Agronomically important thrips: development of species-specific primers in multiplex PCR and microarray assay using internal transcribed spacer 1 (ITS1) sequences for identification

Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms?

Simple Summary

Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis.

Abstract

Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.

DNA barcode, multiplex PCR and qPCR assay for diagnosis of pathogens infecting pulse crops to facilitate safe exchange and healthy conservation of germplasm

The DNA barcodes were developed from ITS region for the identification of fungal plant pathogens namely, Alternaria alternata and A. tenuissima both causing leaf spots, Ascochyta rabiei causing Ascochyta blight, Fusarium oxysporum f. sp. ciceris causing wilt, Macrophomina phaseolina causing dry root rot, Rhizoctonia solani causing web blight and wet root rot, Sclerotium (Athelia) rolfsii causing collar rot, Sclerotinia sclerotiorum causing stem rot and Cercospora canescens and Pseudocercospora cruenta both causing leaf spots in pulse crops. Barcode compliance for A. alternata (DBTPQ001-18), A. tenuissima (DBTPQ002-18), A. rabiei (DBTPQ003-18), F. oxysporum f. sp. ciceris (DBTPQ004-18), M. phaseolina (DBTPQ005-18), R. solani (DBTPQ006-18), S. rolfsii (DBTPQ007-18), S. sclerotiorum (DBTPQ008-18), C. canescens (DBTPQ009-18) and P. cruenta (DBTPQ029-20) have been generated based on the Barcode of Life Data System (BOLD) system. In addition to ITS, other genomic regions were also explored and on the basis of sequence variation they were ranked as TEF-α > SSU > LSU > β-tubulin. These genes could be considered for secondary barcode and phylogenetic relatedness. ITS-based markers for the detection of A. alternata (BAA2aF and BAA2aR) and R. solani (BRS17cF and BRS17cR) were developed which provided 400 bp and 220 bp amplicons, respectively. While, for F. oxysporum f. sp. ciceris, COX1-based marker (FOCox1F and FOCox3R) was developed which amplified 150 bp. The markers proved highly specific and sensitive with detection limit of 0.0001 ng of template DNA using qPCR and simultaneously detected these three pathogens. The DNA barcodes and diagnostics developed are suitable for quick and reliable detection of these pathogens during quarantine processing and field diagnostics.

Species Composition of Thrips (Thysanoptera: Thripidae) in Strawberry High Tunnels in Denmark

Simple Summary

One of the main insect pests in protected strawberry production are thrips, but little is known about which species of thrips are present in the production system. In this study, we identified the thrips species of adults and larvae present in two strawberry cultivars at a commercial strawberry farm in Denmark. The most abundant species found were Frankliniella intonsa, followed by Thrips tabaci. The abundance of thrips peaked in July (temperature range 18–23 °C, mean humidity 65%, mean precipitation 5 mm). More thrips were found in the earlier flowering cultivar. In order to optimize control of thrips, a fundamental first step is knowing which species are present on the target crop.

Abstract

Thrips are a major pest in protected strawberry production. Knowledge of thrips species composition could be instrumental for improved thrips management, but very little is known about which species are present in strawberries grown in high-tunnels in Denmark. Thrips (adults and larvae) were sampled in two strawberry tunnels of the cultivars Murano and Furore from May to August 2018, in the middle and in the edges of the tunnels. The most abundant thrips species found in the tunnels were Frankliniella intonsa and Thrips tabaci adults. Frankliniella intonsa were also the most frequently found species of the immatures sampled, followed by T. tabaci larvae, and other species. The number of thrips differed between the two cultivars, sampling times and location in the tunnel. Frankliniella intonsa was more abundant in the middle of the tunnels, while T. tabaci was more abundant in the edge of the tunnels adjacent to the field margins. The number of thrips peaked by the end of July. Both chemical and biological control should consider species composition and occurrence; hence, a fundamental first step for thrips management is to identify the species present on the target crop.

A rapid field-based assay using recombinase polymerase amplification for identification of Thrips palmi, a vector of tospoviruses

Thrips palmi (Thysanoptera: Thripidae) is an important pest of vegetables, ornamentals, and legumes worldwide. Besides damage caused by feeding, it transmits several tospoviruses. Identification of T. palmi at an early stage is crucial in implementing appropriate pest management strategies. Morpho-taxonomic identification of T. palmi based on the adult stage is time-consuming and needs taxonomic expertise. Here, we report a rapid, on-site, field-based assay for identification of T. palmi based on recombinase polymerase amplification (RPA), its first application in insects. RPA primers designed based on 3' polymorphisms of the Internal Transcribed Spacer 2 region efficiently discriminated T. palmi without any cross-reactivity to other predominant thrips species. RPA was performed with crude DNA, extracted from single T. palmi simply by crushing in sterile distilled water and could be completed within 20 min by holding the reaction tubes in the hand. The assay was further simplified by using fluorescent as well as colorimetric dyes thus eliminating the gel-electrophoresis steps. The presence of T. palmi was visualized by a change in color from dark blue to sky blue. The assay was validated with known thrips specimens and found to be effective in diagnosing the presence of T. palmi in natural vegetation. This on-site, rapid assay for diagnosis of T. palmi can be used by non-expert personnel in the field of quarantine and pest management.

Invasive and Quarantine Risks of Cacopsylla chinensis (Hemiptera: Psyllidae) in East Asia: Hybridization or Gene Flow Between Differentiated Lineages

Pear psyllids are major pests and the causal agents of pear decline disease in orchards. In the past two decades, their outbreaks have raised issues pertaining to invasions and taxonomic identification of the dimorphic Cacopsylla chinensis (Yang and Li) in East Asia. The present study elucidated, as an aid to quarantine management, the invasive origins, differentiation history, and putative gene flow and hybridization between C. chinensis and its sibling species Cacopsylla jukyungi (Kwon). Analyses revealed that the ancestors of C. jukyungi might have diverged from C. chinensis approximately 3.5 million yr ago (Mya) and that differentiation between C. chinensis lineages I and II probably occurred 1.5 Mya. The known overlapping distribution of C. chinensis and C. jukyungi in northeastern China and the two C. chinensis lineages in the Bohai Rim region and Taiwan could be attributed to recent population expansion after the Last Glacial Maximum and/or anthropogenic activities. Analyses of the nuclear gene demonstrated that frequent gene flow between the two C. chinensis lineages and the paraphyletic relationship between C. chinensis and C. jukyungi might be caused by incomplete lineage sorting or hybridization events. On the basis of the current distribution, it is evident that C. jukyungi is not present in middle-southern China, whereas C. chinensis is not distributed in Japan and Korea. Preventing new invasions of Cacopsylla psyllids among geographic regions through the transportation of pear scions is thus pivotal in East Asia, particularly for the possible genetic exchanges among differentiated lineages after secondary invasion events.

Rapid identification of the invasive fall armyworm Spodoptera frugiperda (Lepidoptera, Noctuidae) using species-specific primers in multiplex PCR

The fall armyworm (FAW), Spodoptera frugiperda (Smith), is a major pest native to the Americas. A recent invasion of FAWs from Africa eastward to South Asia, the Indochina Peninsula, and mainland China has received much attention due to the considerable economic losses in agriculture. FAWs can rapidly colonise a new area, likely due to the wide range of host plants, good flying capability, and high egg production. Therefore, a convenient, quick, and accurate tool for FAW identification is urgently required to establish a FAW invasion management strategy. In this study, FAW-specific primers were designed to recognise FAWs on the basis of internal transcribed spacer 1 (ITS1). The results revealed the accurate FAW recognition of the three congeneric species and eight common corn lepidopteran pests, especially at their larval stage. Furthermore, species-specific primers have confirmed their efficacy by using 69 FAW specimens from Taiwan, Thailand, and the United States, with a 96% success rate, excluding 3 decayed specimens. By using the simple, reliable, and convenient FAW-specific primers, a pest management programme can be developed not only to reduce sequencing costs and experimental time from 2 days to 4 h, but eradicate the FAW as soon as it enters a new area.

DNA Barcoding: A Reliable Method for the Identification of Thrips Species (Thysanoptera, Thripidae) Collected on Sticky Traps in Onion Fields

Simple Summary

Thrips species (Insecta, Thysanoptera) identification using traditional approach is not an easy. In the present study, DNA barcoding was used to support the thrips species characterization of a wide collection sampled in onion fields. Our findings confirmed the selected method as a simple and accurate approach identifying major thrips species, characterizing successfully nearly 86% of the samples collected in nine main species. The results here reported underlined the role of genetic markers as a valuable and useful method for species identification, especially when the morphological approach is unsure or even impossible.

Abstract

Several thrips species (Insecta, Thysanoptera) are globally known as important crop pests and vectors of viral diseases, but their identification is difficult because of their small body size and inconspicuous morphological differences. Sequencing variation in the mitochondrial cytochrome c oxidase I (COI) region has been proven to be useful for the identification of species of many groups of insect pests. Here, DNA barcoding has been used to identify thrips species collected with the use of sticky traps placed in an open onion field. A total of 238 thrips specimens were analyzed, 151 of which could be identified to species and 27 to genera belonging to the family Thripidae. Fifty-one specimens could not be assigned to any genus, with the closest BLAST match in the GenBank queries being below 98%, whilst six specimens were not recognized as Thysanoptera. The results indicate that, although there are a few pest thrips species not yet barcoded, most of the species that may cause damage to crops in Europe are represented in GenBank and other databases, enabling correct identification. Additionally, DNA barcoding can be considered a valuable alternative to the classic morphology method for identification of major thrips species.

A multiplex PCR assay for rapid identification of major tospovirus vectors reported in India

BACKGROUND

To date, four thrips vectors have been reported to transmit five different tospoviruses in India. Their identification at an early stage is crucial in formulating appropriate pest management strategies. Since morphometric key-based thrips identification based on the adult stage is time-consuming, there is a need to develop diagnostic tools which are rapid, accurate, and independent of developmental stages. Here, we report a multiplex PCR assay to identify four major thrips vectors viz. Thrips palmi, T. tabaci, Scirtothrips dorsalis, and Frankliniella schultzei present in India.

RESULTS

Cytochrome oxidase subunit III and internal transcribed spacer region 2 were utilized to design species-specific primers. Of 38 pairs of primers tested, primer pairs AG35F-AG36R, AG47F-AG48R, AG87F-AG88R, and AG79F-AG80R amplified 568 bp, 713 bp, 388 bp, and 200 bp products from the DNA templates of T. palmi, S. dorsalis, T. tabaci, and F. schultzei, respectively at same PCR conditions. The specificity of the primer pairs was validated with a large number of known specimens and no cross-reactivity was observed with other thrips species. The multiplex PCR assay with a cocktail of all the four primer pairs detected four thrips vectors efficiently and could discriminate all of them concurrently in a single reaction.

CONCLUSION

The multiplex PCR reported in this study could identify the major thrips vectors reported in India. The assay will be useful in ascertaining distribution profile of major thrips vectors, disease epidemiology, screening large samples, and quarantine.

Pest categorisation of Thrips palmi

The EFSA Panel on Plant Health (PLH) performed a pest categorisation of Thrips palmi (Thysanoptera: Thripidae), for the EU. T. palmi is listed in Annex IAI of 2000/29 EC. Using molecular methods, cryptic speciation has been shown although no new species from the group have been formally described. Here, we consider T. palmi sensu lato as a defined species native to southern Asia, which has spread to tropical and subtropical countries in Asia, the Pacific, North, Central and South America, Africa and Australia. T. palmi has been reported from many different hosts in 20 botanical families; Cucurbitaceae, Solanaceae and Orchidaceae are of primary importance. T. palmi has been intercepted many times on plants from these families. Wild and cultivated hosts are widespread in the EU. However, as a subtropical and tropical species, only a small area of the EU provides climatic conditions where establishment may be possible outdoors. Several host plants are cultivated in glasshouses where conditions may be more favourable for establishment in year-round crops. There have been past outbreaks of T. palmi in EU glasshouses and outdoors in Portugal. T. palmi causes feeding and oviposition damage and populations in Asia are competent vectors of tospoviruses. Impacts could occur on many hosts, especially Cucurbitaceae, Solanaceae and ornamental plants particularly in glasshouses. Phytosanitary measures aim to prevent the entry of T. palmi specifically on cut flowers of Orchidaceae and fruits of Momordica and Solanum melongena. The species meets all the criteria assessed by the PLH Panel to satisfy the definition of a Union quarantine pest, while it does not satisfy all the criteria for it to be regarded as a Union regulated non-quarantine pest (RNQP).

Molecular Identification of Thrips Species Infesting Cotton in the Southeastern United States

Traditional identification of thrips species based on morphology is difficult, laborious, and especially challenging for immature thrips. To support monitoring and management efforts of thrips as consistent and widespread pests of cotton (Gossypium hirsutum L.), a probe-based quantitative PCR (qPCR) assay with crude DNA extraction was developed to allow efficient and specific identification of the primary species of thrips infesting cotton. The assay was applied to identify over 5,000 specimens of thrips (including 3,366 immatures) collected on cotton seedlings from Alabama, Georgia, North Carolina, South Carolina, and Virginia in 2016. One half of all adult samples were examined by morphological identification, which provided a statistically equivalent species composition as the qPCR method. Frankliniella fusca (Hinds) (Thysanoptera: Thripidae) was the dominant species across all the locations (76.8-94.3% of adults and 81.6-98.0% of immatures), followed by Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) in Georgia, North Carolina, and Virginia (4.6-19% of adults and 1.7-17.3% of immatures) or Frankliniella tritici (Fitch) (Thysanoptera: Thripidae) in South Carolina (10.8% of adults and 7.8% of immatures). Thrips tabaci (Lindeman) (Thysanoptera: Thripidae) and Neohydatothrips variabilis (Beach) (Thysanoptera: Thripidae) were occasionally found among adults but were rarely present among immature thrips. These five species of thrips represented 98.2-100% of samples collected across the Southeast. The qPCR assay was demonstrated to be a valuable tool for large-scale monitoring of species composition of thrips at different life stages in cotton. The tool will contribute to a better understanding of thrips population structure in cotton and could assist with development and application of improved management strategies.

Identification of Disease-Transmitting Mosquitoes: Development of Species-Specific Probes for DNA Chip Assay Using Mitochondrial COI and ND2 Genes and Ribosomal Internal Transcribed Spacer 2

Mosquitoes, which transmit infectious diseases, such as malaria and dengue fever, are harmful to human health. Thus, accurate and rapid identification of vectors is a critical step for the control of mosquito-borne diseases. However, phenotypic variations in adults, lack of recognizable features of the immature, and fragility of mosquitoes make identification difficult. Molecular approaches have been widely applied to identify mosquitoes, yet these methods have been focused only on the identification of a few species. This study used sequences of two mitochondrial genes, COI and ND2, and a ribosomal gene, ITS2, to design species-specific probes. Biochips thus developed were able to provide simultaneous identification of nine important medical and veterinary species, including the immature, from genera of Aedes, Anopheles, Armigeres, and Culex. This chip was also applied to samples collected from the field. Despite its inability to resolve the close affinity species of Culex quinquefasciatus and Culex pipiens molestus, pertinent biochips are expected to be applied to a mass screening method.

Prediction of potential barcoding sites on ITS1 by wavelet transform

For sustainable development, biodiversity conservation and life-quality improvement must be simultaneously considered. Molecular techniques have greatly impacted biotechnology. These methods have, in particular, improved the capability to investigate the fine differences among organisms and, as a consequence, to better investigate the effects on environmental factors on them. We propose an approach to support the optimal selection of molecular probes for barcoding application in many biotechnological fields. The aim of our work is specificity maximization. To this purpose, we have integrated a filter system based on wavelet transforms with biological knowledge about the sequence proneness to mutation and post-translational modification. Specifically, we have tested the proposed method on ITS1 sequences that are a region of the rRNA locus. Our analysis has shown the presence of other local relative stable conformations in addition to known cleavage site. Their characteristics differ within the group of mammals selected for our analysis. These variations could be used to design new species-specific barcoding probes or other quick molecular screening tools.