Detection and Molecular Characterization of 'Candidatus Liberibacter asiaticus' and Citrus Tristeza Virus Associated with Citrus Decline in Bhutan

CRISPR/Cas12a-Responsive Smart DNA Hydrogel for Sensitive Electrochemiluminescence Detection of the Huanglongbing Outer Membrane Protein Gene

Citrus Huanglongbing (HLB) is known as the cancer of citrus, where Candidatus Liberibacter asiaticus (CLas) is the most prevalent strain causing HLB. In this study, we report a novel electrochemiluminescence (ECL) biosensor for the highly sensitive detection of the CLas outer membrane protein (Omp) gene by coupling rolling circle amplification (RCA) with a CRISPR/Cas12a-responsive smart DNA hydrogel. In the presence of the target, a large number of amplicons are generated through RCA. The amplicons activate the trans-cleavage activity of CRISPR/Cas12a through hybridizing with crRNA, triggering the response of smart DNA hydrogel to release the encapsulated AuAg nanoclusters (AuAg NCs) on the electrode and therefore leading to a decreased ECL signal. The ECL intensity change (I0 - I) is positively correlated with the concentration of the target in the range 50 fM to 5 nM, with a limit of detection of 40 fM. The performance of the sensor has also been evaluated with 10 samples of live citrus leaves (five HLB negative and five HLB positive), and the result is in excellent agreement with the gold standard qPCR result. The sensing strategy has expanded the ECL versatility for detecting varying levels of dsDNA or ssDNA in plants with high sensitivity.

Uncovering the presence of CVPD disease in citrus varieties of South Sulawesi, Indonesia: A molecular approach

BACKGROUND

The citrus vein phloem degeneration (CVPD) disease is one of important diseases that infects citrus plants and threatens global citrus production and quality due to its severe symptoms and rapid spread. In the 2000s, South Sulawesi Province as one of the citrus producers in Indonesia reported CVPD infection. To date, it is still uncertain as to whether the citrus production center has already been rid of the CVPD infection, keeping in mind the low prevalence of certified citrus saplings use and sub-optimal management of plantations by farmers.

RESULTS

Field observation results revealed varied chlorosis symptoms from young to productive cultivation, which certainly makes it appealing to find out the presence of the causative bacterium, as it has yet to be known whether all the leaves with positive chlorosis symptoms carry the bacterium Candidatus Liberibacter asiaticus. Citrus saplings that appear healthy may carry CVPD pathogens as the incubation period of CVPD pathogens in the host plant spans three to five months. Thus, it is necessary to find the right, rapid way to detect the presence of CVPD pathogens in the citrus plant. The most effective method to use is PCR as the bacterium Candidatus L. asiaticus is non-culturable in vitro, but it is detectable using 16S rDNA. Sampling of leaves with CVPD symptoms was conducted purposively from eight varieties in five citrus cultivation locations, i.e., Pangkep, Sidrap, Bantaeng, Luwu Utara, and Kepulauan Selayar Regencies. DNA isolation was carried out following the Genomic DNA Kit (Geneaid) procedure, followed by detection using the specific pathogenic primer pair OI1 (5' GCG CGT ATG CAA TAC GAG CGG C 3') and OI2c (5' GCC TCG CGA CTT CGC AAC CCA T 3').

CONCLUSION

The PCR visualization result shows seven positive samples with DNA fragments measuring 1160 bp. The seven samples were samples of the Key lime, tangerine, Mandarin (cv. batu 55), and Mandarin (cv. selayar), each being derived from Sidrap, Luwu Utara, and Bantaeng. The average disease incidence rate was 66.56 %. Based on the field observation results, the insect vector Diaphorina citri was nowhere to be found in the five citrus cultivation locations in South Sulawesi.

Plant jasmonic acid mediated contrasting effects of two citrus aphid species on Diaphorina citri Kuwayama

BACKGROUND

Herbivores may influence each other directly and through plant mediated inter-specific interactions. The Asian citrus psyllid (Diaphorina citri Kuwayama) and citrus aphids are key pests that can co-exist on citrus, but their plant-mediated interaction between them is unknown. Here we investigated plant-mediated effect of two citrus aphid species, the polyphagous Aphis spiraecola Patch and the oligophagous Aphis (Toxoptera) citricidus (Kirkaldy) on the feeding behavior and reproduction of Diaphorina citri, and explored the underlying mechanisms.

RESULTS

In comparison with those on aphid free plants, Diaphorina citri had decreased reproduction and reduced phloem feeding on Aphis spiraecola pre-infested plants, while the reproduction and feeding efficiency were increased on Aphis citricidus pre-infested plants. Jasmonic acid (JA) dependent defense was significantly activated by Diaphorina citri feeding on Aphis spiraecola pre-infested plants, but was suppressed by Diaphorina citri feeding on Aphis citricidus pre-infested plants compared with that on aphid free plant. By contrast, only one tested marker gene in salicylic acid (SA) signaling was activated by Diaphorina citri feeding on Aphis spiraecola pre-infested plants. Furthermore, exogenous application of methyl jasmonate, but not SA, conferred resistance against Diaphorina citri in our citrus trials.

CONCLUSION

Our results indicate that pre-infestation by two citrus aphid species differentially altered Diaphorina citri induced citrus JA dependent defense, which resulted in different effect on subsequent Diaphorina citri performance. © 2022 Society of Chemical Industry.

A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris

Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.

Huanglongbing Pandemic: Current Challenges and Emerging Management Strategies

Huanglongbing (HLB, aka citrus greening), one of the most devastating diseases of citrus, has wreaked havoc on the global citrus industry in recent decades. The culprit behind such a gloomy scenario is the phloem-limited bacteria "Candidatus Liberibacter asiaticus" (CLas), which are transmitted via psyllid. To date, there are no effective long-termcommercialized control measures for HLB, making it increasingly difficult to prevent the disease spread. To combat HLB effectively, introduction of multipronged management strategies towards controlling CLas population within the phloem system is deemed necessary. This article presents a comprehensive review of up-to-date scientific information about HLB, including currently available management practices and unprecedented challenges associated with the disease control. Additionally, a triangular disease management approach has been introduced targeting pathogen, host, and vector. Pathogen-targeting approaches include (i) inhibition of important proteins of CLas, (ii) use of the most efficient antimicrobial or immunity-inducing compounds to suppress the growth of CLas, and (iii) use of tools to suppress or kill the CLas. Approaches for targeting the host include (i) improvement of the host immune system, (ii) effective use of transgenic variety to build the host's resistance against CLas, and (iii) induction of systemic acquired resistance. Strategies for targeting the vector include (i) chemical and biological control and (ii) eradication of HLB-affected trees. Finally, a hypothetical model for integrated disease management has been discussed to mitigate the HLB pandemic.

A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World

Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status.

Highly Sensitive and Rapid Detection of Citrus Huanglongbing Pathogen ('Candidatus Liberibacter asiaticus') Using Cas12a-Based Methods

Citrus huanglongbing (HLB) or greening is one of the most devastating diseases of citrus worldwide. Sensitive detection of its causal agent, 'Candidatus Liberibacter asiaticus' (CLas), is critical for early diagnosis and successful management of HLB. However, current nucleic acid-based detection methods are often insufficient for the early detection of CLas from asymptomatic tissue and unsuitable for high-throughput and field-deployable diagnosis of HLB. Here we report the development of the Cas12a-based DNA endonuclease-targeted CRISPR trans reporter (DETECTR) assay for highly specific and sensitive detection of CLas nucleic acids from infected samples. The DETECTR assay, which targets the five-copy nrdB gene specific to CLas, couples isothermal amplification with Cas12a transcleavage of a fluorescent reporter oligonucleotide and enables detection of CLas nucleic acids at the attomolar level. The DETECTR assay was capable of specifically detecting the presence of CLas across different infected citrus, periwinkle, and psyllid samples and shown to be compatible with lateral flow assay technology for potential field-deployable diagnosis. The improvements in detection sensitivity and flexibility of the DETECTR technology position the assay as a potentially suitable tool for early detection of CLas in infected regions.

Development of a real-time RT-PCR method for the detection of Citrus tristeza virus (CTV) and its implication in studying virus distribution in planta

Tristeza is an economically important disease of the citrus caused by Citrus tristeza virus (CTV) of genus Closterovirus and family Closteroviridae. The disease has caused tremendous losses to citrus industry worldwide by killing millions of trees, reducing the productivity and total production. Enormous efforts have been made in many countries to prevent the viral spread and the losses caused by the disease. To understand the reason behind this scenario, studies on virus distribution and tropism in the citrus plants are needed. Different diagnostic methods are available for early CTV detection but none of them is employed for in planta virus distribution study. In this study, a TaqMan RT-PCR-based method to detect and quantify CTV in different tissues of infected Mosambi plants (Citrus sinensis) has been standardized. The assay was very sensitive with the pathogen detection limit of > 0.0595 fg of in vitro-transcribed CTV-RNA. The assay was implemented for virus distribution study and absolute CTV titer quantification in samples taken from Tristeza-infected trees. The highest virus load was observed in the midribs of the symptomatic leaf (4.1 × 10⁷-1.4 × 10⁸/100 mg) and the lowest in partial dead twigs (1 × 10³-1.7 × 10⁴/100 mg), and shoot tip (2.3 × 10³-4.5 × 10³/100 mg). Interestingly, during the peak summer months, the highest CTV load was observed in the feeder roots (3 × 10⁷-1.1 × 10⁸/100 mg) than in the midribs of symptomatic leaf. The viral titer was highest in symptomatic leaf midrib followed by asymptomatic leaf midrib, feeder roots, twig bark, symptomatic leaf lamella, and asymptomatic leaf lamella. Overall, high CTV titer was primarily observed in the phloem containing tissues and low CTV titer in the other tissues. The information would help in selecting tissues with higher virus titer in disease surveillance that have implication in Tristeza management in citrus.

Development of a SYBR Green-based RT-qPCR assay for the detection of Indian citrus ringspot virus

The Indian citrus ringspot virus (ICRSV) that causes ringspot disease, especially to 'Kinnow mandarin' hampers the sustainability of crop production. Presently, the disease is not amenable for control through host resistance or the introduction of chemicals, hence raising virus-free plants is one of the most effective approaches to manage the disease. Consequently, it is necessary to develop rapid, sensitive, specific, and early diagnostic methods for disease control. In the present study, newly designed primers targeting a 164 bp region of the ICRSV coat protein gene were used to develop and optimize a SYBR Green-based quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay, for the detection of ICRSV. The RT-qPCR assay was evaluated and confirmed using viral RNA extracted from ICRSV infected plants maintained in screen house as well as field samples. The standard curves displayed a dynamic linear range across eight log units of ICRSV-cRNA copy number ranging from 9.48.1 fmol (5.709 × 10⁹) to 0.000948 amol (5.709 × 10²), with detection limit of 5.709 × 10² copies per reaction using serial tenfold diluted in vitro transcribed viral cRNA. The developed RT-qPCR is very specific to ICRSV does not react to other citrus pathogens, and approximately 100-fold more sensitive than conventional RT-PCR. Thus, this assay will be useful in laboratories, KVKs, and nurseries for the citrus budwood certification program as well as in plant quarantine stations. To our knowledge, this is the first study of the successful detection of ICRSV by RT-qPCR.