Survey and molecular detection of Sri Lankan cassava mosaic virus in Thailand

Single-tube colorimetric loop-mediated isothermal amplification (LAMP) assay for high-sensitivity detection of SLCMV in cassava from southern India

Sri Lankan cassava mosaic virus (SLCMV) is a major cause for mosaic infections in cassava leaves, resulting in significant economic losses in southern India. SLCMV leads to growth retardation, leaf curl, and chlorosis in the host, with rapid transmission through whitefly insect vectors. Detecting SLCMV promptly is crucial, and the study introduces a novel and efficient colorimetric Loop-mediated isothermal amplification (LAMP) assay for successful detection in 60 min. Three primer sets were designed to target the conserved region of the SLCMV genome, specifically the coat protein gene, making the assay highly specific. The LAMP assay offers rapid and sensitive detection, completing within 60 min in a temperature-controlled water bath or thermal cycler. Compared to PCR techniques, it demonstrates 100 times superior sensitivity. The visual inspection of LAMP tube results using a nucleic acid dye and observing ladder-like pattern bands in a 2 % agarose gel confirms the presence of SLCMV. The assay is specific to SLCMV, showing no false positives or contaminations when tested against other virus. The standardized SLCMV LAMP assay proves technically efficient, providing a rapid, specific, simple, and low-cost solution, streamlining the detection and management of SLCMV.

Role of aminopeptidase N-like in the acquisition of begomoviruses by Bemisia tabaci, the whitefly vector

Sri Lankan cassava mosaic virus (SLCMV) is a prominent causative agent of cassava mosaic disease in Asia and relies on the whitefly Bemisia tabaci cryptic complex for its transmission. However, the molecular mechanisms involved in SLCMV transmission by B. tabaci have yet to be understood. In this study, we identified an aminopeptidase N-like protein (BtAPN) in B. tabaci Asia II 1, an efficient vector of SLCMV, which is involved in the SLCMV transmission process. Through the use of glutathione S-transferase pull-down assay and LC-MS/MS analysis, we demonstrated the interaction between BtAPN and the coat protein (CP) of SLCMV. This interaction was further confirmed in vitro, and we observed an induction of BtAPN gene expression following SLCMV infection. By interfering with the function of BtAPN, the quantities of SLCMV were significantly reduced in various parts of B. tabaci Asia II 1, including the whole body, midgut, hemolymph, and primary salivary gland. Furthermore, we discovered that BtAPN is conserved in B. tabaci Middle East-Asia Minor 1 (MEAM1) and interacts with the CP of tomato yellow leaf curl virus (TYLCV), a begomovirus known to cause severe damage to tomato production. Blocking BtAPN with antibody led to a significant reduction in the quantities of TYLCV in whitefly whole body and organs/tissues. These results demonstrate that BtAPN plays a generic role in interacting with the CP of begomoviruses and positively regulates their acquisition by the whitefly.

Comparative transcriptomics analysis reveals defense mechanisms of Manihot esculenta Crantz against Sri Lanka Cassava MosaicVirus

BACKGROUND

Cassava mosaic disease (CMD), caused by Sri Lankan cassava mosaic virus (SLCMV) infection, has been identified as a major pernicious disease in Manihot esculenta Crantz (cassava) plantations. It is widespread in Southeast Asia, especially in Thailand, which is one of the main cassava supplier countries. With the aim of restricting the spread of SLCMV, we explored the gene expression of a tolerant cassava cultivar vs. a susceptible cassava cultivar from the perspective of transcriptional regulation and the mechanisms underlying plant immunity and adaptation.

RESULTS

Transcriptomic analysis of SLCMV-infected tolerant (Kasetsart 50 [KU 50]) and susceptible (Rayong 11 [R 11]) cultivars at three infection stages-that is, at 21 days post-inoculation (dpi) (early/asymptomatic), 32 dpi (middle/recovery), and 67 dpi (late infection/late recovery)-identified 55,699 expressed genes. Differentially expressed genes (DEGs) between SLCMV-infected KU 50 and R 11 cultivars at (i) 21 dpi to 32 dpi (the early to middle stage), and (ii) 32 dpi to 67 dpi (the middle stage to late stage) were then identified and validated by real-time quantitative PCR (RT-qPCR). DEGs among different infection stages represent genes that respond to and regulate the viral infection during specific stages. The transcriptomic comparison between the tolerant and susceptible cultivars highlighted the role of gene expression regulation in tolerant and susceptible phenotypes.

CONCLUSIONS

This study identified genes involved in epigenetic modification, transcription and transcription factor activities, plant defense and oxidative stress response, gene expression, hormone- and metabolite-related pathways, and translation and translational initiation activities, particularly in KU 50 which represented the tolerant cultivar in this study.

Cassava molecular genetics and genomics for enhanced resistance to diseases and pests

Cassava (Manihot esculenta) is one of the most important sources of dietary calories in the tropics, playing a central role in food and economic security for smallholder farmers. Cassava production is highly constrained by several pests and diseases, mostly cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). These diseases cause significant yield losses, affecting food security and the livelihoods of smallholder farmers. Developing resistant varieties is a good way of increasing cassava productivity. Although some levels of resistance have been developed for some of these diseases, there is observed breakdown in resistance for some diseases, such as CMD. A frequent re-evaluation of existing disease resistance traits is required to make sure they are still able to withstand the pressure associated with pest and pathogen evolution. Modern breeding approaches such as genomic-assisted selection in addition to biotechnology techniques like classical genetic engineering or genome editing can accelerate the development of pest- and disease-resistant cassava varieties. This article summarizes current developments and discusses the potential of using molecular genetics and genomics to produce cassava varieties resistant to diseases and pests.

Constant ratio between the genomic components of bipartite begomoviruses during infection and transmission

The genomic components of multipartite viruses are encapsidated in separate virus particles, and the frequencies of genomic components represent one of the key genetic features. Many begomoviruses of economic significance are bipartite, and the details of the association between their genomic components remain largely unexplored. We first analyzed the temporal dynamics of the quantities of DNA-A and DNA-B and the B/A ratio of the squash leaf curl China virus (SLCCNV) in plants and found that while the quantities of DNA-A and DNA-B varied significantly during infection, the B/A ratio remained constant. We then found that changes in the B/A ratio in agrobacteria inoculum may significantly alter the B/A ratio in plants at 6 days post inoculation, but the differences disappeared shortly thereafter. We next showed that while the quantities of DNA-A and DNA-B among plants infected by agrobacteria, sap transmission and whitefly-mediated transmission differed significantly, the B/A ratios were similar. Further analysis of gene expression revealed that the ratio of the expression of genes encoded by DNA-A and DNA-B varied significantly during infection. Finally, we monitored the temporal dynamics of the quantities of DNA-A and DNA-B and the B/A ratio of another bipartite begomovirus, and a constant B/A ratio was similarly observed. Our findings highlight the maintenance of a constant ratio between the two genomic components of bipartite begomoviruses during infection and transmission, and provide new insights into the biology of begomoviruses.

Comparative analysis of salicylic acid levels and gene expression in resistant, tolerant, and susceptible cassava varieties following whitefly-mediated SLCMV infection

Sri Lankan cassava mosaic virus (SLCMV), the primary pathogen responsible for cassava mosaic disease in cassava plantations, is transmitted via infected cutting stems and the whitefly vector, Bemisia tabaci. To obtain better insights into the defense mechanism of cassava against SLCMV, whiteflies were used to induce SLCMV infection for activating the salicylic acid (SA) signaling pathway, which triggers the innate immune system. The study aimed to investigate the specific interactions between viruliferous whiteflies and SA accumulation in resistant (C33), tolerant (Kasetsart 50; KU50), and susceptible (Rayong 11) cassava cultivars by infecting with SLCMV. Leaf samples were collected at various time points, from 1 to 7 days after inoculation (dai). The SA levels were quantified by gas chromatography-mass spectrometry and validated by quantitative reverse transcription polymerase chain reaction. The SA levels increased in KU50 and C33 plants at 2 and 3 dai, respectively, but remained undetected in Rayong11 plants. The expression of PR-9e, PR-7f5, SPS1, SYP121, Hsf8, and HSP90 increased in infected C33 plants at 4 dai, whereas that of KU50 plants decreased immediately at 2 dai, and that of Rayong11 plants increased at 1 dai but gradually decreased thereafter. These findings strongly indicate that SA plays a crucial role in regulating antiviral defense mechanisms, especially in SLCMV-resistant plants. Altogether, the findings provide valuable insights into the mechanisms underlying the activation of SA-mediated anti-SLCMV defense pathways, and the resistance, tolerance, and susceptibility of cassava, which can aid future breeding programs aimed at enhancing SLCMV resistance.

What Can Be Learned by a Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021?

A synoptic review of plant disease epidemics and outbreaks was made using two complementary approaches. The first approach involved reviewing scientific literature published in 2021, in which quantitative data related to new plant disease epidemics or outbreaks were obtained via surveys or similar methodologies. The second approach involved retrieving new records added in 2021 to the CABI Distribution Database, which contains over a million global geographic records of organisms from over 50,000 species. The literature review retrieved 186 articles, describing studies in 62 categories (pathogen species/species complexes) across more than 40 host species on six continents. Pathogen species with more than five articles were Bursaphelenchus xylophilus, 'Candidatus Liberibacter asiaticus', cassava mosaic viruses, citrus tristeza virus, Erwinia amylovora, Fusarium spp. complexes, F. oxysporum f. sp. cubense, Magnaporthe oryzae, maize lethal necrosis co-infecting viruses, Meloidogyne spp. complexes, Pseudomonas syringae pvs., Puccinia striiformis f. sp. tritici, Xylella fastidiosa, and Zymoseptoria tritici. Automated searches of the CABI Distribution Database identified 617 distribution records new in 2021 of 283 plant pathogens. A further manual review of these records confirmed 15 pathogens reported in new locations: apple hammerhead viroid, apple rubbery wood viruses, Aphelenchoides besseyi, Biscogniauxia mediterranea, 'Ca. Liberibacter asiaticus', citrus tristeza virus, Colletotrichum siamense, cucurbit chlorotic yellows virus, Erwinia rhapontici, Erysiphe corylacearum, F. oxysporum f. sp. cubense Tropical race 4, Globodera rostochiensis, Nothophoma quercina, potato spindle tuber viroid, and tomato brown rugose fruit virus. Of these, four pathogens had at least 25% of all records reported in 2021. We assessed two of these pathogens-tomato brown rugose fruit virus and cucurbit chlorotic yellows virus-to be actively emerging in/spreading to new locations. Although three important pathogens-'Ca. Liberibacter asiaticus', citrus tristeza virus, and F. oxysporum f. sp. cubense-were represented in the results of both our literature review and our interrogation of the CABI Distribution Database, in general, our dual approaches revealed distinct sets of plant disease outbreaks and new records, with little overlap. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Metabolic profiles of Sri Lankan cassava mosaic virus-infected and healthy cassava (Manihot esculenta Crantz) cultivars with tolerance and susceptibility phenotypes

BACKGROUND

Cassava mosaic disease (CMD) of cassava (Manihot esculenta Crantz) has expanded across many continents. Sri Lankan cassava mosaic virus (SLCMV; family Geminiviridae), which is the predominant cause of CMD in Thailand, has caused agricultural and economic damage in many Southeast Asia countries such as Vietnam, Loas, and Cambodia. The recent SLCMV epidemic in Thailand was commonly found in cassava plantations. Current understanding of plant-virus interactions for SLCMV and cassava is limited. Accordingly, this study explored the metabolic profiles of SLCMV-infected and healthy groups of tolerant (TME3 and KU50) and susceptible (R11) cultivars of cassava. Findings from the study may help to improve cassava breeding, particularly when combined with future transcriptomic and proteomic research.

RESULTS

SLCMV-infected and healthy leaves were subjected to metabolite extraction followed by ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS/MS). The resulting data were analyzed using Compound Discoverer software, the mzCloud, mzVault, and ChemSpider databases, and published literature. Of the 85 differential compounds (SLCMV-infected vs healthy groups), 54 were differential compounds in all three cultivars. These compounds were analyzed using principal component analysis (PCA), hierarchical clustering dendrogram analysis, heatmap analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Chlorogenic acid, DL-carnitine, neochlorogenic acid, (E)-aconitic acid, and ascorbyl glucoside were differentially expressed only in TME3 and KU50, with chlorogenic acid, (E)-aconitic acid, and neochlorogenic acid being downregulated in both SLCMV-infected TME3 and KU50, DL-carnitine being upregulated in both SLCMV-infected TME3 and KU50, and ascorbyl glucoside being downregulated in SLCMV-infected TME3 but upregulated in SLCMV-infected KU50. Furthermore, 7-hydroxycoumarine was differentially expressed only in TME3 and R11, while quercitrin, guanine, N-acetylornithine, uridine, vorinostat, sucrose, and lotaustralin were differentially expressed only in KU50 and R11.

CONCLUSIONS

Metabolic profiling of three cassava landrace cultivars (TME3, KU50, and R11) was performed after SLCMV infection and the profiles were compared with those of healthy samples. Certain differential compounds (SLCMV-infected vs healthy groups) in different cultivars of cassava may be involved in plant-virus interactions and could underlie the tolerance and susceptible responses in this important crop.

Analysis of proteomic changes in cassava cv. Kasetsart 50 caused by Sri Lankan cassava mosaic virus infection

BACKGROUND

Sri Lankan cassava mosaic virus (SLCMV) is a plant virus causing significant economic losses throughout Southeast Asia. While proteomics has the potential to identify molecular markers that could assist the breeding of virus resistant cultivars, the effects of SLCMV infection in cassava have not been previously explored in detail.

RESULTS

Liquid Chromatography-Tandem Mass Spectrometry (LC/MS-MS) was used to identify differentially expressed proteins in SLCMV infected leaves, and qPCR was used to confirm changes at mRNA levels. LC/MS-MS identified 1,813 proteins, including 479 and 408 proteins that were upregulated in SLCMV-infected and healthy cassava plants respectively, while 109 proteins were detected in both samples. Most of the identified proteins were involved in biosynthetic processes (29.8%), cellular processes (20.9%), and metabolism (18.4%). Transport proteins, stress response molecules, and proteins involved in signal transduction, plant defense responses, photosynthesis, and cellular respiration, although present, only represented a relatively small subset of the detected differences. RT-qPCR confirmed the upregulation of WRKY 77 (A0A140H8T1), WRKY 83 (A0A140H8T7), NAC 6 (A0A0M4G3M4), NAC 35 (A0A0M5JAB4), NAC 22 (A0A0M5J8Q6), NAC 54 (A0A0M4FSG8), NAC 70 (A0A0M4FEU9), MYB (A0A2C9VER9 and A0A2C9VME6), bHLH (A0A2C9UNL9 and A0A2C9WBZ1) transcription factors. Additional upregulated transcripts included receptors, such as receptor-like serine/threonine-protein kinase (RSTK) (A0A2C9UPE4), Toll/interleukin-1 receptor (TIR) (A0A2C9V5Q3), leucine rich repeat N-terminal domain (LRRNT_2) (A0A2C9VHG8), and cupin (A0A199UBY6). These molecules participate in innate immunity, plant defense mechanisms, and responses to biotic stress and to phytohormones.

CONCLUSIONS

We detected 1,813 differentially expressed proteins infected cassava plants, of which 479 were selectively upregulated. These could be classified into three main biological functional groups, with roles in gene regulation, plant defense mechanisms, and stress responses. These results will help identify key proteins affected by SLCMV infection in cassava plants.

Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics

Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.