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Zou M, Lin A, Wang Y, Yang D, Liu X. The chromosome-level genome assembly of the giant dobsonfly Acanthacorydalis orientalis (McLachlan, 1899). Sci Data 2024; 11:351. [PMID: 38589366 PMCID: PMC11001986 DOI: 10.1038/s41597-024-03194-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
Acanthacorydalis orientalis (McLachlan, 1899) (Megaloptera: Corydalidae) is an important freshwater-benthic invertebrate species that serves as an indicator for water-quality biomonitoring and is valuable for conservation from East Asia. Here, a high-quality reference genome for A. orientalis was constructed using Oxford Nanopore sequencing and High throughput Chromosome Conformation Capture (Hi-C) technology. The final genome size is 547.98 Mb, with the N50 values of contig and scaffold being 7.77 Mb and 50.53 Mb, respectively. The longest contig and scaffold are 20.57 Mb and 62.26 Mb in length, respectively. There are 99.75% contigs anchored onto 13 pseudo-chromosomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed that the completeness of the genome assembly is 99.01%. There are 10,977 protein-coding genes identified, of which 84.00% are functionally annotated. The genome contains 44.86% repeat sequences. This high-quality genome provides substantial data for future studies on population genetics, aquatic adaptation, and evolution of Megaloptera and other related insect groups.
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Affiliation(s)
- Mingming Zou
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Aili Lin
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, China.
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Hoffmann M, Gardein H, Greil H, Erler S. Anatomical, phenological and genetic aspects of the host-parasite relationship between Andrena vaga (Hymenoptera) and Stylops ater (Strepsiptera). Parasitology 2023; 150:744-753. [PMID: 37157059 PMCID: PMC10410535 DOI: 10.1017/s0031182023000483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/10/2023]
Abstract
Stylops ater is an endoparasite of the mining bee Andrena vaga with extreme sexual dimorphism and hypermetamorphosis. Its population structure, parasitization mode, genetic diversity and impact on host morphology were examined in nesting sites in Germany to better understand this highly specialized host–parasite interaction. The shift in host emergence due to stylopization was proven to be especially strong in A. vaga. Around 10% of bees hosted more than 1 Stylops, with at maximum 4. A trend in Stylops' preference for hosts of their own sex and a sex-specific position of extrusion from the host abdomen was found. Invasion of Andrena eggs by Stylops primary larvae was depicted for the first time. Cephalothoraces of female Stylops were smaller in male and pluristylopized hosts, likely due to lower nutrient supply. The genes H3, 18S and cytochrome c oxidase subunit 1 were highly conserved, revealing near-absence of local variation within Stylops. Ovaries of hosts with male Stylops contained poorly developed eggs while those of hosts with female Stylops were devoid of visible eggs, which might be due to a higher protein demand of female Stylops. Male Stylops, which might have a more energy-consuming development, led to a reduction in head width of their hosts. Host masculinization was present in the leaner shape of the metabasitarsus of stylopized females and is interpreted as a by-product of manipulation of the host's endocrine system to shift its emergence. Stylopization intensified tergal hairiness, most strongly in hosts with female Stylops, near the point of parasite extrusion, hinting towards substance-induced host manipulation.
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Affiliation(s)
- Marc Hoffmann
- Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- Institute for Bee Protection, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Hanna Gardein
- Institute for Bee Protection, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Henri Greil
- Institute for Bee Protection, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Silvio Erler
- Institute for Bee Protection, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
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Jaron KS, Parker DJ, Anselmetti Y, Tran Van P, Bast J, Dumas Z, Figuet E, François CM, Hayward K, Rossier V, Simion P, Robinson-Rechavi M, Galtier N, Schwander T. Convergent consequences of parthenogenesis on stick insect genomes. Sci Adv 2022; 8:eabg3842. [PMID: 35196080 PMCID: PMC8865771 DOI: 10.1126/sciadv.abg3842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated reference genomes for five independently evolved parthenogenetic species in the stick insect genus Timema and their closest sexual relatives. Using these references and population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, suggesting that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Parthenogenetic species did not show increased transposable element (TE) accumulation, likely because there is little TE activity in the genus. By using replicated sexual-parthenogenetic comparisons, our study reveals how the absence of sex affects genome evolution in natural populations, providing empirical support for the negative consequences of parthenogenesis as predicted by theory.
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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
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | - Darren J. Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | | | - Patrick Tran Van
- 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
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emeric Figuet
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | | | - Keith Hayward
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Victor Rossier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
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de Almeida LH, Bispo PDC. Perlidae (Plecoptera) from the Paranapiacaba Mountains, Atlantic Forest, Brazil: Diversity and implications of the integrative approach and teneral specimens on taxonomy. PLoS One 2020; 15:e0243393. [PMID: 33301489 PMCID: PMC7728281 DOI: 10.1371/journal.pone.0243393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/20/2020] [Indexed: 11/18/2022] Open
Abstract
The study of complementary sources of biological variation (e.g. morphological, molecular) has allowed a better understanding of biodiversity through the construction of an integrative taxonomy. Using this approach, specimens from the Paranapiacaba Mountains, southeastern Brazil, were studied to update the knowledge on the stonefly family Perlidae from the region, characterize the species, and make associations between nymphs and adults using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. The study also discusses the implications of integrative taxonomy and teneral specimens for the study of South American Perlidae. The molecular data were analyzed using Bayesian inference, Neighbor-joining, and delimiting species methods. Our results revealed that, in general, there was a morphological and molecular congruence between species. In the Paranapiacaba Mountains, three genera and 15 species were recorded: Anacroneuria boraceiensis Froehlich 2004, A. debilis (Pictet 1841) (new record), A. fiorentini De Ribeiro and Froehlich 2007 (new record), A. flintorum Froehlich 2002, A. iporanga Bispo and Froehlich 2004, A. itajaimirim Bispo and Froehlich 2004, A. polita (Burmeister 1913), A. subcostalis Klapálek 1921, A. tupi Bispo and Froehlich 2004 (with a description of the nymph), Kempnyia auberti Froehlich 1996, K. colossica (Navás 1934), K. flava Klapálek 1916, K. neotropica (Jacobson and Bianchi 1905) (including its new junior synonym K. petersorum Froehlich 1996), Kempnyia sp., and Macrogynoplax veneranda Froehlich 1984. COI sequences were obtained for 11 species, five of which had nymphs associated with adults. Among the five associated nymphs, the nymph of A. tupi is described here. The results of this study indicate that the color of adult teneral specimens differs from that of mature specimens. Given this, the synonym of K. neotropica and K. petersorum was proposed since these species have high morphological and molecular similarities and differ only in color patterns. In addition, the previous record of A. petersi Froehlich 2002 from the Paranapiacaba Mountains was invalidated since it was considered a teneral specimen of A. flintorum. These results suggest that the development of an integrative taxonomy is essential to continue advancing the study of Perlidae diversity in South America.
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Affiliation(s)
- Lucas Henrique de Almeida
- Programa de Pós-Graduação em Entomologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Laboratório de Biologia Aquática, Departamento de Ciências Biológicas, Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista, Assis, São Paulo, Brazil
- * E-mail:
| | - Pitágoras da Conceição Bispo
- Laboratório de Biologia Aquática, Departamento de Ciências Biológicas, Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista, Assis, São Paulo, Brazil
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Gamboa M. Hemocyanin and hexamerins expression in response to hypoxia in stoneflies (Plecoptera, Insecta). Arch Insect Biochem Physiol 2020; 105:e21743. [PMID: 32979236 DOI: 10.1002/arch.21743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Many freshwater ecosystems worldwide undergo hypoxia events that can trigger physiological, behavioral, and molecular responses in many organisms. Among such molecular responses, the regulation of the hemocyanin (Hc) protein expression which plays a major role in oxygen transportation within aquatic insects remains poorly understood. The stoneflies (Plecoptera) are aquatic insects that possess a functional Hc in the hemolymph similar to crustacean that co-occurs with a nonfunctional Hc protein, hexamerins (Hx). However, the role of both proteins during hypoxia remains undetermined. Here, we evaluated the effect of hypoxia on the expression of Hc and Hx proteins via a comparison between hypoxia and normoxia amino acid sequence variation and protein expression pattern within 23 stonefly species. We induced short-term hypoxia in wild-caught stoneflies species, sequenced the target region of Hc and Hx by complementary DNA synthesis, characterized the protein biochemistry using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, ultrafiltration, and polarographic fluorometric method, and amplified the genome region of the hypoxia-inducible factor (HIF) transcriptional response element that regulated Hc using genome walking library approach. We found a lack of Hc expression in all examined species during hypoxia conditions, despite recognition of the HIF gene region as a possible regulatory factor of Hc, suggesting that compensatory responses as metabolic changes or behavioral tracheal movements to enhance respiratory efficiency could be possible mechanics to compensate for hypoxia. A short Hc-like novel isoform was detected instead in these 23 species, possibly due to either protein degradation or alternative splicing mechanisms, suggesting that the protein could be performing a different function other than oxygen transportation. Hx during hypoxia was expressed and exhibited species-level amino acid changes, highlighting a possible role during hypoxia. Our results demonstrate that hypoxia could enable a similar potential adaptive response of multiple species regarding specific physiological requirements, thereby shedding light on community behavior in stress environments that may help us to improve conservation practices and biomonitoring.
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Affiliation(s)
- Maribet Gamboa
- Department of Civil and Environmental Engineering, Faculty of Engineering, Ehime University, Matsuyama, Japan
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Abstract
Neuropeptides are among the structurally most diverse signaling molecules and participate in intercellular information transfer from neurotransmission to intrinsic or extrinsic neuromodulation. Many of the peptidergic systems have a very ancient origin that can be traced back to the early evolution of the Metazoa. In recent years, new insights into the evolution of these peptidergic systems resulted from the increasing availability of genome and transcriptome data which facilitated the investigation of the complete neuropeptide precursor sequences. Here we used a comprehensive transcriptome dataset of about 200 species from the 1KITE initiative to study the evolution of single-copy neuropeptide precursors in Polyneoptera. This group comprises well-known orders such as cockroaches, termites, locusts, and stick insects. Due to their phylogenetic position within the insects and the large number of old lineages, these insects are ideal candidates for studying the evolution of insect neuropeptides and their precursors. Our analyses include the orthologs of 21 single-copy neuropeptide precursors, namely ACP, allatotropin, AST-CC, AST-CCC, CCAP, CCHamide-1 and 2, CNMamide, corazonin, CRF-DH, CT-DH, elevenin, HanSolin, NPF-1 and 2, MS, proctolin, RFLamide, SIFamide, sNPF, and trissin. Based on the sequences obtained, the degree of sequence conservation between and within the different polyneopteran lineages is discussed. Furthermore, the data are used to postulate the individual neuropeptide sequences that were present at the time of the insect emergence more than 400 million years ago. The data confirm that the extent of sequence conservation across Polyneoptera is remarkably different between the different neuropeptides. Furthermore, the average evolutionary distance for the single-copy neuropeptides differs significantly between the polyneopteran orders. Nonetheless, the single-copy neuropeptide precursors of the Polyneoptera show a relatively high degree of sequence conservation. Basic features of these precursors in this very heterogeneous insect group are explained here in detail for the first time.
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Wu M, Walser JC, Sun L, Kölliker M. The genetic mechanism of selfishness and altruism in parent-offspring coadaptation. Sci Adv 2020; 6:eaaw0070. [PMID: 31922000 PMCID: PMC6941917 DOI: 10.1126/sciadv.aaw0070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 11/07/2019] [Indexed: 05/04/2023]
Abstract
The social bond between parents and offspring is characterized by coadaptation and balance between altruistic and selfish tendencies. However, its underlying genetic mechanism remains poorly understood. Using transcriptomic screens in the subsocial European earwig, Forficula auricularia, we found the expression of more than 1600 genes associated with experimentally manipulated parenting. We identified two genes, Th and PebIII, each showing evidence of differential coexpression between treatments in mothers and their offspring. In vivo RNAi experiments confirmed direct and indirect genetic effects of Th and PebIII on behavior and fitness, including maternal food provisioning and reproduction, and offspring development and survival. The direction of the effects consistently indicated a reciprocally altruistic function for Th and a reciprocally selfish function for PebIII. Further metabolic pathway analyses suggested roles for Th-restricted endogenous dopaminergic reward, PebIII-mediated chemical communication and a link to insulin signaling, juvenile hormone, and vitellogenin in parent-offspring coadaptation and social evolution.
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Affiliation(s)
- Min Wu
- Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland
- Corresponding author. (M.W.); (M.K.)
| | - Jean-Claude Walser
- Department of Environmental Systems Science, Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland
| | - Lei Sun
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Mathias Kölliker
- Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland
- Corresponding author. (M.W.); (M.K.)
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8
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Song N, Li X, Yin X, Li X, Yin J, Pan P. The mitochondrial genomes of palaeopteran insects and insights into the early insect relationships. Sci Rep 2019; 9:17765. [PMID: 31780743 PMCID: PMC6883079 DOI: 10.1038/s41598-019-54391-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/13/2019] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic relationships of basal insects remain a matter of discussion. In particular, the relationships among Ephemeroptera, Odonata and Neoptera are the focus of debate. In this study, we used a next-generation sequencing approach to reconstruct new mitochondrial genomes (mitogenomes) from 18 species of basal insects, including six representatives of Ephemeroptera and 11 of Odonata, plus one species belonging to Zygentoma. We then compared the structures of the newly sequenced mitogenomes. A tRNA gene cluster of IMQM was found in three ephemeropteran species, which may serve as a potential synapomorphy for the family Heptageniidae. Combined with published insect mitogenome sequences, we constructed a data matrix with all 37 mitochondrial genes of 85 taxa, which had a sampling concentrating on the palaeopteran lineages. Phylogenetic analyses were performed based on various data coding schemes, using maximum likelihood and Bayesian inferences under different models of sequence evolution. Our results generally recovered Zygentoma as a monophyletic group, which formed a sister group to Pterygota. This confirmed the relatively primitive position of Zygentoma to Ephemeroptera, Odonata and Neoptera. Analyses using site-heterogeneous CAT-GTR model strongly supported the Palaeoptera clade, with the monophyletic Ephemeroptera being sister to the monophyletic Odonata. In addition, a sister group relationship between Palaeoptera and Neoptera was supported by the current mitogenomic data.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xinxin Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinghao Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jian Yin
- Xinyang Agriculture and Forestry University, Xinyang, 464001, China
| | - Pengliang Pan
- Xinyang Agriculture and Forestry University, Xinyang, 464001, China
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Andrikou C, Thiel D, Ruiz-Santiesteban JA, Hejnol A. Active mode of excretion across digestive tissues predates the origin of excretory organs. PLoS Biol 2019; 17:e3000408. [PMID: 31356592 PMCID: PMC6687202 DOI: 10.1371/journal.pbio.3000408] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/08/2019] [Accepted: 07/12/2019] [Indexed: 11/21/2022] Open
Abstract
Most bilaterian animals excrete toxic metabolites through specialized organs, such as nephridia and kidneys, which share morphological and functional correspondences. In contrast, excretion in non-nephrozoans is largely unknown, and therefore the reconstruction of ancestral excretory mechanisms is problematic. Here, we investigated the excretory mode of members of the Xenacoelomorpha, the sister group to Nephrozoa, and Cnidaria, the sister group to Bilateria. By combining gene expression, inhibitor experiments, and exposure to varying environmental ammonia conditions, we show that both Xenacoelomorpha and Cnidaria are able to excrete across digestive-associated tissues. However, although the cnidarian Nematostella vectensis seems to use diffusion as its main excretory mode, the two xenacoelomorphs use both active transport and diffusion mechanisms. Based on these results, we propose that digestive-associated tissues functioned as excretory sites before the evolution of specialized organs in nephrozoans. We conclude that the emergence of a compact, multiple-layered bilaterian body plan necessitated the evolution of active transport mechanisms, which were later recruited into the specialized excretory organs.
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Affiliation(s)
- Carmen Andrikou
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Daniel Thiel
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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Wipfler B, Letsch H, Frandsen PB, Kapli P, Mayer C, Bartel D, Buckley TR, Donath A, Edgerly-Rooks JS, Fujita M, Liu S, Machida R, Mashimo Y, Misof B, Niehuis O, Peters RS, Petersen M, Podsiadlowski L, Schütte K, Shimizu S, Uchifune T, Wilbrandt J, Yan E, Zhou X, Simon S. Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proc Natl Acad Sci U S A 2019; 116:3024-3029. [PMID: 30642969 PMCID: PMC6386694 DOI: 10.1073/pnas.1817794116] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.
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Affiliation(s)
- Benjamin Wipfler
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Harald Letsch
- Department für Botanik und Biodiversitätsforschung, Universität Wien, 1030 Vienna, Austria
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84604
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Daniela Bartel
- Department of Integrative Zoology, Universität Wien, 1090 Vienna, Austria
| | - Thomas R Buckley
- New Zealand Arthropod Collection, Manaaki Whenua - Landcare Research, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Janice S Edgerly-Rooks
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA 95053
| | - Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Yuta Mashimo
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Oliver Niehuis
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, 79104 Freiburg, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kai Schütte
- Tierökologie und Naturschutz, Universität Hamburg, 20146 Hamburg, Germany
| | - Shota Shimizu
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Toshiki Uchifune
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
- Yokosuka City Museum, Fukadadai, Kanagawa 238-0016, Japan
| | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Evgeny Yan
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Borissiak Palaeontological Institute, Russian Academy of Sciences, 123 Moscow, Russia
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100083, China
| | - Sabrina Simon
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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Wan Y, Yuan G, He B, Xu B, Xie W, Wang S, Zhang Y, Wu Q, Zhou X. Foccα6, a truncated nAChR subunit, positively correlates with spinosad resistance in the western flower thrips, Frankliniella occidentalis (Pergande). Insect Biochem Mol Biol 2018; 99:1-10. [PMID: 29753712 DOI: 10.1016/j.ibmb.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/07/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs), a molecular target for spinosyns and neonicotinoids, mediate rapid cholinergic transmission in insect central nervous system by binding acetylcholine. Previous studies have shown that mutations in nAChRs contribute to the high level of resistance to these two classes of insecticides. In this study, we identified nine nAChR subunits from a transcriptome of the western flower thrips, Frankliniella occidentalis, including α1-7, β1, and β2. Exon 4 of α4 and exons 3 and 8 of α6 each have two splicing variants, respectively. In addition, altered or incorrect splicing leads to truncated forms of α3, α5, and α6 subunits. The abundance of every nAChRs in both spinosad susceptible and resistant strains was highest in the 1st instar nymph. Significantly more truncated forms of α6 subunit were detected in spinosad resistant strains, whereas, hardly any full-length form was found in the two highly resistant F. occidentalis strains (resistance ratio >104-fold). Under laboratory conditions, spinosad resistance was positively correlated with truncated α6 transcripts. The correlation was later confirmed under the field conditions using five field strains. As the molecular target of spinosad, the percentage of truncated nAChR α6 subunits can be used as a diagnostic tool to detect and quantify spinosad resistance in the field.
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Affiliation(s)
- Yanran Wan
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guangdi Yuan
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bingqing He
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Baoyun Xu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA.
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Song N, Lin A, Zhao X. Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data. PLoS One 2018; 13:e0191826. [PMID: 29381758 PMCID: PMC5790268 DOI: 10.1371/journal.pone.0191826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/11/2018] [Indexed: 01/21/2023] Open
Abstract
It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Aili Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xincheng Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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Wu C, Twort VG, Crowhurst RN, Newcomb RD, Buckley TR. Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction. BMC Genomics 2017; 18:884. [PMID: 29145825 PMCID: PMC5691397 DOI: 10.1186/s12864-017-4245-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/31/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. RESULTS The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. CONCLUSIONS The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.
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Affiliation(s)
- Chen Wu
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Victoria G. Twort
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- Department of Biology, Lund University, Lund, Sweden
| | - Ross N. Crowhurst
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R. Buckley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
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Song N, Li H, Song F, Cai W. Molecular phylogeny of Polyneoptera (Insecta) inferred from expanded mitogenomic data. Sci Rep 2016; 6:36175. [PMID: 27782189 PMCID: PMC5080581 DOI: 10.1038/srep36175] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/06/2016] [Indexed: 02/02/2023] Open
Abstract
The Polyneoptera represents one of the earliest insect radiations, comprising the majority of hemimetabolous orders, in which many species have great economic importance. Here, we sequenced eleven mitochondrial genomes of the polyneopteran insects by using high throughput pooled sequencing technology, and presented a phylogenetic reconstruction for this group based on expanded mitochondrial genome data. Our analyses included 189 taxa, of which 139 species represent all the major polyneopteran lineages. Multiple results support the monophyly of Polyneoptera, the monophyly of Dictyoptera, and the monophyly of Orthoptera. Sister taxon relationships Plecoptera + Dermaptera, and Zoraptera + Embioptera are also supported by most analyses. Within Dictyoptera, the Blattodea is consistently retrieved as paraphyly due to the sister group relationship of Cryptocercus with Isoptera. In addition, the results demonstrate that model selection, data treatment, and outgroup choice can have significant effects on the reconstructed phylogenetic relationships of Polyneoptera.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Fan Song
- Department of Entomology, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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