COI barcode based species-specific primers for identification of five species of stored-product pests from genus Cryptolestes (Coleoptera: Laemophloeidae)

Species-specific markers for Nilaparvata lugens and Sogatella furcifera (Hemiptera: Delphacidae) based on mitochondrial cytochrome oxidase I

Brown planthopper (BPH), Nilaparvata lugens (Stål) and white-backed planthopper (WBPH), Sogatella furcifera (Horváth) are the most destructive sucking insect pests of rice in all rice growing parts of the world. For their accurate identification at early stages, we have developed two species-specific markers (SNL4F and SNL4R for BPH; SNF2F and SNF2R for WBPH) based on mitochondrial cytochrome oxidase I (COI) for their easy detection using Polymerase Chain Reaction (PCR). The markers were developed based on nucleotide differences in COI gene and were subjected to various tests based on PCR-based gel images. The designed primers were cross-checked with five other species, which confirmed their specificity. The primers were also found to be efficient in identification of their respective species (BPH and WBPH) in all the individuals sampled from different regions of India. The lowest detection sensitivity of both the primers was up to 1 ng/µl DNA after testing them through a series of varied DNA concentrations. The species-specific primers developed in this study will help in easy and rapid identification of BPH and WBPH in all the stages of their development and in turn facilitate their timely management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03693-x.

Biology, Ecology, and Behavior of Rusty Grain Beetle (Cryptolestes ferrugineus (Stephens))

Cryptolestes ferrugineus, the rusty grain beetle, is a cosmopolitan pest that has adapted to cool and warm climates due to its unique biology, ecology, and behavior. The rusty grain beetle is a pest of high economic importance; hence, understanding their biology, ecology, and behavior could be useful in designing effective management strategies. An extensive literature survey was conducted using the databases Web of Science and Scopus. Information on country-wise publications from 1949 to 2023 on C. ferrugineus was provided, and a table illustrating the distribution of C. ferrugineus was also presented to demonstrate the global significance of C. ferrugineus. We overviewed their life stages, morphology, and factors influencing their biology, ecology, and behavior, such as refuge-seeking behavior, flight activity, mating behavior, interspecific interaction with other species, movement, and distribution. Mathematical models focusing on C. ferrugineus population dynamics and movement were also presented. In order to advance our knowledge on C. ferrugineus, the following possible avenues for future research were outlined: application of molecular markers and population genetic approaches to understand their evolutionary history; mechanisms responsible for adaptation and resistance to insecticide; interspecific interaction in storage facilities and wider landscapes; and identification of microbial roles in the ecology, behavior, and control of C. ferrugineus.

Current progress on innovative pest detection techniques for stored cereal grains and thereof powders

For stored grains and their powders, pest infestation has always been a knotty problem and thus comprises a serious threat to global food security. Obviously, timely, rapid and accurate pest detection methods are of extreme importance to protect grains from pest mouth. In facing the defects of traditional methods, such as visual inspection, grain flotation and pest trap, diverse innovative approaches progressed fast alternatively, either targeting pest itself or diagnosing pest-induced changes. The former includes machine vision, metabolite analysis, pest-specific protein techniques, molecular techniques, bioacoustics analysis, conductive roller mill, low-field nuclear magnetic resonance spectroscopy and imaging, while the latter consists of thermal imaging, near-infrared spectroscopy and hyperspectral imaging, impact acoustics analysis, soft X-ray imaging and tomography. The principle, operation procedure, pros and cons and application scenarios were discussed for each method. The results herein hope to promote the technical revolution of pest inspection in stored cereal grains and their powders.

A new cost-effective and fast direct PCR protocol for insects based on PBS buffer

Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed a direct PCR workflow that incorporates a 2-min sample preparation in PBS-buffer step for fast and effective universal insect species identification. The developed protocol achieved 100% success rates for amplification in six orders: Mantodea, Phasmatodea, Neuroptera, Odonata, Blattodea and Orthoptera. High and moderate success rates were obtained for five other species: Lepidoptera (97.3%), Coleoptera (93.8%), Diptera (90.5%), Hemiptera (81.8%) and Hymenoptera (75.0%). High-quality sequencing data were also obtained from these amplifiable products, allowing confidence in species identification. The method was sensitive down to 1/4th of a 1-mm fragment of leg or body and its success rates with oven-dried, ethanol-preserved, food, bat guano and museum specimens were 100%, 98.6%, 90.0%, 84.0% and 30.0%, respectively. In addition, the pre-PCR solution (PBS with insect tissues) could be used for further DNA extraction if needed. The workflow will be beneficial in the fields of insect taxonomy and ecological studies due to its low cost, simplicity and applicability to highly degraded specimens.

Distribution of the Related Weevil Species Sitophilus oryzae and S. zeamais (Coleoptera: Curculionidae) in Farmer Stored Grains of China

Sitophilus oryzae (Coleoptera: Curculionidae) and Sitophilus zeamais (Coleoptera: Curculionidae) are major insect pests of farm-stored grains in China. Moreover, their respective distribution and prevalence are not yet assessed for grain storage facilities in China. The two species are often difficult to identify by morphology because they are immature or their presence is only evident from fragments. Species-specific primers were, therefore, designed based on the cytochrome c oxidase subunit I (COI) of 34 populations found throughout China and three foreign populations. Following the validation of this molecular-based approach for species identification, the distribution of the two species in China was determined from 68 different grain storage facilities. The results indicate that S. zeamais is prevalent throughout the country whereas S. oryzae is mainly present in the south and the center of China. It is believed that this distribution pattern is in function of ecological adaptation, mostly determined by temperature and the grain species. This is the first report of its kind, demonstrating the distribution of S. zeamais and S. oryzae in grain storage facilities throughout China and analyzed by species-specific primers of COI.

Random Mating Between Two Widely Divergent Mitochondrial Lineages of Cryptolestes ferrugineus (Coleoptera: Laemophloeidae): A Test of Species Limits in a Phosphine-Resistant Stored Product Pest

Effective pest management relies on accurate delimitation of species and, beyond this, on accurate species identification. Mitochondrial COI sequences are useful for providing initial indications in delimiting species but, despite acknowledged limitations in the method, many studies involving COI sequences and species problems remain unresolved. Here we illustrate how such impasses can be resolved with microsatellite and nuclear sequence data, to assess more directly the amount of gene flow between divergent lineages. We use a population genetics approach to test for random mating between two 8 ± 2% divergent COI lineages of the rusty grain beetle, Cryptolestes ferrugineus (Stephens). This species has become strongly resistant to phosphine, a fumigant used worldwide for disinfesting grain. The possibility of cryptic species would have significant consequences for resistance management, especially if resistance was confined to one mitochondrial lineage. We find no evidence of restricted gene flow or nonrandom mating across the two COI lineages of these beetles, rather we hypothesize that historic population structure associated with early Pleistocene climate changes likely contributed to divergent lineages within this species.

DNA barcoding, species-specific PCR and real-time PCR techniques for the identification of six Tribolium pests of stored products

Flour beetles of the genus Tribolium Macleay (Coleoptera: Tenebrionidae) are important stored product pests in China and worldwide. They are often found or are intercepted in grain depots, flour mills, and entry-exit ports, etc. Traditionally, Tribolium species are identified according to the morphological characteristics of the adult. However, it is almost impossible to rapidly identify adult fragments and non-adult stages based on external morphological characteristics. Molecular techniques for the rapid and accurate identification of Tribolium species are required, particularly for pest monitoring and the quarantine of stored products pests. Here, we establish DNA barcoding, species-specific PCR, and real-time PCR techniques for the identification of six stored-product pest Tribolium species including T. castaneum, T. confusum, T. destructor, T. madens, T. freemani and T. brevicornis. We detected the mitochondrial DNA cytochrome oxidase subunit I (COI) barcodes for Tribolium from 18 geographic populations and 101 individuals, built a Tribolium DNA barcode library, and designed species-specific primers and TaqMan probes for the above six Tribolium species. The three techniques were applied to identify Tribolium collected from stored samples and samples captured from quarantine ports. The results demonstrated that three techniques were all able to identify the six species of Tribolium both rapidly and accurately.

The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA

Psocids are important stored product pests found worldwide that can be spread through grain trade. Most stored-product psocids, including eggs, nymphs, and adults, are very small (~1 mm) and difficult to identify morphologically. Here, we collected 10 economically important stored-product Liposcelis spp. psocids (L. bostrychophila, L. entomophila, L. decolor, L. paeta, L. brunnea, L. corrodens, L. mendax, L. rufa, L. pearmani, and L. tricolor) from 35 geographical locations in 5 countries (China, Czech Republic, Denmark, Germany, and the United States). The ITS2 rDNA gene was extracted and sequenced. The interspecific genetic distance of the stored-product psocids was significantly higher than the intraspecific genetic distance according to the barcoding gap analysis. Ten pairs of species-specific primers based on the ITS2 rDNA were developed for psocid identification. The sensitivity estimation indicated that the species-specific primers could correctly amplify the target ITS2 gene and successfully identify psocids at 1.0 ng/mL. Additionally, these species-specific primers could quantify specificity and identify 10 stored-product psocids; this approach could also be used to accurately identify other stored-product psocids. This work provides a practical approach for the precise examination of 10 stored-product psocid species and also contributes to the development of an identification method using ITS2 rDNA.

The complete mitochondrial genome of Cryptolestes turcicus (Grouvelle) (Coleoptera:Laemophloeidae)

We presented the complete mitogenome of Cryptolestes turcicus (GenBank accession number KT070712) in this study. The total length of mitochondrial DNA is 15 517 bp and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The overall base composition of the genome is A (39.48%), T (37.38%), C (13.97%), and G (9.16%) with an A + T-rich hallmark. The start codon was ATN in all the mitochondrial protein-coding genes, such as ND2, COI, ATP6, ND5, ND4L and ND1 start with ATA, COII, ATP8, ND3, and ND6 genes employing ATT, while the rest using ATG as a start codon. The stop codon was mainly TAA or TAG in most of the mitochondrial protein-coding genes, wherever T(A) was found in COII, COIII, ND4, and ND4L genes. The A + T-rich region is located between 12S rRNA and tRNA(Ile) with a length of 857 bp.

Complete mitochondrial genome of Cryptolestes pusillus (Coleoptera: Laemophloeidae)

In this study, the complete mitochondrial genome of Cryptolestes pusillus (GenBank accession number KT070713) was sequenced by long PCR and primer walking methods. The total length of mitochondrial DNA is 15 502 bp and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a A + T-rich region. The base composition of the genome is A (39.04%), T (37.07%), C (23.4%), and G (14.6%). Except for COI and ATP8 with TCC and ATC as start codon, respectively, the remaining protein-coding genes initiated with the three orthodox start codons. Two complete stop codons (TAA and TAG) and two incomplete stop codons (COIII stop with T and ND5 stop with TA) were used in the protein-coding genes. The A + T-rich region is located between 12s rRNA and tRNA(Ile) with the length of 859 bp. The phylogenetic relationships of Coleoptera species were constructed based on the nucleotide sequences of 13 protein-coding genes of mitogenome using the neighbor-joining method. The molecular-based phylogenetic analysis supported the traditional morphological classification on relationships within Coleoptera species.

The complete mitochondrial genome of Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae)

We determined the complete mitochondrial genome (mitogenome) sequence of Cryptolestes ferrugineus (GenBank accession number KT182067) by the long PCR and primer walking method. The mitochondrial genome is a typical circular DNA molecule of 15 511 bp in length, and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a A + T-rich region (D-loop). The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. The base composition of the genome is A (39.17%), T (37.24%), C (14.22%), and G (9.37%) with an A + T-rich hallmark as that of other invertebrate mitochondrial genomes. All protein-coding genes start with ATN codon and terminate with the stop codon T (AA) or TAG. The A + T-rich region is located between 12S rRNA and tRNA(Ile). In this study, the phylogenetic relationships of Coleoptera species were constructed based on the nucleotides sequences of 13 PCGs of mitogenomes. The molecular-based phylogeny supported the traditional morphological classification on relationships within Coleoptera species.