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Bhattarai UR, Poulin R, Gemmell NJ, Dowle E. Genome assembly and annotation of the mermithid nematode Mermis nigrescens. G3 (BETHESDA, MD.) 2024; 14:jkae023. [PMID: 38301266 PMCID: PMC10989877 DOI: 10.1093/g3journal/jkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. A lack of genomic resources has limited the expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long reads and 10X Chromium link reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 83.98%. mRNA-seq reads from different sized nematodes (≤2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.
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Affiliation(s)
- Upendra R Bhattarai
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - Eddy Dowle
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
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Meunier J. The Biology and Social Life of Earwigs (Dermaptera). ANNUAL REVIEW OF ENTOMOLOGY 2024; 69:259-276. [PMID: 37722682 DOI: 10.1146/annurev-ento-013023-015632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Earwigs are often known for the forceps-like appendage at the end of their abdomen, urban legends about them crawling into human ears, and their roles as pest and biological control agents. However, they are much less known for their social life. This is surprising, as many of the 1,900 species of earwigs show social behaviors toward eggs, juveniles, and adults. These behaviors typically occur during family and group living, which may be obligatory or facultative, last up to several months, and involve only a few to several hundred related or unrelated individuals. Moreover, many individuals can alternate between solitary and group living during their life cycle, an ability that probably prevailed during the emergence of social life. In this review, I detail the diversity of group living and social behavior in earwigs and show how further developing this knowledge in Dermaptera can improve our general understanding of the early evolution of social life in insects.
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Affiliation(s)
- Joël Meunier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS, University of Tours, Tours, France;
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Fricaux T, Le Navenant A, Siegwart M, Rault M, Coustau C, Le Goff G. The Molecular Resistance Mechanisms of European Earwigs from Apple Orchards Subjected to Different Management Strategies. INSECTS 2023; 14:944. [PMID: 38132618 PMCID: PMC10743755 DOI: 10.3390/insects14120944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
To date, apple orchards are among the most treated crops in Europe with up to 35 chemical treatments per year. Combining control methods that reduce the number of pesticide treatments is essential for agriculture and more respectful of the environment, and the use of predatory insects such as earwigs may be valuable to achieve this goal. European earwigs, Forficula auricularia (Dermaptera: Forficulidae) are considered beneficial insects in apple orchards where they can feed on many pests like aphids. The aim of this study was to investigate the potential impact of orchards' insecticide treatments on resistance-associated molecular processes in natural populations of earwigs. Because very few molecular data are presently available on earwigs, our first goal was to identify earwig resistance-associated genes and potential mutations. Using earwigs from organic, integrated pest management or conventional orchards, we identified mutations in acetylcholinesterase 2, α1 and β2 nicotinic acetylcholine receptors. In addition, the expression level of these targets and of some essential detoxification genes were monitored using RT-qPCR. Unexpectedly, earwigs collected in organic orchards showed the highest expression for acetylcholinesterase 2. Four cytochromes P450, one esterase and one glutathione S-transferases were over-expressed in earwigs exposed to various management strategies in orchards. This first study on resistance-associated genes in Forficula auricularia paves the way for future experimental studies aimed at better understanding the potential competition between natural enemies in apple orchards in order to optimize the efficiency of biocontrol.
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Affiliation(s)
- Thierry Fricaux
- Université Côte d’Azur, INRAE, CNRS, ISA, F-06903 Sophia Antipolis, France; (T.F.); (C.C.)
| | - Adrien Le Navenant
- Avignon Université, Aix-Marseille Université, CNRS, IRD, IMBE, Pôle Agrosciences, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France; (A.L.N.); (M.R.)
| | - Myriam Siegwart
- INRAE, Unité PSH, Site Agroparc, F-84914 Avignon, Cedex 9, France;
| | - Magali Rault
- Avignon Université, Aix-Marseille Université, CNRS, IRD, IMBE, Pôle Agrosciences, 301 rue Baruch de Spinoza, BP 21239, F-84916 Avignon, France; (A.L.N.); (M.R.)
| | - Christine Coustau
- Université Côte d’Azur, INRAE, CNRS, ISA, F-06903 Sophia Antipolis, France; (T.F.); (C.C.)
| | - Gaëlle Le Goff
- Université Côte d’Azur, INRAE, CNRS, ISA, F-06903 Sophia Antipolis, France; (T.F.); (C.C.)
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Ming Q, Huang X, He Y, Qin L, Tang Y, Liu Y, Huang Y, Zhang H, Li P. Genome Mining and Screening for Secondary Metabolite Production in the Endophytic Fungus Dactylonectria alcacerensis CT-6. Microorganisms 2023; 11:microorganisms11040968. [PMID: 37110391 PMCID: PMC10142127 DOI: 10.3390/microorganisms11040968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Endophytic fungi are a treasure trove of natural products with great chemical diversity that is largely unexploited. As an alternative to the traditional bioactivity-guided screening approach, the genome-mining-based approach provides a new methodology for obtaining novel natural products from endophytes. In our study, the whole genome of an endophyte, Dactylonectria alcacerensis CT-6, was obtained for the first time. Genomic analysis indicated that D. alcacerensis CT-6 has one 61.8 Mb genome with a G+C content of 49.86%. Gene annotation was extensively carried out using various BLAST databases. Genome collinearity analysis revealed that D. alcacerensis CT-6 has high homology with three other strains of the Dactylonectria genus. AntiSMASH analysis displayed 45 secondary metabolite biosynthetic gene clusters (BGCs) in D. alcacerensis CT-6, and most of them were unknown and yet to be unveiled. Furthermore, only six known substances had been isolated from the fermented products of D. alcacerensis CT-6, suggesting that a great number of cryptic BGCs in D. alcacerensis CT-6 are silent and/or expressed at low levels under conventional conditions. Therefore, our study provides an important basis for further chemical study of D. alcacerensis CT-6 using the gene-mining strategy to awaken these cryptic BGCs for the production of bioactive secondary metabolites.
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Affiliation(s)
- Qianliang Ming
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
- Drug and Instrument Supervision and Inspection Station, 32339 Troops of the Chinese People's Liberation Army, Lhasa 850015, China
| | - Xiuning Huang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yimo He
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Lingyue Qin
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yu Tang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yanxia Liu
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Yuting Huang
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
| | - Hongwei Zhang
- Drug and Instrument Supervision and Inspection Station, 32339 Troops of the Chinese People's Liberation Army, Lhasa 850015, China
| | - Peng Li
- Department of Pharmacognosy, College of Pharmacy, Army Medical University, Chongqing 400038, China
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