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Choi SS, Mc Cartney A, Park D, Roberts H, Brav-Cubitt T, Mitchell C, Buckley TR. Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects. Mol Ecol 2024:e17422. [PMID: 38842022 DOI: 10.1111/mec.17422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 04/17/2024] [Indexed: 06/07/2024]
Abstract
During hybrid speciation, homoeologues combine in a single genome. Homoeologue expression bias (HEB) occurs when one homoeologue has higher gene expression than another. HEB has been well characterized in plants but rarely investigated in animals, especially invertebrates. Consequently, we have little idea as to the role that HEB plays in allopolyploid invertebrate genomes. If HEB is constrained by features of the parental genomes, then we predict repeated evolution of similar HEB patterns among hybrid genomes formed from the same parental lineages. To address this, we reconstructed the history of hybridization between the New Zealand stick insect genera Acanthoxyla and Clitarchus using a high-quality genome assembly from Clitarchus hookeri to call variants and phase alleles. These analyses revealed the formation of three independent diploid and triploid hybrid lineages between these genera. RNA sequencing revealed a similar magnitude and direction of HEB among these hybrid lineages, and we observed that many enriched functions and pathways were also shared among lineages, consistent with repeated evolution due to parental genome constraints. In most hybrid lineages, a slight majority of the genes involved in mitochondrial function showed HEB towards the maternal homoeologues, consistent with only weak effects of mitonuclear incompatibility. We also observed a proteasome functional enrichment in most lineages and hypothesize this may result from the need to maintain proteostasis in hybrid genomes. Reference bias was a pervasive problem, and we caution against relying on HEB estimates from a single parental reference genome.
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Affiliation(s)
- Seung-Sub Choi
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Ann Mc Cartney
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Duckchul Park
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Hester Roberts
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
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2
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Bidoli C, Miccoli A, Buonocore F, Fausto AM, Gerdol M, Picchietti S, Scapigliati G. Transcriptome Analysis Reveals Early Hemocyte Responses upon In Vivo Stimulation with LPS in the Stick Insect Bacillus rossius (Rossi, 1788). INSECTS 2022; 13:insects13070645. [PMID: 35886821 PMCID: PMC9316843 DOI: 10.3390/insects13070645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Non-model insect species such as B. rossius suffer from a profound gap of knowledge regarding the temporal progression of physiological responses following the challenge with bacterial pathogens or cell wall components thereof. The reason for this mostly lies in the lack of genomic/transcriptomic resources, which would provide an unparalleled in-depth capacity in the analysis of molecular, biochemical, and metabolic mechanisms. We present a high-quality transcriptome obtained from high-coverage sequencing of hemocytes harvested from adult stick insect specimens both pre- and post-LPS stimulation. Such a resource served as the basis for a stringent differential gene expression and functional enrichment analyses, the results of which were characterized and discussed in depth. Selected transcripts encoding for C-type lectins and ML-domain containing proteins were further investigated from a phylogenetic perspective. Overall, these findings shed light on the physiological responses driven by a short-term LPS stimulation in the European stick insect. Abstract Despite a growing number of non-model insect species is being investigated in recent years, a greater understanding of their physiology is prevented by the lack of genomic resources. This is the case of the common European stick insect Bacillus rossius (Rossi, 1788): in this species, some knowledge is available on hemocyte-related defenses, but little is known about the physiological changes occurring in response to natural or experimental challenges. Here, the transcriptional signatures of adult B. rossius hemocytes were investigated after a short-term (2 h) LPS stimulation in vivo: a total of 2191 differentially expressed genes, mostly involved in proteolysis and carbohydrate and lipid metabolic processes, were identified in the de novo assembled transcriptome and in-depth discussed. Overall, the significant modulation of immune signals—such as C-type lectins, ML domain-containing proteins, serpins, as well as Toll signaling-related molecules—provide novel information on the early progression of LPS-induced responses in B. rossius.
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Affiliation(s)
- Carlotta Bidoli
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (C.B.); (M.G.)
| | - Andrea Miccoli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
- Correspondence:
| | - Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (C.B.); (M.G.)
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (F.B.); (A.M.F.); (S.P.); (G.S.)
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3
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Sakamoto T, Sasaki S, Yamaguchi N, Nakano M, Sato H, Iwabuchi K, Tabunoki H, Simpson RJ, Bono H. De novo transcriptome analysis for examination of the nutrition metabolic system related to the evolutionary process through which stick insects gain the ability of flight (Phasmatodea). BMC Res Notes 2021; 14:182. [PMID: 33985569 PMCID: PMC8120901 DOI: 10.1186/s13104-021-05600-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/05/2021] [Indexed: 12/02/2022] Open
Abstract
Objective Insects are the most evolutionarily successful groups of organisms, and this success is largely due to their flight ability. Interestingly, some stick insects have lost their flight ability despite having wings. To elucidate the shift from wingless to flying forms during insect evolution, we compared the nutritional metabolism system among flight-winged, flightless-winged, and flightless-wingless stick insect groups. Results Here, we report RNA sequencing of midgut transcriptome of Entoria okinawaensis, a prominent Japanese flightless-wingless stick insect, and the comparative analysis of its transcriptome in publicly available midgut transcriptomes obtained from seven stick insect species. A gene enrichment analysis for differentially expressed genes, including those obtained from winged vs wingless and flight vs flightless genes comparisons, revealed that carbohydrate metabolic process-related genes were highly expressed in the winged stick insect group. We also found that the expression of the mitochondrial enolase superfamily member 1 transcript was significantly higher in the winged stick insect group than in the wingless stick insect group. Our findings could indicate that carbohydrate metabolic processes are related to the evolutionary process through which stick insects gain the ability of flight. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05600-0.
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Affiliation(s)
- Takuma Sakamoto
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.,Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Shunya Sasaki
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Nobuki Yamaguchi
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Miho Nakano
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Hiroki Sato
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Kikuo Iwabuchi
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Hiroko Tabunoki
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.,Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Richard J Simpson
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, VIC, 3086, Australia
| | - Hidemasa Bono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, 411-8540, Japan. .,Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.
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4
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Wu C, Twort VG, Newcomb RD, Buckley TR. Divergent Gene Expression Following Duplication of Meiotic Genes in the Stick Insect Clitarchus hookeri. Genome Biol Evol 2021; 13:6245840. [PMID: 33885769 DOI: 10.1093/gbe/evab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 01/02/2023] Open
Abstract
Some animal groups, such as stick insects (Phasmatodea), have repeatedly evolved alternative reproductive strategies, including parthenogenesis. Genomic studies have found modification of the genes underlying meiosis exists in some of these animals. Here we examine the evolution of copy number, evolutionary rate, and gene expression in candidate meiotic genes of the New Zealand geographic parthenogenetic stick insect Clitarchus hookeri. We characterized 101 genes from a de novo transcriptome assembly from female and male gonads that have homology with meiotic genes from other arthropods. For each gene we determined copy number, the pattern of gene duplication relative to other arthropod orthologs, and the potential for meiosis-specific expression. There are five genes duplicated in C. hookeri, including one also duplicated in the stick insect Timema cristinae, that are not or are uncommonly duplicated in other arthropods. These included two sister chromatid cohesion associated genes (SA2 and SCC2), a recombination gene (HOP1), an RNA-silencing gene (AGO2) and a cell-cycle regulation gene (WEE1). Interestingly, WEE1 and SA2 are also duplicated in the cyclical parthenogenetic aphid Acyrthosiphon pisum and Daphnia duplex, respectively, indicating possible roles in the evolution of reproductive mode. Three of these genes (SA2, SCC2, and WEE1) have one copy displaying gonad-specific expression. All genes, with the exception of WEE1, have significantly different nonsynonymous/synonymous ratios between the gene duplicates, indicative of a shift in evolutionary constraints following duplication. These results suggest that stick insects may have evolved genes with novel functions in gamete production by gene duplication.
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Affiliation(s)
- Chen Wu
- School of Biological Sciences, The University of Auckland, New Zealand.,Manaaki Whenua-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, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand.,Zoology Unit, Finnish Museum of Natural History, LUOMUS, University of Helsinki, Finland
| | - Richard D Newcomb
- School of Biological Sciences, The University of 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, New Zealand.,Manaaki Whenua-Landcare Research, Auckland, New Zealand
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Veenstra JA. Two Lys-vasopressin-like peptides, EFLamide, and other phasmid neuropeptides. Gen Comp Endocrinol 2019; 278:3-11. [PMID: 29705195 DOI: 10.1016/j.ygcen.2018.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 10/25/2022]
Abstract
Phasmid neuropeptide genes were identified in the genomes of two phasmids, Timema cristinae and Clitarchus hookeri. The two species belong to two sisters groups, the Timematodea and Euphasmatodea respectively. Neuropeptide genes were identified using the BLAST+ program on the genome assemblies and the absence of some neuropeptides was confirmed by the concomitant absence of their G-protein coupled receptors. Both genomes were assembled using short reads and the average coverage of the genome is more than 166 times for both species. This makes it virtually impossible that there would not be a single short read for at least one of the conserved transmembrane regions of a GPCR coded by such a genome. Hence, when not a single read can be found for a specific GPCR, it can be concluded that the particular gene is absent from that species. Most previously identified insect neuropeptides are used by these two species. Of the three arthropod allatostatin C related peptides, only allatostatins CC and CCC are present. Both species lack leucokinin, while sulfakinin and dilp8 signaling is absent from Clitarchus, but present in Timema. Interestingly, whereas Timema has lost a vasopressin-related peptide, the gene coding such a peptide is amplified in the Clitarchus genome. Furthermore, while Clitarchus has a specific tryptopyrokinin gene, Timema does not and in this species tryptopyrokinin is coded only by the pyrokinin and periviscerokinin genes. Finally, both species have genes coding EFLamide and its GPCR; in phasmids these genes codes for one (Clitarchus) or two (Timema) EFLamide paracopies.
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Affiliation(s)
- Jan A Veenstra
- INCIA, UMR 5287 CNRS, Université de Bordeaux, allée Geoffroy St Hillaire, CS 50023, 33 615 Pessac Cedex, France.
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6
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Parker DJ, Djordjevic J, Schwander T. Olfactory Proteins in Timema Stick Insects. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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7
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Vizueta J, Rozas J, Sánchez-Gracia A. Comparative Genomics Reveals Thousands of Novel Chemosensory Genes and Massive Changes in Chemoreceptor Repertories across Chelicerates. Genome Biol Evol 2018; 10:1221-1236. [PMID: 29788250 PMCID: PMC5952958 DOI: 10.1093/gbe/evy081] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 12/15/2022] Open
Abstract
Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability of a number of chelicerate genomes constitutes a great opportunity to better characterize gene families involved in this important function in a lineage that emerged and colonized land independently of insects. At the same time, that offers new opportunities and challenges for the study of this interesting animal branch in many translational research areas. Here, we have performed a comprehensive comparative genomics study that explicitly considers the high fragmentation of available draft genomes and that for the first time included complete genome data that cover most of the chelicerate diversity. Our exhaustive searches exposed thousands of previously uncharacterized chemosensory sequences, most of them encoding members of the gustatory and ionotropic receptor families. The phylogenetic and gene turnover analyses of these sequences indicated that the whole-genome duplication events proposed for this subphylum would not explain the differences in the number of chemoreceptors observed across species. A constant and prolonged gene birth and death process, altered by episodic bursts of gene duplication yielding lineage-specific expansions, has contributed significantly to the extant chemosensory diversity in this group of animals. This study also provides valuable insights into the origin and functional diversification of other relevant chemosensory gene families different from receptors, such as odorant-binding proteins and other related molecules.
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Affiliation(s)
- Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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8
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Brand P, Lin W, Johnson BR. The Draft Genome of the Invasive Walking Stick, Medauroidea extradendata, Reveals Extensive Lineage-Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea. G3 (BETHESDA, MD.) 2018; 8:1403-1408. [PMID: 29588379 PMCID: PMC5940134 DOI: 10.1534/g3.118.200204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/21/2018] [Indexed: 12/12/2022]
Abstract
Plant cell wall components are the most abundant macromolecules on Earth. The study of the breakdown of these molecules is thus a central question in biology. Surprisingly, plant cell wall breakdown by herbivores is relatively poorly understood, as nearly all early work focused on the mechanisms used by symbiotic microbes to breakdown plant cell walls in insects such as termites. Recently, however, it has been shown that many organisms make endogenous cellulases. Insects, and other arthropods, in particular have been shown to express a variety of plant cell wall degrading enzymes in many gene families with the ability to break down all the major components of the plant cell wall. Here we report the genome of a walking stick, Medauroidea extradentata, an obligate herbivore that makes uses of endogenously produced plant cell wall degrading enzymes. We present a draft of the 3.3Gbp genome along with an official gene set that contains a diversity of plant cell wall degrading enzymes. We show that at least one of the major families of plant cell wall degrading enzymes, the pectinases, have undergone a striking lineage-specific gene family expansion in the Phasmatodea. This genome will be a useful resource for comparative evolutionary studies with herbivores in many other clades and will help elucidate the mechanisms by which metazoans breakdown plant cell wall components.
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Affiliation(s)
- Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, California 95619
| | - Wei Lin
- Department of Entomology and Nematology, University of California, Davis, California 95616
| | - Brian R Johnson
- Department of Entomology and Nematology, University of California, Davis, California 95616
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9
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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] [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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10
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Twort VG, Dennis AB, Park D, Lomas KF, Newcomb RD, Buckley TR. Positive selection and comparative molecular evolution of reproductive proteins from New Zealand tree weta (Orthoptera, Hemideina). PLoS One 2017; 12:e0188147. [PMID: 29131842 PMCID: PMC5683631 DOI: 10.1371/journal.pone.0188147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/01/2017] [Indexed: 11/18/2022] Open
Abstract
Animal reproductive proteins, especially those in the seminal fluid, have been shown to have higher levels of divergence than non-reproductive proteins and are often evolving adaptively. Seminal fluid proteins have been implicated in the formation of reproductive barriers between diverging lineages, and hence represent interesting candidates underlying speciation. RNA-seq was used to generate the first male reproductive transcriptome for the New Zealand tree weta species Hemideina thoracica and H. crassidens. We identified 865 putative reproductive associated proteins across both species, encompassing a diverse range of functional classes. Candidate gene sequencing of nine genes across three Hemideina, and two Deinacrida species suggests that H. thoracica has the highest levels of intraspecific genetic diversity. Non-monophyly was observed in the majority of sequenced genes indicating that either gene flow may be occurring between the species, or that reciprocal monophyly at these loci has yet to be attained. Evidence for positive selection was found for one lectin-related reproductive protein, with an overall omega of 7.65 and one site in particular being under strong positive selection. This candidate gene represents the first step in the identification of proteins underlying the evolutionary basis of weta reproduction and speciation.
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Affiliation(s)
- Victoria G. Twort
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- * E-mail:
| | | | | | | | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and 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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11
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Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, Dearden PK, Duncan EJ, Grosser S, Rutherford K, Gardner PP, Crowhurst RN, Steinwender B, Tooman LK, Stevens MI, Buckley TR. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution. BMC Genomics 2017; 18:795. [PMID: 29041914 PMCID: PMC5644144 DOI: 10.1186/s12864-017-4197-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/08/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. RESULTS Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes. CONCLUSIONS The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda.
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Affiliation(s)
- Chen Wu
- Landcare Research, Private Bag, Auckland, 92170, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa D Jordan
- The 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
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sarah Bank
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
- Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Freiburg, Germany
| | - Peter K Dearden
- Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Elizabeth J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sefanie Grosser
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-, Martinsried, Germany
| | - Kim Rutherford
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Paul P Gardner
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Bernd Steinwender
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Leah K Tooman
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Mark I Stevens
- South Australian Museum, North Terrace, GPO Box 234, Adelaide, SA, 5001, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Thomas R Buckley
- Landcare Research, Private Bag, Auckland, 92170, New Zealand.
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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De novo transcriptome analysis of the excretory tubules of Carausius morosus (Phasmatodea) and possible functions of the midgut 'appendices'. PLoS One 2017; 12:e0174984. [PMID: 28384348 PMCID: PMC5383107 DOI: 10.1371/journal.pone.0174984] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/18/2017] [Indexed: 01/10/2023] Open
Abstract
The Malpighian tubules are the insect excretory organs, responsible for ion and water homeostasis and elimination of nitrogenous wastes. Post-genomic assays suggest they also metabolize and detoxify xenobiotic compounds and have antimicrobial properties. The Phasmatodea have an additional, unique set of excretory organs referred to predominantly as midgut appendices. Their function and how it compares to phasmid and other insect Malpighian tubules is unknown. Hypotheses include carbonic anhydrase activity, calcium and metal cation sequestration, and xenobiotic transport. This work presents the first comparative transcriptomic analysis of the Phasmatodean excretory organs, using the model insect Carausius morosus. I produced de novo transcriptomes of the midgut appendices, midgut wall, and Malpighian tubules, and looked for differentially expressed genes associated with putative organ functions. The appendices differentially and highly express lipid transport and metabolism proteins, and the biomineralization gene otopetrin. The Malpighian tubules differentially and highly express acid phosphatases and multiple transporter types, while appendices express fat-soluble vitamin and peptide transporters. Many defense proteins such as multidrug resistance proteins, ABC transporters, cytochrome P450's, and glutathione-S-transferases were differentially expressed in specific excretory organs. I hypothesize that the appendices and Malpighian tubules both have defensive / xenobiotic metabolism functions, but each likely target different substrates. Phasmid Malpighian tubules excrete as in other insects, while the appendices may predominantly regulate amino acids, fats, and fat-soluble compounds. Lipid metabolism in insects is poorly understood, and the Phasmatodea may thus serve as a model for studying this further.
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