1
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Schneemann H, De Sanctis B, Welch JJ. Fisher's Geometric Model as a Tool to Study Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041442. [PMID: 38253415 PMCID: PMC11216183 DOI: 10.1101/cshperspect.a041442] [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] [Indexed: 01/24/2024]
Abstract
Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.
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Affiliation(s)
- Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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2
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Szrajer S, Gray D, Ylla G. The genome assembly and annotation of the cricket Gryllus longicercus. Sci Data 2024; 11:708. [PMID: 38942791 PMCID: PMC11213874 DOI: 10.1038/s41597-024-03554-z] [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: 04/16/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
The order Orthoptera includes insects such as grasshoppers, katydids, and crickets, among which there are important species for ecosystem stability and pollination, as well as research organisms in different fields such as neurobiology, ecology, and evolution. Crickets, with more than 2,400 described species, are emerging as novel model research organisms, for their diversity, worldwide distribution, regeneration capacity, and their characteristic acoustic communication. Here we report the assembly and annotation of the first New World cricket, that of Gryllus longicercus Weissman & Gray 2019. The genome assembly, generated by combining 44.54 Gb of long reads from PacBio and 120.44 Gb of short Illumina reads, has a length of 1.85 Gb. The genome annotation yielded 19,715 transcripts from 14,789 gene models.
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Affiliation(s)
- Szymon Szrajer
- Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, 30-387, Poland
| | - David Gray
- Department of Biology, California State University Northridge, Northridge, CA, 91330-8303, USA.
| | - Guillem Ylla
- Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, 30-387, Poland.
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3
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Zhang X, Blaxter M, Wood JMD, Tracey A, McCarthy S, Thorpe P, Rayner JG, Zhang S, Sikkink KL, Balenger SL, Bailey NW. Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution. Nat Commun 2024; 15:5001. [PMID: 38866741 PMCID: PMC11169259 DOI: 10.1038/s41467-024-49344-4] [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: 07/20/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid. Our sampling spanned a social transition during which flatwing fixed and the population went silent. We find long-range linkage disequilibrium around the putative flatwing locus was maintained over time, and hitchhiking genes had functions related to negative flatwing-associated effects. We develop a combinatorial enrichment approach using transcriptome data to test for compensatory, intragenomic coevolution. Temporal changes in genomic selection were distributed genome-wide and functionally associated with the population's transition to silence, particularly behavioural responses to silent environments. Our results demonstrate how 'adaptation begets adaptation'; changes to the sociogenetic environment accompanying rapid trait evolution can generate selection provoking further, compensatory adaptation.
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Affiliation(s)
- Xiao Zhang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China.
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, Fife, UK.
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Peter Thorpe
- School of Medicine, University of St Andrews, St Andrews, Fife, UK
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jack G Rayner
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, Fife, UK
| | - Shangzhe Zhang
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, Fife, UK
| | | | - Susan L Balenger
- College of Biological Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Nathan W Bailey
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, Fife, UK.
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4
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Hayakawa S, Kataoka K, Yamamoto M, Asahi T, Suzuki T. DeepLabCut-based daily behavioural and posture analysis in a cricket. Biol Open 2024; 13:bio060237. [PMID: 38533608 PMCID: PMC11070783 DOI: 10.1242/bio.060237] [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: 11/14/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
Circadian rhythms are indispensable intrinsic programs that regulate the daily rhythmicity of physiological processes, such as feeding and sleep. The cricket has been employed as a model organism for understanding the neural mechanisms underlying circadian rhythms in insects. However, previous studies measuring rhythm-controlled behaviours only analysed locomotive activity using seesaw-type and infrared sensor-based actometers. Meanwhile, advances in deep learning techniques have made it possible to analyse animal behaviour and posture using software that is devoid of human bias and does not require physical tagging of individual animals. Here, we present a system that can simultaneously quantify multiple behaviours in individual crickets - such as locomotor activity, feeding, and sleep-like states - in the long-term, using DeepLabCut, a supervised machine learning-based software for body keypoints labelling. Our system successfully labelled the six body parts of a single cricket with a high level of confidence and produced reliable data showing the diurnal rhythms of multiple behaviours. Our system also enabled the estimation of sleep-like states by focusing on posture, instead of immobility time, which is a conventional parameter. We anticipate that this system will provide an opportunity for simultaneous and automatic prediction of cricket behaviour and posture, facilitating the study of circadian rhythms.
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Affiliation(s)
- Shota Hayakawa
- Department of Advanced Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo 162-8480, Japan
| | - Masanobu Yamamoto
- Division of Sciences for Biological System, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Toru Asahi
- Department of Advanced Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo 162-8480, Japan
- Comprehensive Research Organization, Waseda University, Tokyo 162-8480, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan
| | - Takeshi Suzuki
- Division of Sciences for Biological System, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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5
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Murata K, Kataoka K, Sanno R, Satomura K, Ogura A, Asahi T, Yura K, Suzuki T. Complete mitochondrial genome sequences of two ground crickets, Dianemobius fascipes nigrofasciatus and Polionemobius taprobanensis (Orthoptera: Grylloidea: trigonidiidae). Mitochondrial DNA B Resour 2023; 8:1311-1315. [PMID: 38173920 PMCID: PMC10763891 DOI: 10.1080/23802359.2023.2285400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/11/2023] [Indexed: 01/05/2024] Open
Abstract
The authors sequenced the complete mitochondrial (mt) genomes of the band-legged ground cricket (Dianemobius fascipes nigrofasciatus Matsumura, 1904) and a temperate form of the lawn ground cricket (Polionemobius taprobanensis Walker, 1869), collected in Japan. The length of the mt genome sequences was 15,354 bp in D. fascipes nigrofasciatus and 16,063 bp in P. taprobanensis. Annotation of the mt genome sequences revealed 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The orientation of the genes was the same as in other Grylloidea species, and the order was the same as in other Trigonidiidae species. In our phylogenetic analysis, D. fascipes nigrofasciatus formed a clade with D. fascipes collected in China, and the temperate form of P. taprobanensis formed a clade with P. taprobanensis collected in China. Comparison of the numbers of positions with different amino acid residues encoded by the protein-coding genes implied the separate species status of each member of each of the two pairs of ground crickets. The mt genome sequences of D. fascipes nigrofasciatus and P. taprobanensis will contribute to phylogenetic and taxonomic studies of the Trigonidiidae.
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Affiliation(s)
- Kohyoh Murata
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Kazuhiro Satomura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Atsushi Ogura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Toru Asahi
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Global Consolidated Research Institute for Science Wisdom, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kei Yura
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takeshi Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
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6
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Hirata K, Asahi T, Kataoka K. Spatial and Sexual Divergence of Gut Bacterial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae). MICROBIAL ECOLOGY 2023; 86:2627-2641. [PMID: 37479827 PMCID: PMC10640434 DOI: 10.1007/s00248-023-02265-z] [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: 02/21/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023]
Abstract
The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut compartments, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut bacteriome of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by their gut compartments rather than sex. The species richness and diversity analyses revealed large difference in the bacterial communities between the gut compartments while minor differences were observed between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the gut compartment dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.
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Affiliation(s)
- Kazuya Hirata
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
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7
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Dossey AT, Oppert B, Chu FC, Lorenzen MD, Scheffler B, Simpson S, Koren S, Johnston JS, Kataoka K, Ide K. Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture. Biomolecules 2023; 13:biom13040589. [PMID: 37189337 DOI: 10.3390/biom13040589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.
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8
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De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket ( Tachycines meditationis). Int J Mol Sci 2023; 24:ijms24044005. [PMID: 36835417 PMCID: PMC9966759 DOI: 10.3390/ijms24044005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 02/18/2023] Open
Abstract
Tachycines meditationis (Orthoptera: Rhaphidophoridae: Tachycines) is a widely distributed insect in eastern Asia. This species is common in urban environments, and its unique omnivorous diet may contribute to its success in various habitats. However, molecular studies on the species are scarce. Here, we obtained the first transcriptome sequence of T. meditationis and performed preliminary analyses to test whether the evolution of coding sequences fits the expectations based on the species' ecology. We retrieved 476,495 effective transcripts and annotated 46,593 coding sequences (CDS). We analysed the codon usage and found that directional mutation pressure was the leading cause of codon usage bias in this species. This genome-wide relaxed codon usage pattern in T. meditationis is surprising, given the potentially large population size of this species. Moreover, despite the omnivorous diet, the chemosensory genes of this species do not exhibit codon usage deviating significantly from the genome-level pattern. They also do not seem to experience more gene family expansion than other cave cricket species do. A thorough search for rapidly evolved genes using the dN/dS value showed that genes associated with substance synthesis and metabolic pathways, such as retinol metabolism, aminoacyl-tRNA biosynthesis, and fatty acid metabolism, underwent species-specific positive selection. While some results seem to contradict the species ecology, our transcriptome assembly provides a valuable molecular resource for future studies on camel cricket evolution and molecular genetics for feeding ecology in insects, in general.
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9
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Nakajima Y, Ogura A. Genomics and effective trait candidates of edible insects. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Nakamura T, Ylla G, Extavour CG. Genomics and genome editing techniques of crickets, an emerging model insect for biology and food science. CURRENT OPINION IN INSECT SCIENCE 2022; 50:100881. [PMID: 35123119 DOI: 10.1016/j.cois.2022.100881] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/06/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Most tools available for manipulating gene function in insects have been developed for holometabolous species. In contrast, functional genetics tools for the Hemimetabola are highly underdeveloped. This is a barrier both to understanding ancestral insect biology, and to optimizing contemporary study and manipulation of particular large hemimetabolous orders of crucial economic and agricultural importance like the Orthoptera. For orthopteran insects, including crickets, the rapid spread of next-generation sequencing technology has made transcriptome data available for a wide variety of species over the past decade. Furthermore, whole genome sequences of orthopteran insects with relatively large genome sizes are now available. With these new genome assemblies and the development of genome editing technologies such as the CRISPR-Cas9 system, it has become possible to create gene knock-out and knock-in strains in orthopteran insects. As a result, orthopteran species should become increasingly feasible for laboratory study not only in research fields that have traditionally used insects, but also in agricultural fields that use them as food and feed. In this review, we summarize these recent advances and their relevance to such applications.
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Affiliation(s)
- Taro Nakamura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan.
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA; Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, USA; Howard Hughes Medical Institute, USA
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Mito T, Ishimaru Y, Watanabe T, Nakamura T, Ylla G, Noji S, Extavour CG. Cricket: The third domesticated insect. Curr Top Dev Biol 2022; 147:291-306. [PMID: 35337452 DOI: 10.1016/bs.ctdb.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Many researchers are using crickets to conduct research on various topics related to development and regeneration in addition to brain function, behavior, and biological clocks, using advanced functional and perturbational technologies such as genome editing. Recently, crickets have also been attracting attention as a food source for the next generation of humans. In addition, crickets are increasingly being used as disease models and biological factories for pharmaceuticals. Cricket research has thus evolved over the last century from use primarily in highly important basic research, to use in a variety of applications and practical uses. These insects are now a state-of-the-art model animal that can be obtained and maintained in large quantities at low cost. We therefore suggest that crickets are useful as a third domesticated insect for scientific research, after honeybees and silkworms, contributing to the achievement of global sustainable development goals.
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Affiliation(s)
- Taro Mito
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima City, Tokushima, Japan
| | - Yoshiyasu Ishimaru
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima City, Tokushima, Japan
| | - Takahito Watanabe
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima City, Tokushima, Japan
| | - Taro Nakamura
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States; Laboratory of Bioinformatics and Genome Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Sumihare Noji
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima City, Tokushima, Japan
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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Kataoka K, Togawa Y, Sanno R, Asahi T, Yura K. Dissecting cricket genomes for the advancement of entomology and entomophagy. Biophys Rev 2022; 14:75-97. [PMID: 35340598 PMCID: PMC8921346 DOI: 10.1007/s12551-021-00924-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Significant advances in biophysical methods such as next-generation sequencing technologies have now opened the way to conduct evolutionary and applied research based on the genomic information of greatly diverse insects. Crickets belonging to Orthoptera (Insecta: Polyneoptera), one of the most flourishing groups of insects, have contributed to the development of multiple scientific fields including developmental biology and neuroscience and have been attractive targets in evolutionary ecology for their diverse ecological niches. In addition, crickets have recently gained recognition as food and feed. However, the genomic information underlying their biological basis and application research toward breeding is currently underrepresented. In this review, we summarize the progress of genomics of crickets. First, we outline the phylogenetic position of crickets in insects and then introduce recent studies on cricket genomics and transcriptomics in a variety of fields. Furthermore, we present findings from our analysis of polyneopteran genomes, with a particular focus on their large genome sizes, chromosome number, and repetitive sequences. Finally, how the cricket genome can be beneficial to the food industry is discussed. This review is expected to enhance greater recognition of how important the cricket genomes are to the multiple biological fields and how basic research based on cricket genome information can contribute to tackling global food security.
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Affiliation(s)
- Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Yuki Togawa
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
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13
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Veenstra JA. Identification of cells expressing Calcitonins A and B, PDF and ACP in Locusta migratoria using cross-reacting antisera and in situ hybridization. Peptides 2021; 146:170667. [PMID: 34600039 DOI: 10.1016/j.peptides.2021.170667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022]
Abstract
This work was initiated because an old publication suggested that electrocoagulation of four paraldehyde fuchsin positive cells in the brain of Locusta migratoria might produce a diuretic hormone, the identity of which remains unknown, since none of the antisera to the various putative Locusta diuretic hormones recognizes these cells. The paraldehyde fuchsin positive staining suggests a peptide with a disulfide bridge and the recently identified Locusta calcitonins have both a disulfide bridge and are structurally similar to calcitonin-like diuretic hormone. In situ hybridization and antisera raised to calcitonin-A and -B were used to show where these peptides are expressed in Locusta. Calcitonin-A is produced by neurons and neuroendocrine cells that were previously shown to be immunoreactive to an antiserum to pigment dispersing factor (PDF). The apparent PDF-immunoreactivity in these neurons and neuroendocrine cells is due to crossreactivity with the calcitonin-A precursor. As confirmed by both an PDF-precursor specific antiserum and in situ hybridisation, those calcitonin-A expressing cells do not express PDF. Calcitonin B is expressed by numerous enteroendocrine cells in the midgut as well as the midgut caeca. A guinea pig antiserum to calcitonin A seemed quite specific as it recognized only the calcitonin A expressing cells. However, rabbit antisera to calcitonin-A and-B both crossreacted with neuroendocrine cells in the brain that produce ACP (AKH/corazonin-related peptide), this is almost certainly due to the common C-terminal dipeptide SPamide that is shared between Locusta calcitonin-A, calcitonin-B and ACP.
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Affiliation(s)
- Jan A Veenstra
- INCIA UMR 5287 CNRS, Université de Bordeaux, allée Geoffroy St Hillaire, CS 50023, 33 615 Pessac Cedex, France.
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14
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Satoh A, Takasu M, Yano K, Terai Y. De novo assembly and annotation of the mangrove cricket genome. BMC Res Notes 2021; 14:387. [PMID: 34627387 PMCID: PMC8502352 DOI: 10.1186/s13104-021-05798-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/27/2021] [Indexed: 11/10/2022] Open
Abstract
Objectives The mangrove cricket, Apteronemobius asahinai, shows endogenous activity rhythms that synchronize with the tidal cycle (i.e., a free-running rhythm with a period of ~ 12.4 h [the circatidal rhythm]). Little is known about the molecular mechanisms underlying the circatidal rhythm. We present the draft genome of the mangrove cricket to facilitate future molecular studies of the molecular mechanisms behind this rhythm. Data description The draft genome contains 151,060 scaffolds with a total length of 1.68 Gb (N50: 27 kb) and 92% BUSCO completeness. We obtained 28,831 predicted genes, of which 19,896 (69%) were successfully annotated using at least one of two databases (UniProtKB/SwissProt database and Pfam database).
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Affiliation(s)
- Aya Satoh
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193, Japan. .,School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan.
| | - Miwako Takasu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193, Japan
| | - Kentaro Yano
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Yohey Terai
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Shonan Village, Hayama, Kanagawa, 240-0193, Japan
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15
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Sanno R, Kataoka K, Hayakawa S, Ide K, Nguyen CN, Nguyen TP, Le BTN, Kim OTP, Mineta K, Takeyama H, Takeda M, Sato T, Suzuki T, Yura K, Asahi T. Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-Loving Crickets. Genome Biol Evol 2021; 13:evab222. [PMID: 34554226 PMCID: PMC8511664 DOI: 10.1093/gbe/evab222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Species of infraorder Gryllidea, or crickets, are useful invertebrate models for studying developmental biology and neuroscience. They have also attracted attention as alternative protein sources for human food and animal feed. Mitochondrial genomic information on related invertebrates, such as katydids, and locusts, has recently become available in attempt to clarify the controversial classification schemes, although robust phylogenetic relationships with emphasis on crickets remain elusive. Here, we report newly sequenced complete mitochondrial genomes of crickets to study their phylogeny, genomic rearrangements, and adaptive evolution. First, we conducted de novo assembly of mitochondrial genomes from eight cricket species and annotated protein-coding genes and transfer and ribosomal RNAs using automatic annotations and manual curation. Next, by combining newly described protein-coding genes with public data of the complete Gryllidea genomes and gene annotations, we performed phylogenetic analysis and found gene order rearrangements in several branches. We further analyzed genetic signatures of selection in ant-loving crickets (Myrmecophilidae), which are small wingless crickets that inhabit ant nests. Three distinct approaches revealed two positively selected sites in the cox1 gene in these crickets. Protein 3D structural analyses suggested that these selected sites could influence the interaction of respiratory complex proteins, conferring benefits to ant-loving crickets with a unique ecological niche and morphology. These findings enhance our understanding of the genetic basis of cricket evolution without relying on estimates based on a limited number of molecular markers.
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Affiliation(s)
- Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Shota Hayakawa
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Keigo Ide
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Department of Health Data Science Research, Healthy Aging Innovation Center, Tokyo Metropolitan Geriatric Medical Center, Tokyo, Japan
| | - Chuong N Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thao P Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Binh T N Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Oanh T P Kim
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Haruko Takeyama
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Makio Takeda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan
| | - Toshiyuki Sato
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takeshi Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Japan
| | - Kei Yura
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
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