Evolutionary genomics of three agricultural pest moths reveals rapid evolution of host adaptation and immune-related genes.

BACKGROUND: Understanding the genotype of pest species provides an important baseline for designing integrated pest management (IPM) strategies. Recently developed long-read sequence technologies make it possible to compare genomic features of nonmodel pest species to disclose the evolutionary path underlying the pest species profiles. Here we sequenced and assembled genomes for 3 agricultural pest gelechiid moths: Phthorimaea absoluta (tomato leafminer), Keiferia lycopersicella (tomato pinworm), and Scrobipalpa atriplicella (goosefoot groundling moth). We also compared genomes of tomato leafminer and tomato pinworm with published genomes of Phthorimaea operculella and Pectinophora gossypiella to investigate the gene family evolution related to the pest species profiles. RESULTS: We found that the 3 solanaceous feeding species, P. absoluta, K. lycopersicella, and P. operculella, are clustered together. Gene family evolution analyses with the 4 species show clear gene family expansions on host plant-associated genes for the 3 solanaceous feeding species. These genes are involved in host compound sensing (e.g., gustatory receptors), detoxification (e.g., ABC transporter C family, cytochrome P450, glucose-methanol-choline oxidoreductase, insect cuticle proteins, and UDP-glucuronosyl), and digestion (e.g., serine proteases and peptidase family S1). A gene ontology enrichment analysis of rapid evolving genes also suggests enriched functions in host sensing and immunity. CONCLUSIONS: Our results of family evolution analyses indicate that host plant adaptation and pathogen defense could be important drivers in species diversification among gelechiid moths.

CRISPR-based diagnostics detects invasive insect pests.

Rapid identification of organisms is essential for many biological and medical disciplines, from understanding basic ecosystem processes, disease diagnosis, to the detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than real-time PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a sophisticated laboratory, reduces the risk of cross-contamination, and can be completed in less than 1 h. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

CRISPR-based diagnostics detects invasive insect pests.

Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

DNA barcoding of insects from India: Current status and future perspectives.

Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.

Molecular diversity of Sesamia inferens (Walker, 1856) (Lepidoptera: Noctuidae) from India.

Pink stem borer, Sesamia inferens (Walker, 1856) (Lepidoptera: Noctuidae) is reported to infest many graminaceous crops and cause significant losses. S. inferens cause damage by killing the central shoot and producing a characteristic symptom called "dead heart". Since graminaceous crops are an important source of food for humans and their livestock, impetus should be given on designing efficient management strategies against pink stem borer. The study of genetic variability of pest populations enables to interpret the ecological investigations correctly and also helps to comprehend the dissimilar response of pest to management tactics. The present study was undertaken to evaluate the diversity in S. inferens populations using mitochondrial cytochrome oxidase subunit I sequences from India, Pakistan, China and Indonesia. Analysis revealed a very low nucleotide diversity in Indian populations (π = 0.00981), as compared to a high nucleotide diversity in the sequences outside India (π = 0.4989). The phylogenetic analysis also did not show any clustering among populations within India and Pakistan. However, the nearest neighbour for the Indian and Pakistan population is a sequence from Indonesia followed by China indicating possible ancestral background. This is the maiden attempt to assess the molecular diversity of Indian populations in comparison to populations from other Asian countries. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02678-y.

First report of the poplar leaf miner, Phyllonorycter populifoliella (Treitschke) (Lepidoptera: Gracillariidae) from India.

Here we report about the discovery of the poplar leaf miner, Phyllonorycter populifoliella (Treitschke) in India. The mines of this micromoth were found in noticeable density on the leaves of poplar, Populus sp. (Salicaceae) in the northern mountainous region Ladakh in 2017-2018. We provide short morphological diagnosis, describe bionomics and analyze molecular data of Ph. populifoliella from India comparing sequences with those from other countries in Eurasia where the species is known as native. We also illustrate male and female genitalia, an adult of the moth, the leaf mines and the infestation plot in Ladakh, and discuss the occurrence of the species in the country.

Two new species records of Lecithoceridae (Gelechioidea: Lepidoptera) from India.

The Dalma Wildlife Sanctuary, located in the Dalma Hills about 10 km north of the city of Jamshedpur, Jharkhand, India, is topographically and climatically unique. It encompasses a forested area of over 195 km2 east of the Singhbhum and Saraikela-kharsawan districts of Jharkhand, extending from Chandil about 40 km eastward, running nearly parallel to the National Highway-33 at an altitude of about 280 m. The forests of the sanctuary are "dry peninsular sal" and "northern dry mixed deciduous forest".

A new genus Vittaliana belonging to the tribe Opsiini (Hemiptera: Cicadellidae) from India and its molecular phylogeny.

The new leafhopper genus Vittalianareticulata gen. nov., sp. nov., is described from India, and placed in the tribe Opsiini based on ocelli close to eyes, without carina on anterior margin of the face and bifurcate aedeagus with two gonopores. Phylogenetic analysis with maximum likelihood (ML) using IQtree v1.4.1 of combined data (Histone H3 and 28S rDNA) reveals that the new genus Vittaliana belongs to a clade consisting of Opsius versicolor (Distant, 1908), Opsiini gen. sp., Libengaia sp., Hishimonus phycitis (Distant, 1908) and Yinfomibus menglaensis Du, Liang & Dai (2019) with good branch support, and that the tribe Opsiini is paraphyletic. This resolves the placement of a new genus in the tribe Opsiini under Deltocephalinae.

Tribe reassessment of the subhimalayan leafhopper genus Pseudosubhimalus (Homoptera: Cicadellidae) based on molecular phylogeny.

The phylogeny of the Pseudosubhimalus were investigated using of two different data sets, including 91 taxa and 3853 aligned nucleotide positions from the histone H3, 28S rDNA (D2 & D9-10 region). The results suggest the placement of genus in the tribe Ciacadulini, as it was clustered with Cicadulini genera. Relationships between genera of the Cicadulini were strongly supported and leads placement to tribe Cicadulini from Athysanini. Along with this, genus Pseudosubhimalus Ghauri is revised, and P. trilobatus sp. nov. (Himachal Pradesh: Katrain) is added, described from Indian subcontinent and deposited to National Pusa Collection, IARI, New Delhi, with repository number RRS1.

A new genus of leafhopper subtribe Paraboloponina (Hemiptera: Cicadellidae) with molecular phylogeny of related genera.

A new leafhopper genus Chandra and species Chandra dehradunensis gen. nov., sp. nov. are described, illustrated from India and placed in the subtribe Paraboloponina (Cidadellidae: Deltocephalinae: Drabescini). This genus is closely associated with the genus Parabolopona Webb but differs in shape of the head, placement of antennae, male genitalia and molecular analysis using Histone H3 and COI genes confirmed the difference. The taxonomic and phylogenetic position of Chandra is discussed using morphological characters and preliminary molecular evidence of the new genus and related genus Parabolopona.