Morphological and DNA Barcoding Evidence for Invasive Pest Thrips, Thrips parvispinus (Thripidae: Thysanoptera), Newly Recorded From India

Genetic Diversity and DNA Barcoding of Thrips in Bangladesh

Thrips are economically important pests, and some species transmit plant viruses that are widely distributed and can damage vegetables and cash crops. Although few studies on thrips species have been conducted in Bangladesh, the variation and genetic diversity of thrips species remain unknown. In this study, we collected thrips samples from 16 geographical locations throughout the country and determined the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit 1 (mtCOI) gene in 207 thrips individuals. Phylogenetic analysis revealed ten genera (Thrips, Haplothrips, Megalothrips, Scirtothrips, Frankliniella, Dendrothripoides, Astrothrips, Microcephalothrips, Ayyaria, and Bathrips) and 19 species of thrips to inhabit Bangladesh. Among these, ten species had not been previously reported in Bangladesh. Intraspecific genetic variation was diverse for each species. Notably, Thrips palmi was the most genetically diverse species, containing 14 haplotypes. The Mantel test revealed no correlation between genetic and geographical distances. This study revealed that thrips species are expanding their host ranges and geographical distributions, which provides valuable insights into monitoring the diversity of and control strategies for these pests.

Invasive flower thrips, Thrips parvispinus (Karny) occurrence, host expansion and genetic diversification in a tropical poly-crop ecosystem

BACKGROUND

Invasive black flower thrips Thrips parvispinus (Karny) has recently emerged as a significant threat to Indian chilli production. Identifying T. parvispinus became difficult due to the complex presence of thrips species in Indian chilli and allied ecosystems. Pest management success depends on assessing invasive pests genetic populations and their distribution in newly habituated areas.

METHODS AND RESULTS

The current study investigated the genetic diversity and phylogeographic structure of T. parvispinus across major chilli-growing zones representing different agro-climatic conditions in Tamil Nadu. The species-specific chaetotaxy characteristics of T. parvispinus and molecular analysis of the mtCOI gene were used to confirm that the species T. parvispinus has expanded rapidly in three regions (North Western, Western and Cauvery delta), sparsely in one (Southern) and absent from two (hilly and high rainfall). Fifteen allied crops in chilli/capsicum growing tracts served as host plants for T. parvispinus. A shrub species, namely Littleleaf boxwood, Buxus microphylla Siebold & Zucc., is described as a host plant for the first time. On capsicum and chilli, T. parvispinus and Scirtothrips dorsalis coexisted. Thrips palmi, T. tabaci, Frankliniella schultzei, and Microcephalothrips abdominalis co-occurring alongside T. parvispinus on allied crops.

CONCLUSION

Molecular characterization and haplotype identification help define the genetic composition of T. parvispinus and serve as a foundation for efficient monitoring and creation of Integrated Pest Management (IPM) strategies. As a result, the genetic data presented in this work strongly argues that T. parvispinus as a population is resolving itself towards a fixed state through natural selection that spans its native range globally along with low genetic diversity [Hd: 0.771].

Comparative analysis of the two suborders of Thysanoptera and characterization of the complete mitochondrial genome of Thrips parvispinus

Thrips parvispinus is a serious sucking pest on a number of economically important crops in the oriental region. It has gained importance recently for its drastic range extension distribution as an invasive pest. Here, the complete mitochondrial genome (15,067 bp) of Thrips parvispinus was sequenced and characterized. It possesses 37 genes and the putative noncoding region is duplicated. Comparative analyses of nucleotide diversity, skewness, codon usage bias, and selection pressure in mitochondrial protein-coding genes of the available 31 thrips mitogenomes (24 Terebrantia + 7 Tubulifera) were performed. Phylogenetic analysis showed a sister relationship of T. parvispinus to the clade (T. florum + T. hawaiiensis). Phylogenetic analyses formed the monophyly of subfamilies Phlaeothripinae and Idolothripinae within the family Phlaeothripidae (Suborder Tubulifera). Low nucleotide diversity was indicative of reversal of strand asymmetry in the Tubulifera. Neutrality analysis showed that directional mutation plays a major role in shaping codon usage bias in both suborders. Principal component analysis indicated distinct codon usage patterns in each suborder. Our data suggested weaker selection constrains on Terebrantia than in the Tubulifera. More tubuliferan mitogenomes are required to resolve previous classification hypotheses and elucidate genome evolution in these two suborders.

Shashank P, Kereyagalahalli Mallaiah K, Bedar J. Diagnosis and potential invasion risk of Thrips parvispinus under current and future climate change scenarios

Background and Objective

Invasive thrips, Thrips parvispinus Karny recently reported in India, causing a widespread severe infestation in more than 0.4 million ha of chilli (Capsicum annum L.) growing areas. This species is native to Thailand and most prevalent in other South East Asian countries. Large scale cultivation of the major host plants (chilli and papaya), and favourable climatic conditions in India and other countries similar to native range of Thrips parvispinus expected to favour its further spread and establishment to new areas.

Materials and Methods

The present study was undertaken to confirm invasive thrips species identity through both morphological and molecular approaches and predict its potential invasion using the maximum entropy (MaxEnt) algorithm.

Results

The model predicted species range in respect of discrimination of suitable and unsuitable areas for its occurrence both in current and future climatic scenarios. The model provided a good fit for species distribution with a high value of area under the curve (0.957). The jackknife test indicated annual mean temperature and precipitation were found to be the most important bioclimatic variable in determining the distribution of T. parvispinus. High suitability areas were predicted in the countries wherever its occurrence was reported with high discrimination ability of suitable and unsuitable areas. Key distinguishing morphological characters of T. parvispinus were illustrated through high-resolution scanning electron microscopic images.

Conclusion

The identity of the thrips causing wide spread damage in chilli confirmed through morphological and molecular approaches. Key identifying characters were described through high resolution scanning electron microscopic images for accurate identification of the species. MaxEnt model identified high suitability regions for the potential establishment of T. parvispinus in India and other parts of the world. This study facilitates forecasting of further spread and also suggests imposing strict domestic quarantine measures to curtail its establishment in the new areas.

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 barcoding of selected Scirtothrips species (Thysanoptera) from India

The members of the genus Scirtothrips are highly polyphagous, including major pest and vector species. We applied both morphology and molecular approaches to delimit the selected Scirtothrips species from India. Out of 43 generated barcode sequences, six sequences of three species (S. hitam, S. mangiferae, and S. malayensis) are the novel contribution in global database. The Bayesian (BA) phylogeny clearly distinguishes all the studied species with reciprocal monophyletic criteria and represents multiple clades in S. dorsalis and S. oligochaetus. The high Kimura-2-Parameter (K2P) genetic divergences were observed between the multiple clades of S. dorsalis (4.5-8.8%) and S. oligochaetus (6.4%), which indicating possible existence of cryptic diversity. The current study also provided the morphological keys for six Scirtothrips species including S. hitam as a new record to India.

Molecular footprint of Frankliniella occidentalis from India: a vector of Tospoviruses

The western flower thrips, F. occidentalis is a vector of Tospoviruses and native to Western North America and Mexico. The present study is based on collected F. occidentalis specimens from Karnataka state in southern India and morphologically identified through available keys. The generated DNA barcode data show 99–100% similarity with the database sequences of F. occidentalis. The phylogenetic analysis (NJ, ML, and BA) shows three distinct clades of F. occidentalis in the present dataset with high bootstrap supports and posterior probabilities. The K2P genetic distances further depicted high similarity of the generated sequences from India and Netherlands. The Clade-1 (India + Netherlands) also shows a close relationship with Clade-2 (Kenya) rather than Clade-3 (Canada + USA). This study recorded the first genetic footprint of F. occidentalis in India and indicated the gene flow from the Netherlands to India. The similar molecular techniques may help to detect the invasion of many alien species in the near future and assists the quarantine regulations to protect the native ecosystem.

DNA Barcoding studies on Thrips in India: Cryptic species and Species complexes

Thrips are one of the major sucking pest and vector of plant viruses causing huge economic loss in agriculture. The accurate identification of thrips is crucial for effective pest management strategies. However, morphology based identification has limitations and warrants integration of molecular data. We attempted the largest DNA barcoding initiative on 370 sequences of 89 thrips morphospecies including 104 novel sequences from 39 morphospecies, including the type specimens of four species. The results of multiple species delimitation methods (BIN, ABGD, GMYC and bPTP) were consistent for 73 species (82%) with their morphological identifications. A total of 107 molecular operational taxonomic units (MOTUs) was recovered for 89 morphospecies by superimposing multiple methods and applying a three level nomenclature system. We detected more than one MOTU in 14 morphospecies indicating to have cryptic diversity including, two major vector species (Frankliniella schultzei and Thrips palmi). However, four morphospecies (Thrips moundi, Thrips carthami, Haplothrips andersi and Haplothrips gowdeyi) showed low genetic distances between them with overlapping in barcode gap that requires further analysis with multiple molecular markers and more specimens from wide geographical areas for better taxonomic judgment. We also presented the advantage of simultaneous use of multiple delimitation methods for detection and identification of cryptic species.

Barcoding the food chain: from Sanger to high-throughput sequencing

Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace “environmental DNA”, and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.