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Brink K, Thomas CL, Jones A, Chan TW, Mallon EB. Exploring the ageing methylome in the model insect, Nasonia vitripennis. BMC Genomics 2024; 25:305. [PMID: 38519892 PMCID: PMC10958858 DOI: 10.1186/s12864-024-10211-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The ageing process is a multifaceted phenomenon marked by the gradual deterioration of cellular and organismal functions, accompanied by an elevated susceptibility to diseases. The intricate interplay between genetic and environmental factors complicates research, particularly in complex mammalian models. In this context, simple invertebrate organisms have been pivotal, but the current models lack detectable DNA methylation limiting the exploration of this critical epigenetic ageing mechanism. This study introduces Nasonia vitripennis, the jewel wasp, as an innovative invertebrate model for investigating the epigenetics of ageing. Leveraging its advantages as a model organism and possessing a functional DNA methylation system, Nasonia emerges as a valuable addition to ageing research. RESULTS Whole-genome bisulfite sequencing unveiled dynamic alterations in DNA methylation, with differentially methylated CpGs between distinct time points in both male and female wasps. These changes were associated with numerous genes, enriching for functions related to telomere maintenance, histone methylation, and mRNA catabolic processes. Additionally, other CpGs were found to be variably methylated at each timepoint. Sex-specific effects on epigenetic entropy were observed, indicating differential patterns in the loss of epigenetic stability over time. Constructing an epigenetic clock containing 19 CpGs revealed a robust correlation between epigenetic age and chronological age. CONCLUSIONS Nasonia vitripennis emerges as a promising model for investigating the epigenetics of ageing, shedding light on the intricate dynamics of DNA methylation and their implications for age-related processes. This research not only expands the repertoire of ageing models but also opens avenues for deeper exploration of epigenetic mechanisms in the context of ageing.
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Affiliation(s)
- K Brink
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - C L Thomas
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - A Jones
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstrabe, Muenster, Germany
| | - T W Chan
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, UK
| | - E B Mallon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK.
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Leung K, van de Zande L, Beukeboom LW. Effects of polyploidization and their evolutionary implications are revealed by heritable polyploidy in the haplodiploid wasp Nasonia vitripennis. PLoS One 2023; 18:e0288278. [PMID: 37917617 PMCID: PMC10621845 DOI: 10.1371/journal.pone.0288278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/23/2023] [Indexed: 11/04/2023] Open
Abstract
Recurrent polyploidization occurred in the evolutionary history of most Eukaryota. However, how neopolyploid detriment (sterility, gigantism, gene dosage imbalances) has been overcome and even been bridged to evolutionary advantage (gene network diversification, mass radiation, range expansion) is largely unknown, particularly for animals. We used the parasitoid wasp Nasonia vitripennis, a rare insect system with heritable polyploidy, to begin addressing this knowledge gap. In Hymenoptera the sexes have different ploidies (haploid males, diploid females) and neopolyploids (diploid males, triploid females) occur for various species. Although such polyploids are usually sterile, those of N. vitripennis are reproductively capable and can even establish stable polyploid lines. To assess the effects of polyploidization, we compared a long-established polyploid line, the Whiting polyploid line (WPL) and a newly generated transformer knockdown line (tKDL) for fitness traits, absolute gene expression, and cell size and number. WPL polyploids have high male fitness and low female fecundity, while tKDL polyploids have poor male mate competition ability and high fertility. WPL has larger cells and cell number reduction, but the tKDL does not differ in this respect. Expression analyses of two housekeeping genes indicated that gene dosage is linked to sex irrespective of ploidy. Our study suggests that polyploid phenotypic variation may explain why some polyploid lineages thrive and others die out; a commonly proposed but difficult-to-test hypothesis. This documentation of diploid males (tKDL) with impaired competitive mating ability; triploid females with high fitness variation; and hymenopteran sexual dosage compensation (despite the lack of sex chromosomes) all challenges general assumptions on hymenopteran biology. We conclude that polyploidization is dependent on the duplicated genome characteristics and that genomes of different lines are unequally suited to survive diploidization. These results demonstrate the utility of N. vitripennis for delineating mechanisms of animal polyploid evolution, analogous to more advanced polyploid plant models.
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Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Leo W. Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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Comparative Karyotype Analysis of Parasitoid Hymenoptera (Insecta): Major Approaches, Techniques, and Results. Genes (Basel) 2022; 13:genes13050751. [PMID: 35627136 PMCID: PMC9141968 DOI: 10.3390/genes13050751] [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: 03/18/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
A comprehensive review of main approaches, techniques and results of the chromosome study of parasitic wasps is given. In this group, the haploid chromosome number ranges from n = 3 to 23. Distribution of parasitic wasp species by the chromosome number is bimodal, with two obvious modes at n = 6 and 11. Karyotype analysis based on routinely stained preparations of mitotic chromosomes can be used to identify members of taxonomically complicated parasitoid taxa and to distinguish between them. Morphometric study effectively reveals subtle differences between similar chromosome sets of parasitic wasps. If combined with meiotic analysis and/or cytometric data, information on mitotic karyotypes can highlight pathways of the genome evolution in certain parasitoid taxa. C- and AgNOR-banding as well as staining with base-specific fluorochromes detected important interspecific differences within several groups of parasitic wasps. Fluorescence in situ hybridization (FISH) is successfully used for physical mapping of various DNA sequences on parasitoid chromosomes. These techniques demonstrate that heterochromatic segments are usually restricted to pericentromeric regions of chromosomes of parasitic wasps. Haploid karyotypes carrying one or two nucleolus organizing regions (NORs) are the most frequent among parasitoid Hymenoptera. In combination with chromosome microdissection, FISH could become a powerful tool exploring the genome evolution of parasitic wasps. Perspectives of the comparative cytogenetic study of parasitoid Hymenoptera are outlined.
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Leung K, Ras E, Ferguson KB, Ariëns S, Babendreier D, Bijma P, Bourtzis K, Brodeur J, Bruins MA, Centurión A, Chattington SR, Chinchilla‐Ramírez M, Dicke M, Fatouros NE, González‐Cabrera J, Groot TVM, Haye T, Knapp M, Koskinioti P, Le Hesran S, Lyrakis M, Paspati A, Pérez‐Hedo M, Plouvier WN, Schlötterer C, Stahl JM, Thiel A, Urbaneja A, van de Zande L, Verhulst EC, Vet LEM, Visser S, Werren JH, Xia S, Zwaan BJ, Magalhães S, Beukeboom LW, Pannebakker BA. Next-generation biological control: the need for integrating genetics and genomics. Biol Rev Camb Philos Soc 2020; 95:1838-1854. [PMID: 32794644 PMCID: PMC7689903 DOI: 10.1111/brv.12641] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.
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Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenPO Box 111039700 CCGroningenThe Netherlands
| | - Erica Ras
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureVienna International CentreP.O. Box 1001400ViennaAustria
| | - Kim B. Ferguson
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Simone Ariëns
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | | | - Piter Bijma
- Animal Breeding and GenomicsWageningen University & ResearchPO Box 3386700 AHWageningenThe Netherlands
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureVienna International CentreP.O. Box 1001400ViennaAustria
| | - Jacques Brodeur
- Institut de Recherche en Biologie VégétaleUniversité de Montréal4101 Sherbrooke EstMontréalQuebecCanadaH1X 2B2
| | - Margreet A. Bruins
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Alejandra Centurión
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | - Sophie R. Chattington
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | - Milena Chinchilla‐Ramírez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Marcel Dicke
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Nina E. Fatouros
- Biosystematics GroupWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Joel González‐Cabrera
- Department of Genetics, Estructura de Recerca Interdisciplinar en Biotecnología i Biomedicina (ERI‐BIOTECMED)Unidad Mixta Gestión Biotecnológica de Plagas UV‐IVIA, Universitat de ValènciaDr Moliner 5046100BurjassotValenciaSpain
| | - Thomas V. M. Groot
- Koppert Biological SystemsVeilingweg 142651 BEBerkel en RodenrijsThe Netherlands
| | - Tim Haye
- CABIRue des Grillons 12800DelémontSwitzerland
| | - Markus Knapp
- Koppert Biological SystemsVeilingweg 142651 BEBerkel en RodenrijsThe Netherlands
| | - Panagiota Koskinioti
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureVienna International CentreP.O. Box 1001400ViennaAustria
- Department of Biochemistry and BiotechnologyUniversity of ThessalyBiopolis41500LarissaGreece
| | - Sophie Le Hesran
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
- Koppert Biological SystemsVeilingweg 142651 BEBerkel en RodenrijsThe Netherlands
| | - Manolis Lyrakis
- Institut für PopulationsgenetikVetmeduni ViennaVeterinärplatz 11210ViennaAustria
- Vienna Graduate School of Population GeneticsVetmeduni ViennaVeterinärplatz 11210ViennaAustria
| | - Angeliki Paspati
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Meritxell Pérez‐Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Wouter N. Plouvier
- INRA, CNRS, UMR 1355‐7254400 Route des ChappesBP 167 06903Sophia Antipolis CedexFrance
| | | | - Judith M. Stahl
- CABIRue des Grillons 12800DelémontSwitzerland
- Kearney Agricultural Research and Extension CenterUniversity of California Berkeley9240 South Riverbend AvenueParlierCA93648USA
| | - Andra Thiel
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenPO Box 111039700 CCGroningenThe Netherlands
| | - Eveline C. Verhulst
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Louise E. M. Vet
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
- Netherlands Institute of Ecology (NIOO‐KNAW)Droevendaalsesteeg 106708 PBWageningenThe Netherlands
| | - Sander Visser
- Institute of EntomologyBiology Centre CASBranišovská 31370 05České BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1760370 05České BudějoviceCzech Republic
| | - John H. Werren
- Department of BiologyUniversity of RochesterRochesterNY14627USA
| | - Shuwen Xia
- Animal Breeding and GenomicsWageningen University & ResearchPO Box 3386700 AHWageningenThe Netherlands
| | - Bas J. Zwaan
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution, and Environmental ChangesFaculdade de Ciências da Universidade de LisboaEdifício C2, Campo Grande1749‐016LisbonPortugal
| | - Leo W. Beukeboom
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenPO Box 111039700 CCGroningenThe Netherlands
| | - Bart A. Pannebakker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
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Chaverra-Rodriguez D, Dalla Benetta E, Heu CC, Rasgon JL, Ferree PM, Akbari OS. Germline mutagenesis of Nasonia vitripennis through ovarian delivery of CRISPR-Cas9 ribonucleoprotein. INSECT MOLECULAR BIOLOGY 2020; 29:569-577. [PMID: 32715554 DOI: 10.1111/imb.12663] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
CRISPR/Cas9 gene editing is a powerful technology to study the genetics of rising model organisms, such as the jewel wasp Nasonia vitripennis. However, current methods involving embryonic microinjection of CRISPR reagents are challenging. Delivery of Cas9 ribonucleoprotein into female ovaries is an alternative that has only been explored in a small handful of insects, such as mosquitoes, whiteflies and beetles. Here, we developed a simple protocol for germline gene editing by injecting Cas9 ribonucleoprotein in adult N. vitripennis females using either ReMOT control (Receptor-Mediated Ovary Transduction of Cargo) or BAPC (Branched Amphiphilic Peptide Capsules) as ovary delivery methods. For ReMOT Control we used the Drosophila melanogaster-derived peptide 'P2C' fused to EGFP to visualize the ovary delivery, and fused to Cas9 protein for gene editing of the cinnabar gene using saponin as an endosomal escape reagent. For BAPC we optimized the concentrations of protein, sgRNA and the transfection reagent. We demonstrate delivery of protein cargo such as EGFP and Cas9 into developing oocytes via P2C peptide and BAPC. Additionally, somatic and germline gene editing were demonstrated. This approach will greatly facilitate CRISPR-applied genetic manipulation in this and other rising model organisms.
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Affiliation(s)
- D Chaverra-Rodriguez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - E Dalla Benetta
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - C C Heu
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - J L Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - P M Ferree
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - O S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
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Gokhman VE. Chromosomes of parasitic wasps of the superfamily Chalcidoidea (Hymenoptera): An overview. COMPARATIVE CYTOGENETICS 2020; 14:399-416. [PMID: 36761105 PMCID: PMC9849058 DOI: 10.3897/compcytogen.v14i3.56535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/15/2020] [Indexed: 06/18/2023]
Abstract
An overview of the current knowledge of chromosome sets of the parasitoid superfamily Chalcidoidea is given. Karyotypes of approximately 240 members of this group, i.e. just above one percent of described species, are studied up to now. Techniques for obtaining and analyzing preparations of chalcid chromosomes are outlined, including the so-called "traditional" and "modern" methods of differential staining as well as fluorescence in situ hybridization (FISH). Among the Chalcidoidea, the haploid chromosome number can vary from n = 3 to n = 11, with a clear mode at n = 6 and a second local maximum at n = 10. In this group, most chromosomes are either metacentric or submetacentric, but acrocentrics and/or subtelocentrics also can predominate, especially within karyotypes of certain Chalcidoidea with higher chromosome numbers. The following main types of chromosomal mutations are characteristic of chalcid karyotypes: inversions, fusions, translocations, polyploidy, aneuploidy and B chromosome variation. Although karyotype evolution of this superfamily was mainly studied using phylogenetic reconstructions based on morphological and/or molecular characters, chromosomal synapomorphies of certain groups were also revealed. Taxonomic implications of karyotypic features of the Chalcidoidea are apparently the most important at the species level, especially among cryptic taxa.
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Affiliation(s)
- Vladimir E. Gokhman
- Botanical Garden, Moscow State University, Moscow 119234, RussiaMoscow State UniversityMoscowRussia
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