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Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops. Int J Mol Sci 2022; 23:ijms23179847. [PMID: 36077247 PMCID: PMC9456221 DOI: 10.3390/ijms23179847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 12/03/2022] Open
Abstract
Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.
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Aguirre C, Sánchez E, Olivares N, Hinrichsen P. Multiplex TaqMan Real-Time PCR Assay for Sensitive Detection of Two Weevil Species (Coleoptera: Curculionidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:90-99. [PMID: 33155656 DOI: 10.1093/jee/toaa251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Indexed: 06/11/2023]
Abstract
Rapid and cost-efficient identification of Naupactus species is becoming a key process for the exportation of citrus fruit from Chile and other countries, considering the quarantine regulations for some species of the cosmopolitan genus Naupactus. This study deals with the development of a fast and sensitive detection protocol for Naupactus cervinus (Coleoptera: Curculionidae) (Boheman) and Naupactus xanthographus (Coleoptera: Curculionidae) (Germar) based on multiplex TaqMan Real-time polymerase chain reaction. Both N. cervinus and N. xanthographus primer and probe sets achieved species-specific detection in a linear range from 1 pg/μl to 1 × 10-6 pg/μl, allowing detection of as few as 160 copies of template DNA. Non-target amplifications were not detected and a panel composed of 480 test samples had 100% coincidence with the respective morphological identification.
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Affiliation(s)
- Carlos Aguirre
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11,610, Santiago, Chile
| | - Evelyn Sánchez
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago, Chile
| | - Natalia Olivares
- Instituto de Investigaciones Agropecuarias, INIA-La Cruz, Chorrillos 86, La Cruz, Quillota, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11,610, Santiago, Chile
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Aguirre C, Olivares N, Hinrichsen P. An Efficient Duplex PCR Method for Sex Identification of the European Grapevine Moth Lobesia botrana (Lepidoptera: Tortricidae) at Any Developmental Stage. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:2505-2510. [PMID: 32676656 DOI: 10.1093/jee/toaa155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 06/11/2023]
Abstract
Many genetic studies in insects require sex identification of individuals in all developmental stages. The most common sex chromosome system in lepidopterans is WZ/ZZ; the W chromosome is present only in females. Based on two W chromosome-specific short sequences (CpW2 and CpW5) described in Cydia pomonella (L.) (Lepidoptera: Tortricidae), we identified homologous female-specific sequences in Lobesia botrana Den. & Schiff, a polyphagous and very harmful species present in Chile since 2008. From this starting point, we extended the sequence information using the inverse PCR method, identifying the first W-specific sequences described up to now for the moth. Finally, we developed a duplex PCR method for rapid and sensitive determination of sex in L. botrana from larva to adult. The method showed a detection limit of 1 pg of genomic DNA; a blind panel of samples exhibited exact correspondence with the morphological identification. These results will be very useful for studies requiring sex-specific analyses at any developmental stage, contributing also to the understanding of gene expression in the insect, as well as to the eventual development of control protocols against the moth, such as the development of genetic sexing strains for the implementation of the sterile insect technique.
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Affiliation(s)
- Carlos Aguirre
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
| | - Natalia Olivares
- Instituto de Investigaciones Agropecuarias, INIA-La Cruz, La Cruz, Quillota, Chile
| | - Patricio Hinrichsen
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago, Chile
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Yi Z, Sadiq FA, Wang H, Zhao J, Zhang H, Lu W, Chen W. Establishment and evaluation of a method for efficient screening of Clostridium butyricum. Folia Microbiol (Praha) 2020; 65:917-924. [PMID: 32621129 DOI: 10.1007/s12223-020-00803-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/03/2020] [Indexed: 11/25/2022]
Abstract
At present, the traditional methods for the screening of Clostridium butyricum are not sufficiently selective and efficient. Therefore, it is necessary to establish a targeted and efficient screening method for the detection of C. butyricum. Bioinformatics was used in this study to find C. butyricum specific genes, and species-specific primers were designed based on the conserved regions of the targeted genes, followed by optimization of the PCR conditions. Methodological evaluation was carried out, and the results were compared with the traditional screening method based on Trypticase Sulfite Neomycin (TSN) selective medium. A high-efficiency PCR screening method, targeting C. butyricum species-specific primers, was established. The method was confirmed to have high specificity and sensitivity towards C. butyricum cut-off CFU 103. Compared with the traditional method, the screening success rate of C. butyricum strains increased from 0.61 to 81.91%. The PCR screening method could quickly and accurately detect C. butyricum in samples and dramatically improve screening efficiency.
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Affiliation(s)
- Zhi Yi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
| | - Faizan A Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, Jiangsu Province, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu Province, China.
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122, Jiangsu Province, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, China
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Lanteri AA, del Río MG. Naupactus xanthographus (Germar) species group (Curculionidae: Entiminae: Naupactini): a comprehensive taxonomic treatment. J NAT HIST 2017. [DOI: 10.1080/00222933.2017.1346715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Analia A. Lanteri
- División Entomología, Museo de La Plata, Universidad Nacional de La Plata, CONICET, Buenos Aires, Argentina
| | - María G. del Río
- División Entomología, Museo de La Plata, Universidad Nacional de La Plata, CONICET, Buenos Aires, Argentina
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The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA. Sci Rep 2016; 6:21022. [PMID: 26880378 PMCID: PMC4754681 DOI: 10.1038/srep21022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/14/2016] [Indexed: 11/23/2022] Open
Abstract
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.
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