unable to be detected by old primers. The results of this study indicate that the widespread presence of divergent variants of CBLVd is a major concern for the citrus industry in Pakistan and other countries where virulent isolates of CBLVd are prevalent. These findings suggest the need for future research on effective management and quarantine measures to stop the spread of CBLVd.

Possible Overestimation of Seed Transmission in the Spread of Pospiviroids in Commercial Pepper and Tomato Crops Based on Large-Scale Grow-Out Trials and Systematic Literature Review

Several outbreaks of pospiviroids have been reported in pepper and tomato crops worldwide. Tracing back the origin of the infections has led to different sources. In some cases, the infections were considered to result from seed transmission. Other outbreaks were related to transmission from ornamental crops and weeds. Pospiviroids, in particular potato spindle tuber viroid, are regulated by many countries because they can be harmful to potatoes and tomatoes. Seed transmission has been considered an important pathway of introduction and spread. However, the importance of this pathway can be questioned. This paper presents data on seed transmission from large-scale grow-out trials of infested pepper and tomato seed lots produced under standard seed-industry conditions. In addition, it presents the results of a systematic review of published data on seed transmission and outbreaks in commercial pepper and tomato crops. Based on the results of the grow-out trials and review of the literature, it was concluded that the role of seed transmission in the spread of pospiviroids in practice is possibly overestimated.

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification

Columnea latent viroid (CLVd) is a member of the Pospiviroid family and its naked circular RNA genome typically forms native “rod-like” secondary structures. In this work, the CLVd taxonomy was reevaluated based on sequence similarity and phylogenetic analysis, as well as the evaluation of the symptom development and disease severity of four selected CLVd isolates in a range of host species. The phylogenetic analysis showed that all CLVd isolates were clustered into five distinct clades: (I) severe isolates originally found in tomato crops in Thailand, (II) ornamental isolates, (III) mild isolates originally found in tomato crops in Thailand, and two clades (IV and V) containing mild isolates originating mainly from tomato crops in European countries, with different virulence levels on several hosts. Our analysis demonstrated that some CLVd isolates have a sequence similarity of less than 90% within the species taxon, as well as distinct biological characteristics (symptom development and virulence), both of which are important ICTV criteria for viroid classification. For these reasons, we propose that CLVd should be re-classified into at least three main taxonomic lineages: a “CLVd-tomato Asian lineage” (I), a “CLVd-tomato European lineage” (IV) and a “CLVd-ornamental European lineage” (II), plus two minor lineages (III and V), fitting the ICTV criteria.

Synergistic effects of organic fertilizer and corn straw on microorganisms of pepper continuous cropping soil in China

Because of the large population, large demand, limited arable land and many environmental factors, continuous cropping have become a very common phenomenon in China. However, long-term continuous cropping has caused a series of serious soil-borne diseases, and the yield and quality of crops to drop, which seriously restricted the sustainable development of agricultural industry. Therefore, in order to improve the yield of pepper and reduce the occurrence of soil-borne diseases, it is essential to understand the effect of continuous cropping of pepper on soil microbial community composition and abundance. In this study, high throughput sequencing was used to study the effects of seven treatments of organic fertilizers and corn straw on soil microbial community and function of pepper continuous cropping. The results showed that the yield of all treatments was significantly higher than that of the control. The soil microbial diversity and community composition showed that Proteobacteria and Ascomycota were the most abundant phylum in all treatments. In conclusion, there were significant differences among the seven treatments and the treatment of fowl dung with corn straw was the best fertilizer combination to improve the yield and output value of pepper. Besides, the addition of fowl dung and corn straw not only can improve the community and functions of microorganisms, but also enhance the ability of disease resistance, and ultimately decrease the soil-borne diseases. The results will help to provide scientific basis for rational application of organic fertilizer and corn straw, and overcoming continuous cropping obstacles.

Rasta Disease of Tomato in Ghana is Caused by the Pospiviroids Potato spindle tuber viroid and Tomato apical stunt viroid

Rasta is a virus-like disease of unknown etiology affecting tomato (Solanum lycopersicum) plants in Ghana. Symptoms include stunting; epinasty, crumpling, and chlorosis of leaves; and necrosis of leaf veins, petioles, and stems. Leaf samples with rasta symptoms were collected from commercial tomato fields in Ghana in October 2012 and applied to FTA cards, and RNA extracts were prepared. Reverse-transcription polymerase chain reaction (RT-PCR) tests with primers for Columnea latent viroid, which causes rasta-like symptoms in tomato plants in Mali, were negative, whereas tests with degenerate viroid primer pairs were inconclusive. However, tomato seedlings (Early Pak 7) mechanically inoculated with RNA extracts of 10 of 13 samples developed rasta-like symptoms. In RT-PCR tests with RNA from leaves of the 10 symptomatic seedlings and primers for Potato spindle tuber viroid (PSTVd) or Tomato apical stunt viroid (TASVd), the expected size (approximately 360 bp) of DNA fragment was amplified from eight and two seedlings, respectively. Sequence analyses confirmed that these fragments were from PSTVd and TASVd isolates, and revealed a single PSTVd haplotype and two TASVd haplotypes. The PSTVd and TASVd isolates from Ghana had high nucleotide identities (>94%) with isolates from other geographic regions. In a host range study, PSTVd and TASVd isolates from Ghana induced rasta symptoms in the highly susceptible tomato cultivar Early Pak 7 and mild or no symptoms in Glamour, and symptomless infections in a number of other solanaceous species. PSTVd and TASVd isolates were seed associated and possibly seed transmitted.

Viroid-infected Tomato and Capsicum Seed Shipments to Australia

Pospiviroid species are transmitted through capsicum and tomato seeds. Trade in these seeds represents a route for the viroids to invade new regions, but the magnitude of this hazard has not been adequately investigated. Since 2012, tomato seed lots sent to Australia have been tested for pospiviroids before they are released from border quarantine, and capsicum seed lots have been similarly tested in quarantine since 2013. Altogether, more than 2000 seed lots have been tested. Pospiviroids were detected in more than 10% of the seed lots in the first years of mandatory testing, but the proportion of lots that were infected declined in subsequent years to less than 5%. Six pospiviroid species were detected: Citrus exocortis viroid, Columnea latent viroid, Pepper chat fruit viroid, Potato spindle tuber viroid, Tomato chlorotic dwarf viroid and Tomato apical stunt viroid. They were detected in seed lots exported from 18 countries from every production region. In many seed lots, the detectable fraction (prevalence) of infected seeds was estimated to be very small, as low as 6 × 10⁻⁵ (~1 in 16,000; CI 5 × 10⁻⁶ to 2.5 × 10⁻⁴) for some lots. These findings raise questions about seed production practices, and the study indicates the geographic distributions of these pathogens are uncertain, and there is a continuing threat of invasion.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) designed for fast and sensitive on-site detection of Pepper chat fruit viroid (PCFVd)

Pepper chat fruit viroid (PCFVd) is one of the most important tomato and pepper diseases causing serious losses, affecting productivity, fruit quality and even international seed trade. Reverse transcription Loop-mediated isothermal amplification (RT-LAMP) is a fast and reliable RNA amplification assay, out competing conventional reverse transcription polymerase chain reaction (RT-PCR) in robustness, analytical sensitivity and specificity, and cost-effectiveness. In this work, a PCFVd specific RT-LAMP detection assay, based on a set of six primers was developed. Under the optimized conditions, PCFVd could be detected within 15 min, with a sensitivity of detecting PCFVd that was almost the same as a probe-based qRT-PCR and 10-100 times higher than the available RT-PCR methods. No cross-amplification with other viroids and tomato viruses was observed. The validated assay was also adapted for convenient on-site detection. Besides replacing the full RNA extraction with a simple lysis procedure, several visualization options, of which the use of SYTO9 was the most convenient, were presented to accommodate any in-field application of the method.

A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level

A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.