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Wang CX, Bao HQ, Yan ZC, Wang J, Wang S, Li YX. Knockdown of vitellogenin receptor based on minute insect RNA interference methods affects the initial mature egg load in the pest natural enemy Trichogramma dendrolimi. INSECT SCIENCE 2024. [PMID: 38783625 DOI: 10.1111/1744-7917.13385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Vitellogenin receptor (VgR) plays a crucial role in oogenesis by mediating endocytosis of vitellogenin and a portion of the yolk proteins in many insect species. However, the function of VgR in minute parasitoid wasps is largely unknown. Here, we applied Trichogramma dendrolimi, a minute egg parasitoid, as a study model to investigate the function of VgR in parasitoids. We developed RNA interference (RNAi) methods based on microinjection of prepupae in T. dendrolimi. RNAi employs nanomaterial branched amphipathic peptide capsules (BAPC) as a carrier for double-stranded RNA (dsRNA), significantly enhancing delivery efficiency. Also, artificial hosts without medium were used to culture the injected prepupae in vitro. Utilizing these methods, we found that ovarian growth was disrupted after knockdown of TdVgR, as manifested by the suppressed development of the ovariole and the inhibition of nurse cell internalization by oocytes. Also, the initial mature egg load in the ovary was significantly reduced. Notably, the parasitic capacity of the female adult with ovarian dysplasia was significantly decreased, possibly resulting from the low availability of mature eggs. Moreover, ovarian dysplasia in T. dendrolimi caused by VgR deficiency are conserved despite feeding on different hosts. The results confirmed a critical role of TdVgR in the reproductive ability of T. dendrolimi and provided a reference for gene functional studies in minute insects.
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Affiliation(s)
- Cheng-Xing Wang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hui-Qiao Bao
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Chao Yan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jie Wang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Su Wang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuan-Xi Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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Zhou JC, Dong QJ, Shang D, Ning SF, Zhang HH, Wang Y, Che WN, Dong H, Zhang LS. Posterior concentration of Wolbachia during the early embryogenesis of the host dynamically shapes the tissue tropism of Wolbachia in host Trichogramma wasps. Front Cell Infect Microbiol 2023; 13:1198428. [PMID: 37424778 PMCID: PMC10324615 DOI: 10.3389/fcimb.2023.1198428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction The bacterial endosymbiont, Wolbachia spp. induce thelytokous parthenogenesis in certain parasitoid wasps, such as the egg parasitoid wasps Trichogramma spp. To complete the cycle of vertical transmission, Wolbachia displays efficient transovarial transmission by targeting the reproductive tissues and often exhibits strong tissue-specific tropism in their host. Method The present study aimed to describe the basic Wolbachia distribution patterns that occur during the development of Wolbachia-infected, thelytokous Trichogramma dendrolimi, and T. pretiosum. We used fluorescence in situ hybridization (FISH) to investigate Wolbachia signal dynamics during early embryogenesis (from 30 to 120 min). Wolbachia titers and distributions from the embryo to adult stages of Trichogramma after early embryogenesis were detected by absolute quantitative polymerase chain reaction (AQ-PCR) and FISH. The symmetry ratios (SR) of the Wolbachia signals were calculated using the SR odds ratios in the anterior and posterior parts of the host. The SR was determined to describe Wolbachia tropism during early embryogenesis and various developmental stages of Trichogramma. Results Wolbachia was concentrated in the posterior part of the embryo during early embryogenesis and the various developmental stages of both T. dendrolimi and T. pretiosum. Wolbachia density increased with the number of nuclei and the initial mitotic division frequency during early embryogenesis. The total Wolbachia titer increased with postembryogenesis development in both T. dendrolimi and T. pretiosum. However, the Wolbachia densities relative to body size were significantly lower at the adult and pupal stages than they were at the embryonic stage. Discussion The present work revealed that posterior Wolbachia concentration during early host embryogenesis determined Wolbachia localization in adult wasps. By this mechanism, Wolbachia exhibits efficient vertical transmission across generations by depositing only female Wolbachia-infected offspring. The results of this study describe the dynamics of Wolbachia during the development of their Trichogramma host. The findings of this investigation helped clarify Wolbachia tropism in Trichogramma wasps.
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Affiliation(s)
- Jin-Cheng Zhou
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian-Jin Dong
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Dan Shang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Su-Fang Ning
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Huan-Huan Zhang
- Institute of Vegetable, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Ying Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Wu-Nan Che
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Hui Dong
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Li-Sheng Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Sperling AL, Glover DM. Parthenogenesis in dipterans: a genetic perspective. Proc Biol Sci 2023; 290:20230261. [PMID: 36946111 PMCID: PMC10031431 DOI: 10.1098/rspb.2023.0261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
Parthenogenesis has been documented in almost every phylum of animals, and yet this phenomenon is largely understudied. It has particular importance in dipterans since some parthenogenetic species are also disease vectors and agricultural pests. Here, we present a catalogue of parthenogenetic dipterans, although it is likely that many more remain to be identified, and we discuss how their developmental biology and interactions with diverse environments may be linked to different types of parthenogenetic reproduction. We discuss how the advances in genetics and genomics have identified chromosomal loci associated with parthenogenesis. In particular, a polygenic cause of facultative parthenogenesis has been uncovered in Drosophila mercatorum, allowing the corresponding genetic variants to be tested for their ability to promote parthenogenesis in another species, Drosophila melanogaster. This study probably identifies just one of many routes that could be followed in the evolution of parthenogenesis. We attempt to account for why the phenomenon has evolved so many times in the dipteran order and why facultative parthenogenesis appears particularly prevalent. We also discuss the significance of coarse genomic changes, including non-disjunction, aneuploidy, and polyploidy and how, together with changes to specific genes, these might relate to both facultative and obligate parthenogenesis in dipterans and other parthenogenetic animals.
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Affiliation(s)
- A. L. Sperling
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - D. M. Glover
- Department of Genetics, University of Cambridge, Cambridge, UK
- California Institute of Technology, Pasadena, CA, USA
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5
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Greenberg LO, Huigens ME, Groot AT, Cusumano A, Fatouros NE. Finding an egg in a haystack: variation in chemical cue use by egg parasitoids of herbivorous insects. CURRENT OPINION IN INSECT SCIENCE 2023; 55:101002. [PMID: 36535578 DOI: 10.1016/j.cois.2022.101002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Egg parasitoids of herbivorous insects use an interplay of short- and long-range chemical cues emitted by hosts and host plants to find eggs to parasitize. Volatile compounds that attract egg parasitoids can be identified via behavioral assays and used to manipulate parasitoid behavior in the field for biological control of herbivorous pests. However, how and when a particular cue will be used varies over the life of an individual, as well as at and below species level. Future research should expand taxonomic coverage to explore variation in chemical cue use in more natural, dynamic settings. More nuanced understanding of the variability of egg parasitoid host-finding strategies will aid in disentangling the underlying genetics and further enhancing biological control.
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Affiliation(s)
- Liana O Greenberg
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | - Martinus E Huigens
- Education and Student Affairs, Wageningen University, Wageningen, the Netherlands
| | - Astrid T Groot
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, the Netherlands
| | - Antonino Cusumano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Nina E Fatouros
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands.
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Zhang X, Jiang Z, Jiao X, Yu Y, Wang Z, Hou Y, Duan G, Du W, Ruan C, Zhang J, Hu Y. Genome Assembly and Comparative Analysis of the Egg Parasitoid Wasp Trichogramma dendrolimi Shed Light on the Composition and Evolution of Olfactory Receptors and Venoms. INSECTS 2023; 14:144. [PMID: 36835713 PMCID: PMC9960361 DOI: 10.3390/insects14020144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Trichogramma dendrolimi is one of the most successfully industrialized Trichogramma species used to control agricultural and forestry pests in China. However, the molecular mechanisms underlying its host recognition and parasitism remain largely unknown, partially due to the limited genome information of this parasitoid wasp. Here, we present a high-quality de novo assembly of T. dendrolimi through a combination of Illumina and PacBio sequencing technologies. The final assembly had a length of 215.2 Mb and contains 316 scaffolds with a scaffold N50 size of 1.41 Mb. Repetitive sequences with a length of 63.4 Mb and 12,785 protein-coding genes were identified. Significantly expanded gene families were identified to be involved in the development and regulatory processes, while remarkably contracted gene families were involved in the transport processes in T. dendrolimi. The olfactory and venom-associated genes were identified in T. dendrolimi and 24 other hymenopteran species, using uniform methods combining BLAST and HMM profiling. The identified venom genes of T. dendrolimi were enriched in antioxidant activity, tricarboxylic acid cycle, response to oxidative stress and cell redox homeostasis. Our study provides an important resource for comparative genomics and functional studies to interpret the molecular mechanisms underlying host recognition and parasitism of Trichogramma species.
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Affiliation(s)
- Xue Zhang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Zhuo Jiang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Xilin Jiao
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Yang Yu
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Zhenan Wang
- Department of Plant Pathology, College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yangyang Hou
- Department of Entomology, College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Guohua Duan
- Department of Plant Pathology, College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Wenmei Du
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Changchun Ruan
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Junjie Zhang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Ying Hu
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
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7
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Wu X, Bhatia N, Grozinger CM, Yi SV. Comparative studies of genomic and epigenetic factors influencing transcriptional variation in two insect species. G3 GENES|GENOMES|GENETICS 2022; 12:6693626. [PMID: 36137211 PMCID: PMC9635643 DOI: 10.1093/g3journal/jkac230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022]
Abstract
Different genes show different levels of expression variability. For example, highly expressed genes tend to exhibit less expression variability. Genes whose promoters have TATA box and initiator motifs tend to have increased expression variability. On the other hand, DNA methylation of transcriptional units, or gene body DNA methylation, is associated with reduced gene expression variability in many species. Interestingly, some insect lineages, most notably Diptera including the canonical model insect Drosophila melanogaster, have lost DNA methylation. Therefore, it is of interest to determine whether genomic features similarly influence gene expression variability in lineages with and without DNA methylation. We analyzed recently generated large-scale data sets in D. melanogaster and honey bee (Apis mellifera) to investigate these questions. Our analysis shows that increased gene expression levels are consistently associated with reduced expression variability in both species, while the presence of TATA box is consistently associated with increased gene expression variability. In contrast, initiator motifs and gene lengths have weak effects limited to some data sets. Importantly, we show that a sequence characteristics indicative of gene body DNA methylation is strongly and negatively associate with gene expression variability in honey bees, while it shows no such association in D. melanogaster. These results suggest the evolutionary loss of DNA methylation in some insect lineages has reshaped the molecular mechanisms concerning the regulation of gene expression variability.
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Affiliation(s)
| | - Neharika Bhatia
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, GA 30332, USA
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University , University Park, PA 16801, USA
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, GA 30332, USA
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara , Santa Barbara, CA 93106, USA
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Wu Y, Fang H, Liu X, Michaud JP, Xu H, Zhao Z, Zhang S, Li Z. Laboratory evaluation of the compatibility of Beauveria bassiana with the egg parasitoid Trichogramma dendrolimi (Hymenoptera: Trichogrammatidae) for joint application against the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae). PEST MANAGEMENT SCIENCE 2022; 78:3608-3619. [PMID: 35598075 DOI: 10.1002/ps.7003] [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: 08/10/2021] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The entomopathogenic fungus Beauveria bassiana and the egg parasitoid Trichogramma dendrolimi can both contribute to biological control of the global fruit borer Grapholita molesta. To derive insights for optimizing their combined application in augmentation programs, we assayed fungal pathogenicity to both G. molesta (eggs, larvae and adults) and adult parasitoids, and assessed wasp acquisition and transmission of fungal spores following their emergence from B. bassiana-treated host eggs. RESULTS Concentrations of 108 conidia mL-1 of B. bassiana and higher caused virtually complete mortality of G. molesta larvae, but less than 30% mortality of eggs, and female moths surviving treatments had reduced fecundity. More than 80% of adult T. dendrolimi survived B. bassiana treatments of 107 conidia mL-1 , and more than 60% survived 109 conidia mL-1 , with surviving females achieving reproductive success equivalent to controls. Parasitoid females preferred healthy eggs over B. bassiana-infected ones in choice tests; wasps emerging from treated eggs carried about 104 conidia each and contributed an additional 11% host mortality in trials combining both agents. CONCLUSION Our results indicate that combined applications of B. bassiana and T. dendrolimi can have complimentary impacts on G. molesta, the wasps compensating for low fungal pathogenicity to eggs and their progeny potentially aiding in subsequent disease transmission. Although foraging wasps tended to avoid infected eggs, negative interactions between the two agents might be further mitigated by timing B. bassiana applications from late instar larva to early moth stage, and T. dendrolimi releases several days later to coincide with peak oviposition periods. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yanan Wu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Haibo Fang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - J P Michaud
- Department of Entomology, Kansas State University, Agricultural Research Center-Hays, Hays, KS, USA
| | - Haoyang Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhihua Zhao
- Jiangsu Giastone Biotechnology Co., Ltd, China
| | - Songdou Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhen Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Kamiyama T, Shimada-Niwa Y, Tanaka H, Katayama M, Kuwabara T, Mori H, Kunihisa A, Itoh T, Toyoda A, Niwa R. Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica. DNA Res 2022; 29:6605221. [PMID: 35686927 PMCID: PMC9233498 DOI: 10.1093/dnares/dsac019] [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: 01/19/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.
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Affiliation(s)
- Takumi Kamiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
| | - Yuko Shimada-Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency (JST) , Tokyo 102-0076, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Minami Katayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takayoshi Kuwabara
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Hitoha Mori
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Akari Kunihisa
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
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10
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Yan ZC, Qi GY, Yao TY, Li YX. Mitochondrial Genomes of Two Asexual Trichogramma (Hymenoptera: Trichogrammatidae) Strains and Comparison with Their Sexual Relatives. INSECTS 2022; 13:insects13060549. [PMID: 35735886 PMCID: PMC9224637 DOI: 10.3390/insects13060549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023]
Abstract
Simple Summary Sexual reproduction is dominant in animals, while asexual lineages are rare and evolutionarily short-lived. However, sexual reproduction has substantial costs, such as male production, inputs to courtship and mating, increased risk of predator exposure, and sexually transmitted diseases. A large body of theories has been proposed to explain the paradox of sex. One favored explanation is that asexuals are more likely to accumulate a greater number of deleterious mutations, known as Muller’s ratchet. Trichogramma is a genus of egg parasitoid wasps and is widely used as a biological control agent for agricultural and forest pests. With asexual lineages in at least 16 species, Trichogramma provides an excellent model to investigate the causes and consequences of asexual reproduction. In this study, we sequenced and assembled two asexual Trichogramma mitogenomes, representing two divergent origins of asexual reproduction. The asexual T. pretiosum is induced by the endosymbiont Wolbachia, while T. cacoeciae presumably originates from interspecific hybridization. To test Muller’s ratchet hypothesis, we compared these two asexual mitogenomes with their sexual relatives and found no association between asexual reproduction and mutation accumulation. This study provides a basis for further investigation into mitochondrial evolution and asexual reproduction in Trichogramma. Abstract Despite its substantial costs, sexual reproduction dominates in animals. One popular explanation for the paradox of sex is that asexual reproduction is more likely to accumulate deleterious mutations than sexual reproduction. To test this hypothesis, we compared the mitogenomes of two asexual wasp strains, Trichogramma cacoeciae and T. pretiosum, to their sexual relatives. These two asexual strains represent two different transition mechanisms in Trichogramma from sexual to asexual reproduction. Asexual T. pretiosum is induced by Wolbachia, while T. cacoeciae presumably originated from interspecific hybridization. We sequenced and assembled complete mitochondrial genomes of asexual T. cacoeciae and T. pretiosum. Compared to four sexual relatives, we found no evidence of higher mutation accumulation in asexual Trichogramma mitogenomes than in their sexual relatives. We also did not detect any relaxed selection in asexual Trichogramma mitogenomes. In contrast, the intensified selection was detected in Nad1 and Nad4 of the asexual T. pretiosum mitogenome, suggesting more purifying selection. In summary, no higher mitochondrial mutation accumulation was detected in these two asexual Trichogramma strains. This study provides a basis for further investigating mitochondrial evolution and asexual reproduction in Trichogramma.
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Affiliation(s)
- Zhi-Chao Yan
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
| | - Guang-Yuan Qi
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
| | - Tian-Yi Yao
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
| | - Yuan-Xi Li
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (Z.-C.Y.); (G.-Y.Q.); (T.-Y.Y.)
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Nanjing Agricultural University), Ministry of Agriculture, Nanjing 210095, China
- Correspondence:
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Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue. Nat Commun 2022; 13:1608. [PMID: 35338130 PMCID: PMC8956670 DOI: 10.1038/s41467-022-29273-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/03/2022] [Indexed: 02/05/2023] Open
Abstract
Cytoplasmic incompatibility (CI) results when Wolbachia bacteria-infected male insects mate with uninfected females, leading to embryonic lethality. “Rescue” of viability occurs if the female harbors the same Wolbachia strain. CI is caused by linked pairs of Wolbachia genes called CI factors (CifA and CifB). The co-evolution of CifA-CifB pairs may account in part for the incompatibility patterns documented in insects infected with different Wolbachia strains, but the molecular mechanisms remain elusive. Here, we use X-ray crystallography and AlphaFold to analyze the CI factors from Wolbachia strain wMel called CidAwMel and CidBwMel. Substituting CidAwMel interface residues with those from CidAwPip (from strain wPip) enables the mutant protein to bind CidBwPip and rescue CidBwPip-induced yeast growth defects, supporting the importance of CifA-CifB interaction in CI rescue. Sequence divergence in CidAwPip and CidBwPip proteins affects their pairwise interactions, which may help explain the complex incompatibility patterns of mosquitoes infected with different wPip strains. Wolbachia induced cytoplasmic incompatibility (CI) is caused by linked pairs of genes named cifA and cifB. Here, authors show that the residues at interfaces of the CidA-CidB complex is crucial for their binding and contribute to the diversity of CI.
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12
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Xu H, Ye X, Yang Y, Yang Y, Sun YH, Mei Y, Xiong S, He K, Xu L, Fang Q, Li F, Ye G, Lu Z. Comparative Genomics Sheds Light on the Convergent Evolution of Miniaturized Wasps. Mol Biol Evol 2021; 38:5539-5554. [PMID: 34515790 PMCID: PMC8662594 DOI: 10.1093/molbev/msab273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Miniaturization has occurred in many animal lineages, including insects and vertebrates, as a widespread trend during animal evolution. Among Hymenoptera, miniaturization has taken place in some parasitoid wasp lineages independently, and may have contributed to the diversity of species. However, the genomic basis of miniaturization is little understood. Diverged approximately 200 Ma, Telenomus wasps (Platygastroidea) and Trichogramma wasps (Chalcidoidea) have both evolved to a highly reduced body size independently, representing a paradigmatic example of convergent evolution. Here, we report a high-quality chromosomal genome of Telenomus remus, a promising candidate for controlling Spodoptera frugiperda, a notorious pest that has recently caused severe crop damage. The T. remus genome (129 Mb) is characterized by a low density of repetitive sequence and a reduction of intron length, resulting in the shrinkage of genome size. We show that hundreds of genes evolved faster in two miniaturized parasitoids Trichogramma pretiosum and T. remus. Among them, 38 genes exhibit extremely accelerated evolutionary rates in these miniaturized wasps, possessing diverse functions in eye and wing development as well as cell size control. These genes also highlight potential roles in body size regulation. In sum, our analyses uncover a set of genes with accelerated evolutionary rates in Tri. pretiosum and T. remus, which might be responsible for their convergent adaptations to miniaturization, and thus expand our understanding on the evolutionary basis of miniaturization. Additionally, the genome of T. remus represents the first genome resource of superfamily Platygastroidea, and will facilitate future studies of Hymenoptera evolution and pest control.
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Affiliation(s)
- Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
- Institute of Artificial Intelligence, College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Le Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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13
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Walsh AT, Triant DA, Le Tourneau JJ, Shamimuzzaman M, Elsik CG. Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. Nucleic Acids Res 2021; 50:D1032-D1039. [PMID: 34747465 PMCID: PMC8728238 DOI: 10.1093/nar/gkab1018] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023] Open
Abstract
We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.
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Affiliation(s)
- Amy T Walsh
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Deborah A Triant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Md Shamimuzzaman
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.,Division of Plant Science & Technology, University of Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
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14
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Olfactory Sensilla and Olfactory Genes in the Parasitoid Wasp Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae). INSECTS 2021; 12:insects12110998. [PMID: 34821797 PMCID: PMC8620382 DOI: 10.3390/insects12110998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Parasitic wasps are the major natural enemies of many organisms, and therefore they are broadly used in the biological control of numerous agricultural and horticultural pests. For example, Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae) is a tiny natural egg parasitoid of various agricultural pest insects, including Plutella xylostella, Helicoverpa armigera, Spodoptera frugiperda and Ectomyelois ceratoniae. However, how T. pretiosum seek and localise host insect eggs is still not clear. The olfactory system is critical in guiding insect behaviours, including mating, feeding and oviposition, which play pivotal roles in the interactions between parasitoid wasps and their hosts. This project aimed to investigate T. pretiosum major olfactory tissue (antennae) and the olfactory genes, including odorant binding proteins (OBPs) and odorant receptors (ORs). T. pretiosum adult antennae were examined under scanning electron microscopy, and four types of olfactory sensilla were observed. Using T. pretiosum genome, 22 OBPs and 105 ORs were identified, which were further compared with olfactory genes of other Hymenoptera insect species. The expression patterns of OBPs between T. pretiosum male and female adults were examined to identify female- or male-specific OBPs. This study enriches our knowledge of T. pretiosum olfactory system and will help better use it in the integrated pest management (IPM) for many insect pest species. Abstract Trichogramma pretiosum Riley (Hymenoptera: Trichogrammatidae) is a tiny natural egg parasitoid of several agricultural pest insects, which has been widely used in the biological control for Plutella xylostella, Helicoverpa armigera, Spodoptera frugiperda and Ectomyelois ceratoniae. However, limited studies have been conducted on T. pretiosum olfactory system, which is critical in regulating insect behaviours. In this study, T. pretiosum adult antennae were investigated under ascanning electron microscopy (SEM). Four types of olfactory sensilla were observed, including chaetica sensilla (CS), trichoid sensilla (TS), faleate sensilla (FS) and placoid sensilla (PS). Using T. pretiosum genome, 22 putative odorant binding proteins (OBPs) and 105 odorant receptors (ORs) were identified, which were further compared with olfactory genes of Apis mellifera, Nasonia vitripennis and Diachasma alloeum. The expression patterns of OBPs between T. pretiosum male and female adults were examined by quantitative real time PCR (qRT-PCR) approaches. Three female-specific OBPs (TpreOBP19, TpreOBP15 and TpreOBP3) were identified, which may play crucial roles in T. pretiosum host-seeking and oviposition behaviours. This study enriches our knowledge of T. pretiosum olfactory genes and improves our understanding of its olfactory system.
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15
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Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proc Biol Sci 2021; 288:20211720. [PMID: 34547909 PMCID: PMC8456138 DOI: 10.1098/rspb.2021.1720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/31/2021] [Indexed: 11/12/2022] Open
Abstract
While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.
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Affiliation(s)
- Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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16
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Chen J, Fang G, Pang L, Sheng Y, Zhang Q, Zhou Y, Zhou S, Lu Y, Liu Z, Zhang Y, Li G, Shi M, Chen X, Zhan S, Huang J. Neofunctionalization of an ancient domain allows parasites to avoid intraspecific competition by manipulating host behaviour. Nat Commun 2021; 12:5489. [PMID: 34531391 PMCID: PMC8446075 DOI: 10.1038/s41467-021-25727-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 08/16/2021] [Indexed: 02/08/2023] Open
Abstract
Intraspecific competition is a major force in mediating population dynamics, fuelling adaptation, and potentially leading to evolutionary diversification. Among the evolutionary arms races between parasites, one of the most fundamental and intriguing behavioural adaptations and counter-adaptations are superparasitism and superparasitism avoidance. However, the underlying mechanisms and ecological contexts of these phenomena remain underexplored. Here, we apply the Drosophila parasite Leptopilina boulardi as a study system and find that this solitary endoparasitic wasp provokes a host escape response for superparasitism avoidance. We combine multi-omics and in vivo functional studies to characterize a small set of RhoGAP domain-containing genes that mediate the parasite's manipulation of host escape behaviour by inducing reactive oxygen species in the host central nervous system. We further uncover an evolutionary scenario in which neofunctionalization and specialization gave rise to the novel role of RhoGAP domain in avoiding superparasitism, with an ancestral origin prior to the divergence between Leptopilina specialist and generalist species. Our study suggests that superparasitism avoidance is adaptive for a parasite and adds to our understanding of how the molecular manipulation of host behaviour has evolved in this system.
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Affiliation(s)
- Jiani Chen
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Gangqi Fang
- grid.9227.e0000000119573309CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lan Pang
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yifeng Sheng
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qichao Zhang
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuenan Zhou
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sicong Zhou
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yueqi Lu
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhiguo Liu
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XKey Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yixiang Zhang
- grid.9227.e0000000119573309CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Guiyun Li
- grid.9227.e0000000119573309CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Shi
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XKey Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Xuexin Chen
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XKey Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XState Key Lab of Rice Biology, Zhejiang University, Hangzhou, China
| | - Shuai Zhan
- grid.9227.e0000000119573309CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China ,grid.410726.60000 0004 1797 8419CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jianhua Huang
- grid.13402.340000 0004 1759 700XInstitute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XKey Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China
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17
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Yang Y, Ye X, Dang C, Cao Y, Hong R, Sun YH, Xiao S, Mei Y, Xu L, Fang Q, Xiao H, Li F, Ye G. Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation. BMC Biol 2021; 19:145. [PMID: 34315471 PMCID: PMC8314478 DOI: 10.1186/s12915-021-01081-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Background Hymenoptera comprise extremely diverse insect species with extensive variation in their life histories. The Dryinidae, a family of solitary wasps of Hymenoptera, have evolved innovations that allow them to hunt using venom and a pair of chelae developed from the fore legs that can grasp prey. Dryinidae larvae are also parasitoids of Auchenorrhyncha, a group including common pests such as planthoppers and leafhoppers. Both of these traits make them effective and valuable for pest control, but little is yet known about the genetic basis of its dual adaptation to parasitism and predation. Results We sequenced and assembled a high-quality genome of the dryinid wasp Gonatopus flavifemur, which at 636.5 Mb is larger than most hymenopterans. The expansion of transposable elements, especially DNA transposons, is a major contributor to the genome size enlargement. Our genome-wide screens reveal a number of positively selected genes and rapidly evolving proteins involved in energy production and motor activity, which may contribute to the predatory adaptation of dryinid wasp. We further show that three female-biased, reproductive-associated yellow genes, in response to the prey feeding behavior, are significantly elevated in adult females, which may facilitate the egg production. Venom is a powerful weapon for dryinid wasp during parasitism and predation. We therefore analyze the transcriptomes of venom glands and describe specific expansions in venom Idgf-like genes and neprilysin-like genes. Furthermore, we find the LWS2-opsin gene is exclusively expressed in male G. flavifemur, which may contribute to partner searching and mating. Conclusions Our results provide new insights into the genome evolution, predatory adaptation, venom evolution, and sex-biased genes in G. flavifemur, and present genomic resources for future in-depth comparative analyses of hymenopterans that may benefit pest control. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01081-6.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Cong Dang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yunshen Cao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Rui Hong
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Shan Xiao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Le Xu
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Huamei Xiao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.,Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, College of Life Sciences and Resource Environment, Yichun University, Yichun, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
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18
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Wu X, Galbraith DA, Chatterjee P, Jeong H, Grozinger CM, Yi SV. Lineage and Parent-of-Origin Effects in DNA Methylation of Honey Bees (Apis mellifera) Revealed by Reciprocal Crosses and Whole-Genome Bisulfite Sequencing. Genome Biol Evol 2021; 12:1482-1492. [PMID: 32597952 PMCID: PMC7502210 DOI: 10.1093/gbe/evaa133] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Parent-of-origin methylation arises when the methylation patterns of a particular allele are dependent on the parent it was inherited from. Previous work in honey bees has shown evidence of parent-of-origin-specific expression, yet the mechanisms regulating such pattern remain unknown in honey bees. In mammals and plants, DNA methylation is known to regulate parent-of-origin effects such as genomic imprinting. Here, we utilize genotyping of reciprocal European and Africanized honey bee crosses to study genome-wide allele-specific methylation patterns in sterile and reproductive individuals. Our data confirm the presence of allele-specific methylation in honey bees in lineage-specific contexts but also importantly, though to a lesser degree, parent-of-origin contexts. We show that the majority of allele-specific methylation occurs due to lineage rather than parent-of-origin factors, regardless of the reproductive state. Interestingly, genes affected by allele-specific DNA methylation often exhibit both lineage and parent-of-origin effects, indicating that they are particularly labile in terms of DNA methylation patterns. Additionally, we re-analyzed our previous study on parent-of-origin-specific expression in honey bees and found little association with parent-of-origin-specific methylation. These results indicate strong genetic background effects on allelic DNA methylation and suggest that although parent-of-origin effects are manifested in both DNA methylation and gene expression, they are not directly associated with each other.
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Affiliation(s)
- Xin Wu
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - David A Galbraith
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University
| | - Paramita Chatterjee
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Hyeonsoo Jeong
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University
| | - Soojin V Yi
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
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19
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Pinto BJ, Weis JJ, Gamble T, Ode PJ, Paul R, Zaspel JM. A chromosome-level genome assembly of the parasitoid wasp, Cotesia glomerata (Hymenoptera: Braconidae). J Hered 2021; 112:558-564. [PMID: 34043785 DOI: 10.1093/jhered/esab032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet under-studied hymenopterans, are parasitoid wasps in the family Braconidae. Among this under-studied group are braconid wasps in the genus Cotesia; a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing technologies, including Oxford Nanopore, whole-genome shotgun sequencing, and 3-D chromatin contact information (Hi-C). Our assembly is one of the most contiguous, complete, and publicly available hymenopteran genomes, represented by 3,355 scaffolds with a scaffold N50 of ~28Mb and a BUSCO score of ~99%. Given the genome sizes found in closely related species, our genome assembly was ~50% larger than expected, which was apparently induced by runaway amplification of three types of repetitive elements: simple repeats, Long Terminal Repeats (LTRs), and Long Interspersed Nuclear Elements (LINEs). This assembly is another step forward for genomics across this hyper-diverse, yet understudied, order of insects. The assembled genomic data and metadata files are publicly available via Figshare (https://doi.org/10.6084/m9.figshare.13010549).
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Affiliation(s)
- Brendan J Pinto
- Department of Integrative Biology, University of Texas at Austin, TX, USA.,Milwaukee Public Museum, Milwaukee, WI, USA
| | | | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.,Bell Museum of Natural History, University of Minnesota, St Paul, MN, USA
| | - Paul J Ode
- Colorado State University, Ft. Collins, CO, USA
| | - Ryan Paul
- Colorado State University, Ft. Collins, CO, USA
| | - Jennifer M Zaspel
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
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20
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Ferguson KB, Visser S, Dalíková M, Provazníková I, Urbaneja A, Pérez‐Hedo M, Marec F, Werren JH, Zwaan BJ, Pannebakker BA, Verhulst EC. Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest. INSECT MOLECULAR BIOLOGY 2021; 30:188-209. [PMID: 33305885 PMCID: PMC8048687 DOI: 10.1111/imb.12688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/25/2020] [Accepted: 12/07/2020] [Indexed: 05/14/2023]
Abstract
Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.
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Affiliation(s)
- K. B. Ferguson
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - S. Visser
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - M. Dalíková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - I. Provazníková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- European Molecular Biology LaboratoryHeidelbergGermany
| | - A. Urbaneja
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - M. Pérez‐Hedo
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - F. Marec
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
| | - J. H. Werren
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - B. J. Zwaan
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - B. A. Pannebakker
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - E. C. Verhulst
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
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21
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Jaron KS, Bast J, Nowell RW, Ranallo-Benavidez TR, Robinson-Rechavi M, Schwander T. Genomic Features of Parthenogenetic Animals. J Hered 2021; 112:19-33. [PMID: 32985658 PMCID: PMC7953838 DOI: 10.1093/jhered/esaa031] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.
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Affiliation(s)
- Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
- Reuben W. Nowell is now at the Department of Zoology, University of Oxford, Oxford, UK
| | | | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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22
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Huang J, Chen J, Fang G, Pang L, Zhou S, Zhou Y, Pan Z, Zhang Q, Sheng Y, Lu Y, Liu Z, Zhang Y, Li G, Shi M, Chen X, Zhan S. Two novel venom proteins underlie divergent parasitic strategies between a generalist and a specialist parasite. Nat Commun 2021; 12:234. [PMID: 33431897 PMCID: PMC7801585 DOI: 10.1038/s41467-020-20332-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/25/2020] [Indexed: 12/23/2022] Open
Abstract
Parasitoids are ubiquitous in natural ecosystems. Parasitic strategies are highly diverse among parasitoid species, yet their underlying genetic bases are poorly understood. Here, we focus on the divergent adaptation of a specialist and a generalist drosophilid parasitoids. We find that a novel protein (Lar) enables active immune suppression by lysing the host lymph glands, eventually leading to successful parasitism by the generalist. Meanwhile, another novel protein (Warm) contributes to a passive strategy by attaching the laid eggs to the gut and other organs of the host, leading to incomplete encapsulation and helping the specialist escape the host immune response. We find that these diverse parasitic strategies both originated from lateral gene transfer, followed with duplication and specialization, and that they might contribute to the shift in host ranges between parasitoids. Our results increase our understanding of how novel gene functions originate and how they contribute to host adaptation.
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Affiliation(s)
- Jianhua Huang
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China. .,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China.
| | - Jiani Chen
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Gangqi Fang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lan Pang
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Sicong Zhou
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Yuenan Zhou
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Zhongqiu Pan
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Qichao Zhang
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Yifeng Sheng
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Yueqi Lu
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Zhiguo Liu
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Yixiang Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Guiyun Li
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Shi
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China.,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China
| | - Xuexin Chen
- Institute of Insect Sciences, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China. .,Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, 310058, Hangzhou, China. .,State Key Lab of Rice Biology, Zhejiang University, 310058, Hangzhou, China.
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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23
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Ye X, Xiong S, Teng Z, Yang Y, Wang J, Yu K, Wu H, Mei Y, Yan Z, Cheng S, Yin C, Wang F, Yao H, Fang Q, Song Q, Werren JH, Ye G, Li F. Amino acid synthesis loss in parasitoid wasps and other hymenopterans. eLife 2020; 9:e59795. [PMID: 33074103 PMCID: PMC7593089 DOI: 10.7554/elife.59795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/17/2020] [Indexed: 11/17/2022] Open
Abstract
Insects utilize diverse food resources which can affect the evolution of their genomic repertoire, including leading to gene losses in different nutrient pathways. Here, we investigate gene loss in amino acid synthesis pathways, with special attention to hymenopterans and parasitoid wasps. Using comparative genomics, we find that synthesis capability for tryptophan, phenylalanine, tyrosine, and histidine was lost in holometabolous insects prior to hymenopteran divergence, while valine, leucine, and isoleucine were lost in the common ancestor of Hymenoptera. Subsequently, multiple loss events of lysine synthesis occurred independently in the Parasitoida and Aculeata. Experiments in the parasitoid Cotesia chilonis confirm that it has lost the ability to synthesize eight amino acids. Our findings provide insights into amino acid synthesis evolution, and specifically can be used to inform the design of parasitoid artificial diets for pest control.
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Affiliation(s)
- Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
- Department of Biology, University of RochesterRochesterUnited States
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Ziwen Teng
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yi Yang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Kaili Yu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Huizi Wu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Sammy Cheng
- Department of Biology, University of RochesterRochesterUnited States
| | - Chuanlin Yin
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Fang Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Hongwei Yao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of MissouriColumbiaUnited States
| | - John H Werren
- Department of Biology, University of RochesterRochesterUnited States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
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24
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Ferguson KB, Kursch-Metz T, Verhulst EC, Pannebakker BA. Hybrid Genome Assembly and Evidence-Based Annotation of the Egg Parasitoid and Biological Control Agent Trichogramma brassicae. G3 (BETHESDA, MD.) 2020; 10:3533-3540. [PMID: 32792343 PMCID: PMC7534424 DOI: 10.1534/g3.120.401344] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/04/2020] [Indexed: 11/26/2022]
Abstract
Trichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister species T. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genus Trichogramma, but also for research into molecular evolution, ecology, and breeding of T. brassicae.
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Affiliation(s)
- Kim B Ferguson
- Wageningen University, Laboratory of Genetics, Wageningen, The Netherlands
| | - Tore Kursch-Metz
- Technische Universität Darmstadt, Department of Biology, Darmstadt, Germany
- AMW Nützlinge GmbH, Pfungstadt, Germany
| | - Eveline C Verhulst
- Wageningen University, Laboratory of Entomology, Wageningen, The Netherlands
| | - Bart A Pannebakker
- Wageningen University, Laboratory of Genetics, Wageningen, The Netherlands
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25
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SSizer: Determining the Sample Sufficiency for Comparative Biological Study. J Mol Biol 2020; 432:3411-3421. [DOI: 10.1016/j.jmb.2020.01.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/26/2019] [Accepted: 01/18/2020] [Indexed: 01/25/2023]
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26
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Distinct epigenomic and transcriptomic modifications associated with Wolbachia-mediated asexuality. PLoS Pathog 2020; 16:e1008397. [PMID: 32187233 PMCID: PMC7105135 DOI: 10.1371/journal.ppat.1008397] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/30/2020] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are maternally transmitted intracellular bacteria that induce a range of pathogenic and fitness-altering effects on insect and nematode hosts. In parasitoid wasps of the genus Trichogramma, Wolbachia infection induces asexual production of females, thus increasing transmission of Wolbachia. It has been hypothesized that Wolbachia infection accompanies a modification of the host epigenome. However, to date, data on genome-wide epigenomic changes associated with Wolbachia are limited, and are often confounded by background genetic differences. Here, we took sexually reproducing Trichogramma free of Wolbachia and introgressed their genome into a Wolbachia-infected cytoplasm, converting them to Wolbachia-mediated asexuality. Wolbachia was then cured from replicates of these introgressed lines, allowing us to examine the genome-wide effects of wasps newly converted to asexual reproduction while controlling for genetic background. We thus identified gene expression and DNA methylation changes associated with Wolbachia-infection. We found no overlaps between differentially expressed genes and differentially methylated genes, indicating that Wolbachia-infection associated DNA methylation change does not directly modulate levels of gene expression. Furthermore, genes affected by these mechanisms exhibit distinct evolutionary histories. Genes differentially methylated due to the infection tended to be evolutionarily conserved. In contrast, differentially expressed genes were significantly more likely to be unique to the Trichogramma lineage, suggesting host-specific transcriptomic responses to infection. Nevertheless, we identified several novel aspects of Wolbachia-associated DNA methylation changes. Differentially methylated genes included those involved in oocyte development and chromosome segregation. Interestingly, Wolbachia-infection was associated with higher levels of DNA methylation. Additionally, Wolbachia infection reduced overall variability in gene expression, even after accounting for the effect of DNA methylation. We also identified specific cases where alternative exon usage was associated with DNA methylation changes due to Wolbachia infection. These results begin to reveal distinct genes and molecular pathways subject to Wolbachia induced epigenetic modification and/or host responses to Wolbachia-infection. Wolbachia is an extremely common endosymbiotic infection of arthropods and nematodes. One of the reasons why Wolbachia can so successfully infect diverse species is the bacterium’s ability to profoundly alter the reproductive behavior of its host. It has been proposed that Wolbachia may modify host’s epigenetic programs to alter its reproductive behavior. However, it has been difficult to study how epigenetic programs change with Wolbachia infection, due to the confounding effects of genetic backgrounds. Here, we studied host transcriptome and epigenome changes associated with Wolbachia infection in a homogenous genetic background, by carrying out an innovative introgression scheme. By doing so, we show, for the first time, high-resolution molecular consequences of intracellular infection and offer insights into epigenetic and transcriptomic regulation of invertebrates.
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27
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Yang L, Yang Y, Liu MM, Yan ZC, Qiu LM, Fang Q, Wang F, Werren JH, Ye GY. Identification and Comparative Analysis of Venom Proteins in a Pupal Ectoparasitoid, Pachycrepoideus vindemmiae. Front Physiol 2020; 11:9. [PMID: 32038312 PMCID: PMC6993573 DOI: 10.3389/fphys.2020.00009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
Parasitoid wasps inject venom containing complex bioactive compounds to regulate the immune response and development of host arthropods and sometime paralyze host arthropods. Although extensive studies have been conducted on the identification of venom proteins in larval parasitoids, relatively few studies have examined the pupal parasitoids. In our current study, a combination of transcriptomic and proteomic methods was used to identify 64 putative venom proteins from Pachycrepoideus vindemmiae, an ectoparasitoid of Drosophila. Expression analysis revealed that 20 tested venom proteins have 419-fold higher mean expression in the venom apparatus than in other wasp tissues, indicating their specialization to venom. Comparisons of venom proteins from P. vindemmiae and other five species spanning three parasitoid families detected a core set of "ancient" orthologs in Pteromalidae. Thirty-five venom proteins of P. vindemmiae were assigned to the orthologous groups by reciprocal best matches with venoms of other pteromalids, while the remaining 29 were not. Of the 35 categories, twenty-seven have orthologous relationships with Nasonia vitripennis venom proteins and 25 with venoms of Pteromalus puparum. More distant relationships detected that five and two venom proteins of P. vindemmiae are orthologous with venoms of two Figitidae parasitoids and a Braconidae representative, respectively. Moreover, twenty-two venoms unique to P. vindemmiae were also detected, indicating considerable interspecific variation of venom proteins in parasitoids. Phylogenetic reconstruction based on a set of single-copy genes clustered P. vindemmiae with P. puparum, N. vitripennis, and other members of the family Pteromalidae. These findings provide strong evidence that P. vindemmiae venom proteins are well positioned for future functional and evolutionary studies.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Ming-Ming Liu
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhi-Chao Yan
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Li-Ming Qiu
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Gong-Yin Ye
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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28
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Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE, Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B, Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann M, Perry T, Peters RS, Poynton HC, Prpic NM, Qu J, Rotenberg D, Schal C, Schoville SD, Scully ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S. Gene content evolution in the arthropods. Genome Biol 2020; 21:15. [PMID: 31969194 PMCID: PMC6977273 DOI: 10.1186/s13059-019-1925-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/26/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. RESULTS Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. CONCLUSIONS These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
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Affiliation(s)
- Gregg W. C. Thomas
- 0000 0001 0790 959Xgrid.411377.7Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN USA
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münsterss, 48149 Münster, Germany ,0000 0001 2287 2617grid.9026.dInstitute for Bioinformatics and Chemoinformatics, University of Hamburg, Hamburg, Germany ,Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
| | - Daniel S. T. Hughes
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000000419368729grid.21729.3fPresent Address: Institute for Genomic Medicine, Columbia University, New York, NY 10032 USA
| | - Shwetha C. Murali
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000000122986657grid.34477.33Present Address: Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
| | - Monica Poelchau
- 0000 0001 2113 2895grid.483014.aNational Agricultural Library, USDA, Beltsville, MD 20705 USA
| | - Karl Glastad
- 0000 0001 2097 4943grid.213917.fSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA ,0000 0004 1936 8972grid.25879.31Present Address: Penn Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Clare A. Anstead
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Nadia A. Ayoub
- grid.268042.aDepartment of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA 24450 USA
| | - Phillip Batterham
- 0000 0001 2179 088Xgrid.1008.9School of BioSciences Science Faculty, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Michelle Bellair
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,Present Address: CooperGenomics, Houston, TX USA
| | - Greta J. Binford
- 0000 0004 1936 9043grid.259053.8Department of Biology, Lewis & Clark College, Portland, OR 97219 USA
| | - Hsu Chao
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yolanda H. Chen
- 0000 0004 1936 7689grid.59062.38Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | - Christopher Childers
- 0000 0001 2113 2895grid.483014.aNational Agricultural Library, USDA, Beltsville, MD 20705 USA
| | - Huyen Dinh
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Harsha Vardhan Doddapaneni
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jian J. Duan
- 0000 0004 0404 0958grid.463419.dBeneficial Insects Introduction Research Unit, United States Department of Agriculture, Agricultural Research Service, Newark, DE USA
| | - Shannon Dugan
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Lauren A. Esposito
- 0000 0004 0461 6769grid.242287.9Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118 USA
| | - Markus Friedrich
- 0000 0001 1456 7807grid.254444.7Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Jessica Garb
- 0000 0000 9620 1122grid.225262.3Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA 01854 USA
| | - Robin B. Gasser
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Michael A. D. Goodisman
- 0000 0001 2097 4943grid.213917.fSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Dawn E. Gundersen-Rindal
- 0000 0004 0404 0958grid.463419.dUSDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD USA
| | - Yi Han
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Alfred M. Handler
- 0000 0004 0404 0958grid.463419.dUSDA-ARS, Center for Medical, Agricultural, and Veterinary Entomology, 1700 S.W. 23rd Drive, Gainesville, FL 32608 USA
| | - Masatsugu Hatakeyama
- 0000 0001 0699 0373grid.410590.9Division of Insect Sciences, National Institute of Agrobiological Sciences, Owashi, Tsukuba, 305-8634 Japan
| | - Lars Hering
- 0000 0001 1089 1036grid.5155.4Department of Zoology, Institute of Biology, University of Kassel, 34132 Kassel, Germany
| | - Wayne B. Hunter
- 0000 0004 0404 0958grid.463419.dUSDA ARS, U. S. Horticultural Research Laboratory, Ft. Pierce, FL 34945 USA
| | - Panagiotis Ioannidis
- 0000 0001 2322 4988grid.8591.5Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland ,0000 0004 0635 685Xgrid.4834.bPresent Address: Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, Vassilika Vouton, 70013 Heraklion, Greece
| | - Joy C. Jayaseelan
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Divya Kalra
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Abderrahman Khila
- 0000 0001 2150 7757grid.7849.2Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, 69364 Lyon, France
| | - Pasi K. Korhonen
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Carol Eunmi Lee
- 0000 0001 0701 8607grid.28803.31Department of Integrative Biology, University of Wisconsin, Madison, WI 53706 USA
| | - Sandra L. Lee
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yiyuan Li
- 0000 0001 2168 0066grid.131063.6Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences, Notre Dame, IN 46556 USA
| | - Amelia R. I. Lindsey
- 0000 0001 2222 1582grid.266097.cDepartment of Entomology, University of California Riverside, Riverside, CA USA ,0000 0001 0790 959Xgrid.411377.7Present Address: Department of Biology, Indiana University, Bloomington, IN USA
| | - Georg Mayer
- 0000 0001 1089 1036grid.5155.4Department of Zoology, Institute of Biology, University of Kassel, 34132 Kassel, Germany
| | - Alistair P. McGregor
- 0000 0001 0726 8331grid.7628.bDepartment of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP UK
| | - Duane D. McKenna
- 0000 0000 9560 654Xgrid.56061.34Department of Biological Sciences, University of Memphis, 3700 Walker Ave, Memphis, TN 38152 USA
| | - Bernhard Misof
- 0000 0001 2216 5875grid.452935.cCenter for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Mala Munidasa
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Monica Munoz-Torres
- 0000 0001 2231 4551grid.184769.5Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, USA ,0000 0004 4665 2899grid.497331.bPresent Address: Phoenix Bioinformatics, 39221 Paseo Padre Parkway, Ste. J., Fremont, CA 94538 USA
| | - Donna M. Muzny
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Oliver Niehuis
- grid.5963.9Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University of Freiburg, 79104 Freiburg (Brsg.), Germany
| | - Nkechinyere Osuji-Lacy
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Subba R. Palli
- 0000 0004 1936 8438grid.266539.dDepartment of Entomology, University of Kentucky, Lexington, KY 40546 USA
| | - Kristen A. Panfilio
- 0000 0000 8809 1613grid.7372.1School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL UK
| | - Matthias Pechmann
- 0000 0000 8580 3777grid.6190.eCologne Biocenter, Zoological Institute, Department of Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Trent Perry
- 0000 0001 2179 088Xgrid.1008.9School of BioSciences Science Faculty, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ralph S. Peters
- 0000 0001 2216 5875grid.452935.cCentre of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Helen C. Poynton
- 0000 0004 0386 3207grid.266685.9School for the Environment, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Nikola-Michael Prpic
- 0000 0001 2364 4210grid.7450.6Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, Georg-August-Universität Göttingen, Göttingen, Germany ,0000 0001 2364 4210grid.7450.6Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jiaxin Qu
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Dorith Rotenberg
- 0000 0001 2173 6074grid.40803.3fDepartment of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606 USA
| | - Coby Schal
- 0000 0001 2173 6074grid.40803.3fDepartment of Entomology and W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695 USA
| | - Sean D. Schoville
- 0000 0001 2167 3675grid.14003.36Department of Entomology, University of Wisconsin-Madison, Madison, USA
| | - Erin D. Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research, Manhattan, KS 66502 USA
| | - Evette Skinner
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Daniel B. Sloan
- 0000 0004 1936 8083grid.47894.36Department of Biology, Colorado State University, Ft. Collins, CO USA
| | - Richard Stouthamer
- 0000 0001 2222 1582grid.266097.cDepartment of Entomology, University of California Riverside, Riverside, CA USA
| | - Michael R. Strand
- 0000 0004 1936 738Xgrid.213876.9Department of Entomology, University of Georgia, Athens, GA USA
| | - Nikolaus U. Szucsich
- 0000 0001 2169 5989grid.252381.fPresent Address: Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR USA
| | - Asela Wijeratne
- 0000 0000 9560 654Xgrid.56061.34Department of Biological Sciences, University of Memphis, 3700 Walker Ave, Memphis, TN 38152 USA ,0000 0001 2112 4115grid.425585.bNatural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Neil D. Young
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Eduardo E. Zattara
- 0000 0001 2112 473Xgrid.412234.2INIBIOMA, Univ. Nacional del Comahue – CONICET, Bariloche, Argentina
| | - Joshua B. Benoit
- 0000 0001 2179 9593grid.24827.3bDepartment of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Evgeny M. Zdobnov
- 0000 0001 2322 4988grid.8591.5Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland
| | - Michael E. Pfrender
- 0000 0001 2168 0066grid.131063.6Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences, Notre Dame, IN 46556 USA
| | - Kevin J. Hackett
- 0000 0004 0404 0958grid.463419.dCrop Production and Protection, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705 USA
| | - John H. Werren
- 0000 0004 1936 9174grid.16416.34Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Kim C. Worley
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Richard A. Gibbs
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Ariel D. Chipman
- 0000 0004 1937 0538grid.9619.7Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - Robert M. Waterhouse
- 0000 0001 2165 4204grid.9851.5Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münsterss, 48149 Münster, Germany ,0000 0001 2287 2617grid.9026.dInstitute for Bioinformatics and Chemoinformatics, University of Hamburg, Hamburg, Germany ,0000 0001 1014 8330grid.419495.4Department Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Matthew W. Hahn
- 0000 0001 0790 959Xgrid.411377.7Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN USA
| | - Stephen Richards
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000 0004 1936 9684grid.27860.3bPresent Address: UC Davis Genome Center, University of California, Davis, CA 95616 USA
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29
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Rago A, Werren JH, Colbourne JK. Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis. PLoS Genet 2020; 16:e1008518. [PMID: 31986136 PMCID: PMC7004391 DOI: 10.1371/journal.pgen.1008518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 02/06/2020] [Accepted: 11/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sexual dimorphism requires regulation of gene expression in developing organisms. These developmental differences are caused by differential expression of genes and isoforms. The effect of expressing a gene is also influenced by which other genes are simultaneously expressed (functional interactions). However, few studies have described how these processes change across development. We compare the dynamics of differential expression, isoform switching and functional interactions in the sexual development of the model parasitoid wasp Nasonia vitripennis, a system that permits genome wide analysis of sex bias from early embryos to adults. We find relatively little sex-bias in embryos and larvae at the gene level, but several sub-networks show sex-biased functional interactions in early developmental stages. These networks provide new candidates for hymenopteran sex determination, including histone modification. In contrast, sex-bias in pupae and adults is driven by the differential expression of genes. We observe sex-biased isoform switching consistently across development, but mostly in genes that are already differentially expressed. Finally, we discover that sex-biased networks are enriched by genes specific to the Nasonia clade, and that those genes possess the topological properties of key regulators. These findings suggest that regulators in sex-biased networks evolve more rapidly than regulators of other developmental networks.
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Affiliation(s)
- Alfredo Rago
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY, United States of America
| | - John K. Colbourne
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
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30
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Sharko FS, Nedoluzhko AV, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen'ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG. A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum. PLoS One 2019; 14:e0226485. [PMID: 31869362 PMCID: PMC6927652 DOI: 10.1371/journal.pone.0226485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect-the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, compared to other chalcid wasps the gene content of M. amalphitanum is remarkably conserved. Intriguingly, we observed significant changes in M. amalphitanum transposable element dynamics over time, in which an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Overall, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.
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Affiliation(s)
- Fedor S. Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Artem V. Nedoluzhko
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Nord University, Faculty of Biosciences and Aquaculture, Bodø, Norway
| | - Brandon M. Lê
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | | | | | | | - Alexey S. Sokolov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Alexander M. Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Polilov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Irina R. Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Egor B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Konstantin G. Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
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31
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Martinson EO, Siebert AL, He M, Kelkar YD, Doucette LA, Werren JH. Evaluating the evolution and function of the dynamic Venom Y protein in ectoparasitoid wasps. INSECT MOLECULAR BIOLOGY 2019; 28:499-508. [PMID: 30636014 PMCID: PMC6606371 DOI: 10.1111/imb.12565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Venom of the parasitoid wasp Nasonia vitripennis changes the metabolism and gene expression in its fly host Sarcophaga bullata to induce developmental arrest, suppression of the immune response and various other venom effects. Yet, the venom of ectoparasitoid wasps has not been fully characterized. A major component of N. vitripennis venom is an uncharacterized, high-expressing protein referred to as Venom Y. Here we describe the evolutionary history and possible functions of this venom protein. We found that Venom Y is a relatively young gene that has duplicated to form two distinct paralogue groups. A copy of Venom Y has been recruited as a venom protein in at least five wasp species. Functional analysis found that Venom Y affects detoxification and immunity genes in envenomated fly hosts. Many of these genes are fat-body specific, suggesting that Venom Y may have a targeted effect on fat body tissue. We also show that Venom Y may mitigate negative effects of other venom proteins. Finally, protein sequencing indicates that Venom Y is post-translationally modified. This study contributes to elucidating parasitoid venom by using RNA interference knockdown to investigate venom protein function in the context of the whole venom cocktail.
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Affiliation(s)
- Ellen O. Martinson
- Biology Department, University of Rochester, Rochester, NY 14627 USA
- Current Address: Department of Entomology, University of Georgia, Athens, Georgia 30602 USA
| | - Aisha L. Siebert
- Translational Biomedical Science Department, University of Rochester School of Medicine and Dentistry, Rochester NY 14627 USA
- Current Address: Department of Urology, Northwestern University, Chicago, IL 60611 USA
| | - Mengni He
- Biology Department, University of Rochester, Rochester, NY 14627 USA
- Current Address: Johns Hopkins University, Baltimore, MD 21218 USA
| | | | - Luticha A. Doucette
- Biology Department, University of Rochester, Rochester, NY 14627 USA
- Current Address: Mayor’s Office of Innovation, Rochester, NY 14614 USA
| | - John H. Werren
- Biology Department, University of Rochester, Rochester, NY 14627 USA
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32
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Segar ST, Volf M, Sisol M, Pardikes NA, Souto-Vilarós D. Chemical cues and genetic divergence in insects on plants: conceptual cross pollination between mutualistic and antagonistic systems. CURRENT OPINION IN INSECT SCIENCE 2019; 32:83-90. [PMID: 31113637 DOI: 10.1016/j.cois.2018.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/20/2018] [Accepted: 11/25/2018] [Indexed: 06/09/2023]
Abstract
Cascading or reciprocal genetic diversification of herbivores, parasitoids, and pollinators can track chemotypic variation in host resources, and can lead to non-overlapping communities. Because plants simultaneously interact with both pollinators and herbivores, models investigating the genetic divergence of antagonistic herbivores and mutualistic pollinators should be merged in order to study how both processes interact using a common conceptual and methodological approach. We expect insects to mediate divergence in many systems, with outcomes depending on the level of pollinator or herbivore specialisation, and the relative selective pressures they impose. Applying approaches widely used to study insect pollinators, for example genomic tools and integration of behavioural, genetic and chemical data, to both pollinators and herbivores in the same system will facilitate our understanding of patterns of genetic divergence across multiple interacting species.
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Affiliation(s)
- Simon T Segar
- Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic; Department of Crop and Environment Sciences, Harper Adams University, UK.
| | - Martin Volf
- Molecular Interaction Ecology Group, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Mentap Sisol
- New Guinea Binatang Research Centre, Madang, Papua New Guinea
| | | | - Daniel Souto-Vilarós
- Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
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33
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Tvedte ES, Logsdon JM, Forbes AA. Sex loss in insects: causes of asexuality and consequences for genomes. CURRENT OPINION IN INSECT SCIENCE 2019; 31:77-83. [PMID: 31109677 DOI: 10.1016/j.cois.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/03/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Boasting a staggering diversity of reproductive strategies, insects provide attractive models for the comparative study of the causes and consequences of transitions to asexuality. We provide an overview of some contemporary studies of reproductive systems in insects and compile an initial database of asexual insect genome resources. Insect systems have already yielded some important insights into various mechanisms by which sex is lost, including genetic, endosymbiont-mediated, and hybridization. Studies of mutation and substitution after loss of sex provide the strongest empirical support for hypothesized effects of asexuality, whereas there is mixed evidence for ecological hypotheses such as increased parasite load and altered niche breadth in asexuals. Most hypotheses have been explored in a select few taxa (e.g. stick insects, aphids), such that much of the great taxonomic breadth of insects remain understudied. Given the variation in the proximate causes of asexuality in insects, we argue for expanding the taxonomic breadth of study systems. Despite some challenges for investigating sex in insects, the increasing cost-effectiveness of genomic sequencing makes data generation for closely-related asexual and sexual lineages increasingly feasible.
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Affiliation(s)
- Eric S Tvedte
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States.
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA, United States
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34
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Minelli A, Fusco G. No limits: Breaking constraints in insect miniaturization. ARTHROPOD STRUCTURE & DEVELOPMENT 2019; 48:4-11. [PMID: 30496889 DOI: 10.1016/j.asd.2018.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 06/09/2023]
Abstract
Small arthropods are not simply scaled-down versions of their larger closest relatives, as changes in morphology and functional characters are largely governed by scaling laws. These same scaling laws set strict limits to size change toward smaller sizes. The evolution of extreme miniaturized forms involves the breaking of these constraints, by means of design innovations that allow evolutionary change to evade the limits posed by scaling laws. Here we review several cases studies in insects and other arthropods that illustrate this evolutionary path. We examine morphologies commonly recurring in miniaturized forms but not exclusive to them, morphologies exclusive to miniaturized forms and novel functional solutions supported by unconventional morphologies. We also discuss miniaturization and its evolvability taking into consideration arthropod postembryonic development and modular body organization. The modification of features commonly supposed not to change appears as a recurring pattern in arthropod miniaturization.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via Ugo Bassi 58B, I 35131, Padova, Italy.
| | - Giuseppe Fusco
- Department of Biology, University of Padova, Via Ugo Bassi 58B, I 35131, Padova, Italy.
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Jeong H, Wu X, Smith B, Yi SV. Genomic Landscape of Methylation Islands in Hymenopteran Insects. Genome Biol Evol 2018; 10:2766-2776. [PMID: 30239702 PMCID: PMC6195173 DOI: 10.1093/gbe/evy203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2018] [Indexed: 01/31/2023] Open
Abstract
Recent genome-wide DNA methylation analyses of insect genomes accentuate an intriguing contrast compared with those in mammals. In mammals, most CpGs are heavily methylated, with the exceptions of clusters of hypomethylated sites referred to as CpG islands. In contrast, DNA methylation in insects is localized to a small number of CpG sites. Here, we refer to clusters of methylated CpGs as “methylation islands (MIs),” and investigate their characteristics in seven hymenopteran insects with high-quality bisulfite sequencing data. Methylation islands were primarily located within gene bodies. They were significantly overrepresented in exon–intron boundaries, indicating their potential roles in splicing. Methylated CpGs within MIs exhibited stronger evolutionary conservation compared with those outside of MIs. Additionally, genes harboring MIs exhibited higher and more stable levels of gene expression compared with those that do not harbor MIs. The effects of MIs on evolutionary conservation and gene expression are independent and stronger than the effect of DNA methylation alone. These results indicate that MIs may be useful to gain additional insights into understanding the role of DNA methylation in gene expression and evolutionary conservation in invertebrate genomes.
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Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Xin Wu
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Brandon Smith
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
| | - Soojin V Yi
- School of Biological Sciences, Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
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