Unexpected High Intragenomic Variation in Two of Three Major Pest Thrips Species Does Not Affect Ribosomal Internal Transcribed Spacer 2 (ITS2) Utility for Thrips Identification

Ultra-deep sequencing of 45S rDNA to discern intragenomic diversity in three Chrysodeixis species for molecular identification

Species identification is necessary to prevent introductions of exotic plant pests through global trade. Many of these pests are understudied and lack publicly available DNA sequence data on which rapid molecular identification methods can be based. One such lineage is the genus Chrysodeixis, which includes three species of potential concern for United States trade initiatives: C. includens, C. chalcites, and C. eriosoma. Here we describe a method to generate robust 45S rDNA profiles using long read sequencing in order to clarify evolutionary relationships and develop a real-time PCR identification technique. Such an identification tool will be useful in rapidly differentiating between Chrysodeixis species of quarantine concern where traditional morphological identification methods are insufficient. Molecular methods such as this greatly reduce the time spent identifying each specimen, allow for detection of eDNA, vastly increase throughput, and increase the probability of detection. The methods presented here will be generally adaptable to any understudied lepidopteran taxa that necessitates a molecular diagnostic assay and, with adjustment or testing of the primers, could be applied to any group for which development of rDNA profiles in a benchtop setting would prove useful.

Integrative Insight into Relationships between Florivorous Thrips Haplothrips leucanthemi and H. niger (Insecta, Thysanoptera)

Haplothrips niger is recognized as a parthenogenetic form of H. leucanthemi and is also considered to be a pest in clover-seed plantations. On the contrary, some researchers highlight the distinctiveness of H. niger and H. leucanthemi. Taking into account these two points of view, as well as the lack of molecular studies investigating the relationship between the mentioned thrips, we decided to perform analyses of both mitochondrial (COI) and nuclear markers (28S and ITS2) to determine the genetic diversity of H. leucanthemi and H. niger. Additionally, as a part of an integrative approach, we determined and analyzed their microbiota profiles, based on high-throughput 16S rRNA gene sequencing. The results of the molecular analyses revealed high intraspecific diversity of H. leucanthemi and did not support the distinctiveness of H. niger. The identified microbiota profiles were similar in both species and the performed analyses also did not support the distinctiveness of H. niger. Significant differences were, in turn, observed between H. leucanthemi and H. niger larvae. Moreover, two known endosymbiotic bacteria were found in the analyzed microbiota profiles (i.e., Wolbachia and Rickettsia). Nevertheless, these symbionts were not predominantly found in the bacterial communities that are associated with H. niger and thus, its impact on the parthenogenetic mode of its reproduction seems less likely.

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.