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Mumoki FN, Yusuf AA, Pirk CWW, Crewe RM. Hydroxylation patterns associated with pheromone synthesis and composition in two honey bee subspecies Apis mellifera scutellata and A. m. capensis laying workers. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 114:103230. [PMID: 31470083 DOI: 10.1016/j.ibmb.2019.103230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Colony losses due to social parasitism in the form of reproductive workers of the Apis mellifera capensis clones results from the production of queen-like pheromonal signals coupled with ovarian activation in these socially parasitic honey bees. While the behavioral attributes of these social parasites have been described, their genetic attributes require more detailed exploration. Here, we investigate the production of mandibular gland pheromones in queenless workers of two sub-species of African honey bees; A. m. scutellata (low reproductive potential) and A. m. capensis clones (high reproductive potential). We used standard techniques in gas chromatography to assess the amounts of various pheromone components present, and qPCR to assess the expression of cytochrome P450 genes cyp6bd1 and cyp6as8, thought to be involved in the caste-dependent hydroxylation of acylated stearic acid in queens and workers, respectively. We found that, for both subspecies, the quality and quantity of the individual pheromone components vary with age, and that from the onset, A. m. capensis parasites make use of gene pathways typically upregulated in queens in achieving reproductive dominance. Due to the high production of 9-hydroxy-decenoic acid (9-HDA) the precursor to the queen substance 9-oxo-decenoic acid (9-ODA) in newly emerged capensis clones, we argue that clones are primed for parasitism upon emergence and develop into fully fledged parasites depending on the colony's social environment.
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Affiliation(s)
- Fiona N Mumoki
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa.
| | - Abdullahi A Yusuf
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa.
| | - Christian W W Pirk
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa.
| | - Robin M Crewe
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, Pretoria, South Africa.
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202
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Zaworra M, Nauen R. New approaches to old problems: Removal of phospholipase A 2 results in highly active microsomal membranes from the honey bee, Apis mellifera. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 161:68-76. [PMID: 31685199 DOI: 10.1016/j.pestbp.2019.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/08/2019] [Accepted: 04/29/2019] [Indexed: 06/10/2023]
Abstract
Over the last 50 years numerous studies were published by insect toxicologists using native microsomal membrane preparations in order to investigate in vitro cytochrome P450-(P450) mediated oxidative metabolism of xenobiotics, including insecticides. Whereas the preparation of active microsomal membranes from many pest insect species is straightforward, their isolation from honey bees, Apis mellifera (Hymenoptera: Apidae) remained difficult, if not impossible, due to the presence of a yet unidentified endogenous inhibitory factor released during abdominal gut membrane isolation. Thus hampering in vitro toxicological studies on microsomal oxidative phase 1 metabolism of xenobiotics, including compounds of ecotoxicological concern. The use of microsomal membranes rather than individually expressed P450s offers advantages and allows to develop a better understanding of phase 1 driven metabolic fate of foreign compounds. Here we biochemically investigated the problems associated with the isolation of active honey bee microsomes and developed a method resulting in highly active native microsomal preparations from adult female worker abdomens. This was achieved by removal of the abdominal venom gland sting complex prior to microsomal membrane preparation. Molecular sieve chromatography of the venom sac content leads to the identification of phospholipase A2 as the enzyme responsible for the immediate inhibition of cytochrome P450 activity in microsomal preparations. The substrate specificity of functional honey bee microsomes was investigated with different fluorogenic substrates, and revealed a strong preference for coumarin over resorufin derivatives. Furthermore we were able to demonstrate the metabolism of insecticides by honey bee microsomes using an approach coupled to LC-MS/MS analysis of hydroxylated metabolites. Our work provides access to a new and simple in vitro tool to study honey bee phase 1 metabolism of xenobiotics utilising the entire range of microsomal cytochrome P450s.
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Affiliation(s)
- Marion Zaworra
- Bayer AG, Crop Science Division, R&D, Alfred Nobel Str. 50, D-40789 Monheim, Germany; University of Bonn, INRES, Molecular Phytomedicine, Karlrobert-Kreiten-Str. 13, D-53115 Bonn, Germany
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Alfred Nobel Str. 50, D-40789 Monheim, Germany.
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203
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Comparative Analysis of Intra- and Inter-Specific Genomic Variability in the Peach Potato Aphid, Myzus persicae. INSECTS 2019; 10:insects10100368. [PMID: 31652640 PMCID: PMC6835256 DOI: 10.3390/insects10100368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022]
Abstract
The availability of genomic data in the last decade relating to different aphid species has allowed the analysis of the genomic variability occurring among such species, whereas intra-specific variability has hitherto very largely been neglected. In order to analyse the intra-genomic variability in the peach potato aphid, Myzus persicae, comparative analyses were performed revealing several clone-specific gene duplications, together with numerous deletions/rearrangements. Our comparative approach also allowed us to evaluate the synteny existing between the two M. persicae clones tested and between the peach potato aphid and the pea aphid, Acyrthosiphon pisum. Even if part of the observed rearrangements are related to a low quality of some assembled contigs and/or to the high number of contigs present in these aphid genomes, our evidence reveals that aphid clones are genetically more different than expected. These results suggest that the choice of performing genomes sequencing combining different biotypes/populations, as revealed in the case of the soybean aphid, Aphis glycines, is unlikely to be very informative in aphids. Interestingly, it is possible that the holocentric nature of aphid chromosomes favours genome rearrangements that can be successively inherited transgenerationally via the aphid's apomictic (parthenogenetic) mode of reproduction. Lastly, we evaluated the structure of the cluster of genes coding for the five histones (H1, H2A, H2B, H3 and H4) in order to better understand the quality of the two M. persicae genomes and thereby to improve our knowledge of this functionally important gene family.
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204
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205
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Berenbaum MR, Liao LH. Honey Bees and Environmental Stress: Toxicologic Pathology of a Superorganism. Toxicol Pathol 2019; 47:1076-1081. [PMID: 31581932 DOI: 10.1177/0192623319877154] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As a eusocial species, Apis mellifera, the European honey bee, is effectively a superorganism-a group of genetically related individuals functioning as a collective unit. Because the unit of selection is the colony and not the individual, standard methods for assessing toxicologic pathology can miss colony-level responses to stress. For over a decade, US populations of honeybees have experienced severe annual losses attributed to a variety of environmental stressors varying temporally and geographically; differentiating among those stressors is accordingly a high priority. Social interactions among individuals in this social species, however, mean that the "footprint" of stressors such as pesticides, phytochemicals, pathogens, and parasites may be most discernible in individuals that did not themselves directly encounter the stressor. For example, neurotoxic effects of pesticides on nurse bees may impair their behavioral responses to queen-destined larvae, which may then emerge as adults with altered anatomy or physiology. Similarly, pesticide-induced size alterations in nurse hypopharyngeal glands, which produce royal jelly, the exclusive food of larval and adult queens, may disproportionately affect the queen's (and thus colony) health. Thus, evaluating toxicologic pathology in the honeybee requires a new perspective and development of assays that preserve the social context that ultimately determines colony health.
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Affiliation(s)
- May R Berenbaum
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ling-Hsiu Liao
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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206
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Mandrioli M, Melchiori G, Panini M, Chiesa O, Giordano R, Mazzoni E, Manicardi GC. Analysis of the extent of synteny and conservation in the gene order in aphids: A first glimpse from the Aphis glycines genome. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 113:103228. [PMID: 31446034 DOI: 10.1016/j.ibmb.2019.103228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
In the last decade several insect genomes have been sequenced, but for most the chromosomal mapping of the identified scaffolds/annotated genes is not available. The lack of this information makes it difficult to analyse various genetic aspects, including the presence of genome rearrangements and the extent of synteny within and across species. We mapped five multigenic DNA families (major and minor rDNAs, histone gene cluster, esterases and carotenoid desaturases) and seven scaffolds corresponding to 9 Mb of the soybean aphid, Aphis glycines, genome and identified loci spanning the four soybean aphid chromosomes. A comparative analysis of the localization of the annotated A. glycines genes with respect to the peach potato aphid, Myzus persicae, and the fly, Drosophila melanogaster, evidenced a lower degree of synteny between the two aphid species than in the aphid-fly comparison. Only 1.4 genes per syntenic block were observed in aphids in contrast to 2.3 genes per block in flies. This higher chromosomal rearrangement rate in aphids could be explained considering that they possess holocentric chromosomes that can favour the stabilization and inheritance of chromosomal rearrangements. Lastly, our experiments did not detect the presence of chimeric assemblies in the newly available A. glycines biotype 1 genome, differently from what reported in assembled genome of other aphid species, suggesting that chromosomal mapping can be used to ascertain the quality of assembled genomes.
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Affiliation(s)
- Mauro Mandrioli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy.
| | - Giulia Melchiori
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
| | - Michela Panini
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Olga Chiesa
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rosanna Giordano
- Puerto Rico Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc., San Juan, PR, USA
| | - Emanuele Mazzoni
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Gian Carlo Manicardi
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
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207
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Alburaki M, Karim S, Lamour K, Adamczyk J, Stewart SD. RNA-seq reveals disruption of gene regulation when honey bees are caged and deprived of hive conditions. ACTA ACUST UNITED AC 2019; 222:jeb.207761. [PMID: 31413101 DOI: 10.1242/jeb.207761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/06/2019] [Indexed: 11/20/2022]
Abstract
In this study, we present phenotypic and genetic data characterizing the impact of imidacloprid and caging stress on honey bee Apis mellifera physiological responses and regulation of 45 genes using targeted-RNA seq. The term 'caging stress' characterizes the effects of depriving honey bees of all hive aspects and conditions. Two cohorts of 1 day old sister bees were subjected to different conditions. One cohort was caged and fed different imidacloprid-tainted sugar solutions and the second was marked and introduced back to its natal hive. Physiological bee parameters and diet behavior were monitored daily for caged bees over several weeks. Bee samples from both cohorts were sampled weekly for RNA sequencing and oxidative stress analyses. Imidacloprid induced significant protein damage and post-ingestive aversion responses in caged bees, leading to lower tainted syrup consumption and higher water intake compared with the controls. No differentially expressed genes were observed among caged bees in regards to imidacloprid treatment. However, significant upregulation in antioxidant genes was recorded in caged bees as compared with hive bees, with overwhelming downregulation in all gene categories in caged bees at week 4. We identified two sets of genes that were constantly regulated in caged bees, including Rsod with unknown function in insects that could potentially characterize caging stress in honey bees.
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Affiliation(s)
| | - Shahid Karim
- The University of Southern Mississippi, Department of Cell and Molecular Biology Sciences, Hattiesburg, MS 39406, USA
| | - Kurt Lamour
- The University of Tennessee, Entomology and Plant Pathology Department, Knoxville, TN 37996, USA
| | - John Adamczyk
- USDA-ARS Thad Cochran Horticulture Laboratory, Poplarville, MS 39470, USA
| | - Scott D Stewart
- The University of Tennessee, Department of Entomology and Plant Pathology, West Tennessee Research and Education Center, Jackson, TN 38301, USA
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208
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Yagound B, Smith NMA, Buchmann G, Oldroyd BP, Remnant EJ. Unique DNA Methylation Profiles Are Associated with cis-Variation in Honey Bees. Genome Biol Evol 2019; 11:2517-2530. [PMID: 31406991 PMCID: PMC6740151 DOI: 10.1093/gbe/evz177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is an important epigenetic modification that mediates diverse processes such as cellular differentiation, phenotypic plasticity, and genomic imprinting. Mounting evidence suggests that local DNA sequence variation can be associated with particular DNA methylation states, indicating that the interplay between genetic and epigenetic factors may contribute synergistically to the phenotypic complexity of organisms. Social insects such as ants, bees, and wasps have extensive phenotypic plasticity manifested in their different castes, and this plasticity has been associated with variation in DNA methylation. Yet, the influence of genetic variation on DNA methylation state remains mostly unknown. Here we examine the importance of sequence-specific methylation at the genome-wide level, using whole-genome bisulfite sequencing of the semen of individual honey bee males. We find that individual males harbor unique DNA methylation patterns in their semen, and that genes that are more variable at the epigenetic level are also more likely to be variable at the genetic level. DNA sequence variation can affect DNA methylation by modifying CG sites directly, but can also be associated with local variation in cis that is not CG-site specific. We show that covariation in sequence polymorphism and DNA methylation state contributes to the individual-specificity of epigenetic marks in social insects, which likely promotes their retention across generations, and their capacity to influence evolutionary adaptation.
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Affiliation(s)
- Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Nicholas M A Smith
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
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209
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Alshukri B, Astarita F, Al‐Esawy M, El Halim HMESA, Pennacchio F, Gatehouse AMR, Edwards MG. Targeting the potassium ion channel genes SK and SH as a novel approach for control of insect pests: efficacy and biosafety. PEST MANAGEMENT SCIENCE 2019; 75:2505-2516. [PMID: 31207012 PMCID: PMC6771844 DOI: 10.1002/ps.5516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Potassium ion channels play a critical role in the generation of electrical signals and thus provide potential targets for control of insect pests by RNA interference. RESULTS Genes encoding the small conductance calcium-activated potassium channel (SK) and the voltage-gated potassium channel (SH) were knocked down in Tribolium castaneum by injection and oral delivery of dsRNA (dsTcSK and dsTcSH, respectively). Irrespective of the delivery mechanism a dose-dependent effect was observed for knockdown (KD) of gene expression and insect mortality for both genes. Larvae fed a 400 ng dsRNA mg-1 diet showed significant gene (P < 0.05) knockdown (98% and 83%) for SK and SH, respectively, with corresponding mortalities of 100% and 98% after 7 days. When injected (248.4 ng larva-1 ), gene KD was 99% and 98% for SK and SH, causing 100% and 73.4% mortality, respectively. All developmental stages tested (larvae, early- and late-stage pupae and adults) showed an RNAi-sensitive response for both genes. LC50 values were lower for SK than SH, irrespective of delivery method, demonstrating that the knockdown of SK had a greater effect on larval mortality. Biosafety studies using adult honeybee Apis mellifera showed that there were no significant differences either in expression levels or mortality of honeybees orally dosed with dsTcSK and dsTcSH compared to control-fed bees. Similarly, there was no significant difference in the titre of deformed wing virus, used as a measure of immune suppression, between experimental and control bees. CONCLUSION This study demonstrates the potential of using RNAi targeting neural receptors as a technology for the control of T. castaneum. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Baida Alshukri
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
| | - Federica Astarita
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
- Department of Agricultural Sciences, Laboratory of Entomology “E. Tremblay”University of Napoli “Federico II”PorticiItaly
| | - Mushtaq Al‐Esawy
- Institute of Neuroscience, Newcastle UniversityNewcastle‐upon‐TyneUK
- Department of Plant ProtectionUniversity of KufaIraq
| | - Hesham Mohamed El Sayed Abd El Halim
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
- Entomology Department, Faculty of ScienceBenha UniversityBenhaEgypt
| | - Francesco Pennacchio
- Department of Agricultural Sciences, Laboratory of Entomology “E. Tremblay”University of Napoli “Federico II”PorticiItaly
| | | | - Martin Gethin Edwards
- School of Natural and Environmental Sciences, Newcastle UniversityNewcastle‐upon‐TyneUK
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210
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Altaye SZ, Meng L, Lu Y, Li J. The Emerging Proteomic Research Facilitates in-Depth Understanding of the Biology of Honeybees. Int J Mol Sci 2019; 20:ijms20174252. [PMID: 31480282 PMCID: PMC6747239 DOI: 10.3390/ijms20174252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023] Open
Abstract
Advances in instrumentation and computational analysis in proteomics have opened new doors for honeybee biological research at the molecular and biochemical levels. Proteomics has greatly expanded the understanding of honeybee biology since its introduction in 2005, through which key signaling pathways and proteins that drive honeybee development and behavioral physiology have been identified. This is critical for downstream mechanistic investigation by knocking a gene down/out or overexpressing it and being able to attribute a specific phenotype/biochemical change to that gene. Here, we review how emerging proteome research has contributed to the new understanding of honeybee biology. A systematic and comprehensive analysis of global scientific progress in honeybee proteome research is essential for a better understanding of research topics and trends, and is potentially useful for future research directions.
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Affiliation(s)
- Solomon Zewdu Altaye
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lifeng Meng
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yao Lu
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianke Li
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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211
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Lim S, Jung J, Yunusbaev U, Ilyasov R, Kwon HW. Characterization and its implication of a novel taste receptor detecting nutrients in the honey bee, Apis mellifera. Sci Rep 2019; 9:11620. [PMID: 31406120 PMCID: PMC6690930 DOI: 10.1038/s41598-019-46738-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
Umami taste perception indicates the presence of amino acids, which are essential nutrients. Although the physiology of umami perception has been described in mammals, how insects detect amino acids remains unknown except in Drosophila melanogaster. We functionally characterized a gustatory receptor responding to L-amino acids in the western honey bee, Apis mellifera. Using a calcium-imaging assay and two-voltage clamp recording, we found that one of the honey bee's gustatory receptors, AmGr10, functions as a broadly tuned amino acid receptor responding to glutamate, aspartate, asparagine, arginine, lysine, and glutamine, but not to other sweet or bitter compounds. Furthermore, the sensitivity of AmGr10 to these L-amino acids was dramatically enhanced by purine ribonucleotides, like inosine-5'-monophosphate (IMP). Contact sensory hairs in the mouthpart of the honey bee responded strongly to glutamate and aspartate, which house gustatory receptor neurons expressing AmGr10. Interestingly, AmGr10 protein is highly conserved among hymenopterans but not other insects, implying unique functions in eusocial insects.
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Affiliation(s)
- Sooho Lim
- Department of Life Sciences & Convergence Research Center for Insect Vectors, College of Life Science and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, Republic of Korea
| | - Jewon Jung
- Department of Life Sciences & Convergence Research Center for Insect Vectors, College of Life Science and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, Republic of Korea
| | - Ural Yunusbaev
- Department of Life Sciences & Convergence Research Center for Insect Vectors, College of Life Science and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, Republic of Korea
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Russia
| | - Rustem Ilyasov
- Department of Life Sciences & Convergence Research Center for Insect Vectors, College of Life Science and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, Republic of Korea
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Russia
| | - Hyung Wook Kwon
- Department of Life Sciences & Convergence Research Center for Insect Vectors, College of Life Science and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon, 22012, Republic of Korea.
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212
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Chen D, Chen H, Du Y, Zhou D, Geng S, Wang H, Wan J, Xiong C, Zheng Y, Guo R. Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection. INSECTS 2019; 10:insects10080245. [PMID: 31405016 PMCID: PMC6723323 DOI: 10.3390/insects10080245] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in cis and trans fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to N. ceranae invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.
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Affiliation(s)
- Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huazhi Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Du
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dingding Zhou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sihai Geng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haipeng Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jieqi Wan
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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213
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Yunusbaev UB, Kaskinova MD, Ilyasov RA, Gaifullina LR, Saltykova ES, Nikolenko AG. The Role of Whole-Genome Studies in the Investigation of Honey Bee Biology. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541906019x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Metabolomics-based biomarker discovery for bee health monitoring: A proof of concept study concerning nutritional stress in Bombus terrestris. Sci Rep 2019; 9:11423. [PMID: 31388077 PMCID: PMC6684606 DOI: 10.1038/s41598-019-47896-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/24/2019] [Indexed: 02/06/2023] Open
Abstract
Bee pollinators are exposed to multiple natural and anthropogenic stressors. Understanding the effects of a single stressor in the complex environmental context of antagonistic/synergistic interactions is critical to pollinator monitoring and may serve as early warning system before a pollination crisis. This study aimed to methodically improve the diagnosis of bee stressors using a simultaneous untargeted and targeted metabolomics-based approach. Analysis of 84 Bombus terrestris hemolymph samples found 8 metabolites retained as potential biomarkers that showed excellent discrimination for nutritional stress. In parallel, 8 significantly altered metabolites, as revealed by targeted profiling, were also assigned as candidate biomarkers. Furthermore, machine learning algorithms were applied to the above-described two biomarker sets, whereby the untargeted eight components showed the best classification performance with sensitivity and specificity up to 99% and 100%, respectively. Based on pathway and biochemistry analysis, we propose that gluconeogenesis contributed significantly to blood sugar stability in bumblebees maintained on a low carbohydrate diet. Taken together, this study demonstrates that metabolomics-based biomarker discovery holds promising potential for improving bee health monitoring and to identify stressor related to energy intake and other environmental stressors.
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215
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Garczynski SF, Hendrickson CA, Harper A, Unruh TR, Dhingra A, Ahn SJ, Choi MY. Neuropeptides and peptide hormones identified in codling moth, Cydia pomonella (Lepidoptera: Tortricidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 101:e21587. [PMID: 31271487 DOI: 10.1002/arch.21587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/19/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
The codling moth, Cydia pomonella, is a worldwide pest of pome fruits. Neuropeptides regulate most physiological functions in insects and represent new targets for the development of control agents. The only neuropeptides reported from the codling moth to date are the allatostatin A family peptides. To identify other neuropeptides and peptide hormones from codling moth, we analyzed head transcriptomes, identified 50 transcripts, and predicted 120 prepropeptides for the codling moth neuropeptides and peptide hormones. All transcripts were amplified, and these sequences were verified. One of the notable findings in this study is that diapause hormones (DHs) reported from Tortricid moths, including the codling moth, do not have the WFGPRL sequence in C-terminal ends in the pban genes. The C-terminal motif is critical to characterize insect DH peptides, and always conserved in pban/dh genes in Lepidoptera and many insect orders. Interestingly, the WFGPRL sequence was produced only from the capa gene in the codling moth. The allatostatin A-family encoding transcript predicted nine peptides, seven of which, as expected, are identical to those previously isolated from the moth. We also identified new codling moth orthologs of insect neuropeptides including CCHamides, allatostatin CC, RYamides, and natalisins. The information provided in this study will benefit future codling moth investigations using peptidoproteomics to determine peptide presence and functions.
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Affiliation(s)
| | | | - Artemus Harper
- Department of Horticulture, Washington State University, Pullman, Washington
| | - Thomas R Unruh
- Yakima Agricultural Research Laboratory, USDA-ARS, Wapato, Washington
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, Washington
| | - Seung-Joon Ahn
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon
- Horticultural Crops Research Unit, USDA-ARS, Corvallis, Oregon
| | - Man-Yeon Choi
- Horticultural Crops Research Unit, USDA-ARS, Corvallis, Oregon
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216
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Rubin BER, Jones BM, Hunt BG, Kocher SD. Rate variation in the evolution of non-coding DNA associated with social evolution in bees. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180247. [PMID: 31154980 PMCID: PMC6560270 DOI: 10.1098/rstb.2018.0247] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2019] [Indexed: 11/12/2022] Open
Abstract
The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Benjamin E. R. Rubin
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Beryl M. Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
| | - Brendan G. Hunt
- Department of Entomology, University of Georgia, Griffin, GA, USA
| | - Sarah D. Kocher
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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217
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Lin Y, Shao Q, Zhang M, Lu C, Fleming J, Su S. Royal jelly-derived proteins enhance proliferation and migration of human epidermal keratinocytes in an in vitro scratch wound model. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:175. [PMID: 31299973 PMCID: PMC6626366 DOI: 10.1186/s12906-019-2592-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/04/2019] [Indexed: 12/28/2022]
Abstract
Background Skin injury is inevitable in daily life. In recent years, with the increasing morbidity of diseases such as diabetes and metabolic disorders, chronic wounds have become a considerable challenge in clinical practice. Royal jelly, reported to have multifarious biological and physiological properties, has been used as a remedy for a variety of wounds since ancient times. However, the active components and mechanisms underlying the wound-healing properties of royal jelly are still largely unknown. Methods Water-soluble proteins of royal jelly were fractionated and investigated for the proliferative and migratory effects on human epidermal keratinocytes (HaCaT) in an in vitro wound healing model. The proteins present in bioactive fractions were characterised and quantified using Label-free protein quantification method. The potential functions of these proteins in biological systems were further analysed using bioinformatic tools. Results A protein fraction, mainly containing major royal jelly proteins 2 (MRJP2), MRJP3 and MRJP7, stimulated proliferative and migratory activities in HaCaT cells without visible cytotoxicity. It exerted the greatest effects on the growth of HaCaT cells in the first 48 h. Furthermore, when treated with this protein fraction, the closure rates of the in vitro scratch wound were significantly increased. Functional analysis indicated that MRJP2, MRJP3 and MRJP7 were associated with carbohydrate transport and metabolism. Conclusions We fractionated the water-soluble proteins of royal jelly and identified one fraction (Fraction 2) that induced both proliferative and migratory effects on a human epidermal keratinocyte cell line. Major royal jelly proteins (MRJP2, MRJP3 and/or MRJP7) were speculated to possess potential wound-healing bioactivity. This is the first report that royal jelly may improve wound closure via MRJP-induced cellular proliferation and migration. These proteins may be valuable lead compounds for the development of novel wound healing medications. Our findings would facilitate better understanding of the wound repair mechanisms of royal jelly.
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218
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Guo R, Chen D, Diao Q, Xiong C, Zheng Y, Hou C. Transcriptomic investigation of immune responses of the Apis cerana cerana larval gut infected by Ascosphaera apis. J Invertebr Pathol 2019; 166:107210. [PMID: 31211962 DOI: 10.1016/j.jip.2019.107210] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/19/2022]
Abstract
Chalkbrood is the most common fungal disease in honeybees. The objective of this study was to reveal immune responses in the Apis cerana cerana larval gut following Ascosphaera apis invasion. Combining a previously assembled transcriptome of A. c. cerana larval gut and the high-throughput sequencing data obtained in this study, 6152 differentially expressed genes (DEGs) were clustered into eight profiles. Trend analysis showed three significant up-regulated profiles (p ≤ 0.05) and three down-regulated profiles. Gene Ontology (GO) term analysis suggested that DEGs within significant up-regulated and down-regulated clusters were enriched in 46 and 38 functional groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated a majority of DEGs were involved in ribosome structure or function, carbon metabolism, biosynthesis of amino acids, and oxidative phosphorylation. In addition, 142 and 14 DEGs were annotated in the cellular immune- and humoral immune-related pathways, respectively. Further investigation indicated that DEGs up-regulated in cellular immune and humoral immune pathways outnumbered those that were down-regulated. Moreover, immune responses of A. c. cerana and Apis mellifera ligustica larvae were compared and studied to decipher resistance of eastern honeybee larvae to A. apis. These results demonstrated that a large number of genes involved in immunity-related pathways were activated by A. apis. Our findings provided valuable information for elucidating the molecular mechanisms underlying immune responses of A. c. cerana larvae to A. apis infection and pathogen-host interactions during chalkbrood infection.
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Affiliation(s)
- Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
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219
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Melicher D, Wilson ES, Bowsher JH, Peterson SS, Yocum GD, Rinehart JP. Long-Distance Transportation Causes Temperature Stress in the Honey Bee, Apis mellifera (Hymenoptera: Apidae). ENVIRONMENTAL ENTOMOLOGY 2019; 48:681-701. [PMID: 30927358 PMCID: PMC6554651 DOI: 10.1093/ee/nvz027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 06/09/2023]
Abstract
Pollination services provided by the honey bee, Apis mellifera (Hymenoptera: Apidae, Linnaeus, 1758) have broad economic impacts and are necessary for production of a diversity of important crops. Hives may be transported multiple times per year to provide pollination. To test how temperature may contribute to transportation stress, temperature sensors were placed in hives in different locations and orientations on the trailer during shipping. Colony size prior to shipping significantly contributed to loss of population immediately after shipping which contributed to colony failure with smaller colonies more likely to fail and fail faster. Colony size also affects thermoregulation and temperature stress. Internal hive temperature varies significantly based on location and orientation. While colonies near the front and rear of the trailer and those oriented toward the center aisle had significantly different average internal temperatures, colony size best predicts loss of thermoregulation. Additionally, we profiled gene expression at departure, on arrival, and after a recovery period to identify transcriptional responses to transportation. Functional and enrichment analysis identified increased methylation and decreased ribosomal and protein-folding activity. Pheromone and odorant-binding transcripts were up-regulated after transportation. After recovery, transcripts associated with defense response, immune activity, and heat shock decreased, while production of antibiotic peptides increased. We conclude that hives experience considerable temperature stress possibly caused by turbulent airflow in exposed locations. Transportation stress should be considered an important component of annual colony losses which can be mitigated with improved management strategies.
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Affiliation(s)
- Dacotah Melicher
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Service, Fargo, ND
| | - Elisabeth S Wilson
- Department of Biological Sciences, North Dakota State University, Fargo, ND
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, ND
| | | | - George D Yocum
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Service, Fargo, ND
| | - Joseph P Rinehart
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Service, Fargo, ND
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220
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Skelly J, Pushparajan C, Duncan EJ, Dearden PK. Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting. INSECT MOLECULAR BIOLOGY 2019; 28:392-408. [PMID: 30548465 DOI: 10.1111/imb.12560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Embryonic terminal patterning and moulting are critical developmental processes in insects. In Drosophila and Tribolium both of these processes are regulated by the Torso-activation cassette (TAC). The TAC consists of a common receptor, Torso, ligands Trunk and prothoracicotropic hormone (PTTH), and the spatially restricted protein Torso-like, with combinations of these elements acting mechanistically to activate the receptor in different developmental contexts. In order to trace the evolutionary history of the TAC we determined the presence or absence of TAC components in the genomes of arthropods. Our analyses reveal that Torso, Trunk and PTTH are evolutionarily labile components of the TAC with multiple individual or combined losses occurring in the arthropod lineages leading to and within the insects. These losses are often correlated, with both ligands and receptor missing from the genome of the same species. We determine that the PTTH gene evolved in the common ancestor of Hemiptera and Holometabola, and is missing from the genomes of a number of species with experimentally demonstrated PTTH activity, implying another molecule may be involved in ecdysis in these species. In contrast, the torso-like gene is a common component of pancrustacean genomes.
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Affiliation(s)
- J Skelly
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
| | - C Pushparajan
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
| | - E J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - P K Dearden
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
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221
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Liu F, Shi T, Qi L, Su X, Wang D, Dong J, Huang ZY. lncRNA profile of Apis mellifera and its possible role in behavioural transition from nurses to foragers. BMC Genomics 2019; 20:393. [PMID: 31113365 PMCID: PMC6528240 DOI: 10.1186/s12864-019-5664-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/01/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The behavioural transition from nurses to foragers in honey bees is known to be affected by intrinsic and extrinsic factors, including colony demography, hormone levels, brain chemistry and structure, and gene expression in the brain. However, the molecular mechanism underlying this behavioural transition of honey bees is still obscure. RESULTS Through RNA sequencing, we performed a comprehensive analysis of lncRNAs and mRNAs in honey bee nurses and foragers. Nurses and foragers from both typical colonies and single-cohort colonies were used to prepare six libraries to generate 49 to 100 million clear reads per sample. We obtained 6863 novel lncRNAs, 1480 differentially expressed lncRNAs between nurses and foragers, and 9308 mRNAs. Consistent with previous studies, lncRNAs showed features distinct from mRNAs, such as shorter lengths, lower exon numbers, and lower expression levels compared to mRNAs. Bioinformatic analysis showed that differentially expressed genes were mostly involved in the regulation of sensory-related events, such as olfactory receptor activity and odorant binding, and enriched Wnt and FoxO signaling pathways. Moreover, we found that lncRNAs TCONS_00356023, TCONS_00357367, TCONS_00159909 and mRNAs dop1, Kr-h1 and HR38 may play important roles in behavioural transition in honey bees. CONCLUSION This study characterized the expression profile of lncRNAs in nurses and foragers and provided a framework for further study of the role of lncRNAs in honey bee behavioural transition.
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Affiliation(s)
- Fang Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Tengfei Shi
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Lei Qi
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Xin Su
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230000 Anhui China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Zachary Y. Huang
- Department of Entomology, Michigan State University, East Lansing, MI 48824 USA
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222
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Darwinian black box selection for resistance to settled invasive Varroa destructor parasites in honey bees. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02001-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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223
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Drukewitz SH, von Reumont BM. The Significance of Comparative Genomics in Modern Evolutionary Venomics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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224
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Conlon BH, Aurori A, Giurgiu AI, Kefuss J, Dezmirean DS, Moritz RFA, Routtu J. A gene for resistance to the Varroa mite (Acari) in honey bee (Apis mellifera) pupae. Mol Ecol 2019; 28:2958-2966. [PMID: 30916410 DOI: 10.1111/mec.15080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/21/2022]
Abstract
Social insect colonies possess a range of defences which protect them against highly virulent parasites and colony collapse. The host-parasite interaction between honey bees (Apis mellifera) and the mite Varroa destructor is unusual, as honey bee colonies are relatively poorly defended against this parasite. The interaction has existed since the mid-20th Century, when Varroa switched host to parasitize A. mellifera. The combination of a virulent parasite and relatively naïve host means that, without acaricides, honey bee colonies typically die within 3 years of Varroa infestation. A consequence of acaricide use has been a reduced selective pressure for the evolution of Varroa resistance in honey bee colonies. However, in the past 20 years, several natural-selection-based breeding programmes have resulted in the evolution of Varroa-resistant populations. In these populations, the inhibition of Varroa's reproduction is a common trait. Using a high-density genome-wide association analysis in a Varroa-resistant honey bee population, we identify an ecdysone-induced gene significantly linked to resistance. Ecdysone both initiates metamorphosis in insects and reproduction in Varroa. Previously, using a less dense genetic map and a quantitative trait loci analysis, we have identified Ecdysone-related genes at resistance loci in an independently evolved resistant population. Varroa cannot biosynthesize ecdysone but can acquire it from its diet. Using qPCR, we are able to link the expression of ecdysone-linked resistance genes to Varroa's meals and reproduction. If Varroa co-opts pupal compounds to initiate and time its own reproduction, mutations in the host's ecdysone pathway may represent a key selection tool for honey bee resistance and breeding.
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Affiliation(s)
- Benjamin H Conlon
- Molecular Ecology, Institute of Biology/Zoology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.,Department of Biology, Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Adriana Aurori
- University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | | | | | - Daniel S Dezmirean
- University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Robin F A Moritz
- Molecular Ecology, Institute of Biology/Zoology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.,University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania.,Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Jarkko Routtu
- Molecular Ecology, Institute of Biology/Zoology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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225
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Liang C, Wang Y, Wang Y, Chen X, Guo H. Telomerase Reverse Transcriptase Gene from Greasyback Shrimp Metapenaeus ensis: Isolation, Genomic Organization and Expression Pattern Analysis. Zoolog Sci 2019; 34:419-428. [PMID: 28990474 DOI: 10.2108/zs160130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Telomerase reverse transcriptase (TERT), a catalytic subunit of telomerase, plays a key role in the activity and biological functions of telomerase. In the present study we isolated and characterized the full-length cDNA and DNA sequences of the TERT gene (MeTERT) from Metapenaeus ensis. MeTERT cDNA was 4239 bp in length, which consisted of a 369 bp 5'UTR, a 3231 bp open reading frame encoding 1076 amino acids, and a 639 bp 3'UTR. The genomic DNA of MeTERT had only two introns, similar to beetle (two introns) and silkworm (intronless). The MeTERT protein showed only 5.2-7.9% identity with other known TERTs but contained all the four primary TERT domains of the N-terminal TEN, RNA binding domain (TRBD), reverse transcriptase (RT) and C-terminus CTE. Expression pattern analysis by RT-qPCR showed that, the MeTERT mRNA transcripts could be detected in all the tested samples, with relatively higher expression level in the gill, mysis, Oka organ and egg, but lower level in muscle, ovary, in vitro cultured 3-d Oka organ cells and heart. The significant decrease of MeTERT expression in the in vitro cultured 3-d Oka organ primary cells compared with their source tissue of Oka organ may have contributed to the cellular mitosisarrest. Thus trans-activation of TERT gene may be a candidate in attempts to immortalize in vitro cultured shrimp cells. This work will lay a solid foundation for future studies of the biological functions of telomerase in crustaceans.
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Affiliation(s)
- Cuicui Liang
- 1 Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,2 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yuhao Wang
- 3 Qingdao No.2 Middle School of Shandong Province, Qingdao 266061, China
| | - Yujie Wang
- 3 Qingdao No.2 Middle School of Shandong Province, Qingdao 266061, China
| | - Xuemei Chen
- 1 Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,2 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Huarong Guo
- 1 Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,2 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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226
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Dhaygude K, Nair A, Johansson H, Wurm Y, Sundström L. The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host. BMC Genomics 2019; 20:301. [PMID: 30991952 PMCID: PMC6469114 DOI: 10.1186/s12864-019-5665-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/02/2019] [Indexed: 02/05/2023] Open
Abstract
Background Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. The wood ant Formica exsecta (Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well-established model for studies of ecological characteristics and evolutionary conflict. Results In this study, we sequenced and assembled draft genomes for F. exsecta and its endosymbiont Wolbachia. The F. exsecta draft genome is 277.7 Mb long; we identify 13,767 protein coding genes, for which we provide gene ontology and protein domain annotations. This is also the first report of a Wolbachia genome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) from Wolbachia to F. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes. Conclusion We present the first draft genome of ant F. exsecta, and its endosymbiont Wolbachia (wFex), and show considerable rates of gene transfer from the symbiont to the host. We expect that especially the F. exsecta genome will be valuable resource in further exploration of the molecular basis of the evolution of social organization. Electronic supplementary material The online version of this article (10.1186/s12864-019-5665-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kishor Dhaygude
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.
| | - Abhilash Nair
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Helena Johansson
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland
| | - Yannick Wurm
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
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227
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Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera. G3-GENES GENOMES GENETICS 2019; 9:1055-1063. [PMID: 30792192 PMCID: PMC6469410 DOI: 10.1534/g3.118.200857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNA-seq has proven to be a powerful tool to unravel various aspects of the transcriptome, especially the quantification of alternative splicing (AS) that leads to isoform diversity. The honey bee (Apis mellifera) is an important model organism for studying the molecular underpinnings of behavioral plasticity and social behavior, and recent RNA-seq studies of honey bees have revealed AS patterns and their regulation by DNA methylation. However, tissue-specific AS patterns have not been fully explored. In this paper, we characterized AS patterns in two different honey bee tissue types, and also explored their conservation and regulation. We used the RNA-seq data from brain and fat body to improve the existing models of honey bee genes and identified tissue-specific AS patterns. We found that AS genes show high conservation between honey bee and Drosophila melanogaster. We also confirmed and extended previous findings of a correlation between gene body DNA methylation and AS patterns, providing further support for the role of DNA methylation in regulating AS. In addition, our analysis suggests distinct functional roles for tissue-specific alternatively spliced genes. Taken together, our work provides new insights into the conservation and dynamics of AS patterns across different tissue types.
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Comparative transcriptomics of social insect queen pheromones. Nat Commun 2019; 10:1593. [PMID: 30962449 PMCID: PMC6453924 DOI: 10.1038/s41467-019-09567-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 03/19/2019] [Indexed: 12/18/2022] Open
Abstract
Queen pheromones are chemical signals that mediate reproductive division of labor in eusocial animals. Remarkably, queen pheromones are composed of identical or chemically similar compounds in some ants, wasps and bees, even though these taxa diverged >150MYA and evolved queens and workers independently. Here, we measure the transcriptomic consequences of experimental exposure to queen pheromones in workers from two ant and two bee species (genera: Lasius, Apis, Bombus), and test whether they are similar across species. Queen pheromone exposure affected transcription and splicing at many loci. Many genes responded consistently in multiple species, and the set of pheromone-sensitive genes was enriched for functions relating to lipid biosynthesis and transport, olfaction, production of cuticle, oogenesis, and histone (de)acetylation. Pheromone-sensitive genes tend to be evolutionarily ancient, positively selected, peripheral in the gene coexpression network, hypomethylated, and caste-specific in their expression. Our results reveal how queen pheromones achieve their effects, and suggest that ants and bees use similar genetic modules to achieve reproductive division of labor.
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Wallberg A, Bunikis I, Pettersson OV, Mosbech MB, Childers AK, Evans JD, Mikheyev AS, Robertson HM, Robinson GE, Webster MT. A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC Genomics 2019; 20:275. [PMID: 30961563 PMCID: PMC6454739 DOI: 10.1186/s12864-019-5642-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/24/2019] [Indexed: 01/27/2023] Open
Abstract
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Results Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor > 98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features. Conclusions The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics. Electronic supplementary material The online version of this article (10.1186/s12864-019-5642-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mai-Britt Mosbech
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna K Childers
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA.,USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | - Jay D Evans
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | | | - Hugh M Robertson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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230
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019. [PMID: 30935422 DOI: 10.1101/201731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department 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
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department 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
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department 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
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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Panfilio KA, Vargas Jentzsch IM, Benoit JB, Erezyilmaz D, Suzuki Y, Colella S, Robertson HM, Poelchau MF, Waterhouse RM, Ioannidis P, Weirauch MT, Hughes DST, Murali SC, Werren JH, Jacobs CGC, Duncan EJ, Armisén D, Vreede BMI, Baa-Puyoulet P, Berger CS, Chang CC, Chao H, Chen MJM, Chen YT, Childers CP, Chipman AD, Cridge AG, Crumière AJJ, Dearden PK, Didion EM, Dinh H, Doddapaneni HV, Dolan A, Dugan S, Extavour CG, Febvay G, Friedrich M, Ginzburg N, Han Y, Heger P, Holmes CJ, Horn T, Hsiao YM, Jennings EC, Johnston JS, Jones TE, Jones JW, Khila A, Koelzer S, Kovacova V, Leask M, Lee SL, Lee CY, Lovegrove MR, Lu HL, Lu Y, Moore PJ, Munoz-Torres MC, Muzny DM, Palli SR, Parisot N, Pick L, Porter ML, Qu J, Refki PN, Richter R, Rivera-Pomar R, Rosendale AJ, Roth S, Sachs L, Santos ME, Seibert J, Sghaier E, Shukla JN, Stancliffe RJ, Tidswell O, Traverso L, van der Zee M, Viala S, Worley KC, Zdobnov EM, Gibbs RA, Richards S. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biol 2019; 20:64. [PMID: 30935422 PMCID: PMC6444547 DOI: 10.1186/s13059-019-1660-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. RESULTS The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. CONCLUSIONS With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.
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Affiliation(s)
- Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany.
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK.
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Deniz Erezyilmaz
- Department of Biochemistry and Cell Biology and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
- Present address: Department of Physiology, Anatomy and Genetics and Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, OX1 3SR, UK
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA, 02481, USA
| | - Stefano Colella
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
- Present address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, INRA, IRD, CIRAD, SupAgro, University of Montpellier, Montpellier, France
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Robert M Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
- Present address: Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Present address: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Present address: Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745, Jena, Germany
| | - Elizabeth J Duncan
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David Armisén
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Barbara M I Vreede
- Department 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
| | | | - Chloé S Berger
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Chun-Che Chang
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mei-Ju M Chen
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Yen-Ta Chen
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Ariel D Chipman
- Department 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
| | - Andrew G Cridge
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Antonin J J Crumière
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Peter K Dearden
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: School of Life Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gérard Febvay
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Neta Ginzburg
- Department 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
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter Heger
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Thorsten Horn
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Yi-Min Hsiao
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Tamsin E Jones
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Stefan Koelzer
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | | | - Megan Leask
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Chien-Yueh Lee
- National Agricultural Library, Beltsville, MD, 20705, USA
| | - Mackenzie R Lovegrove
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
| | - Hsiao-Ling Lu
- Department of Entomology/Institute of Biotechnology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Yong Lu
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Patricia J Moore
- Department of Entomology, University of Georgia, 120 Cedar St., Athens, GA, 30602, USA
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Subba R Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Leslie Pick
- Department of Entomology and Program in Molecular & Cell Biology, University of Maryland, College Park, MD, 20742, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Peter N Refki
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
- Present address: Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Rose Richter
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Present address: Earthworks Institute, 185 Caroline Street, Rochester, NY, 14620, USA
| | - Rolando Rivera-Pomar
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de Buenos Aires, Pergamino, Argentina
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Siegfried Roth
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Lena Sachs
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - M Emília Santos
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jan Seibert
- Institute for Zoology: Developmental Biology, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Essia Sghaier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Jayendra N Shukla
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
- Present address: Department of Biotechnology, Central University of Rajasthan (CURAJ), NH-8, Bandarsindri, Ajmer, 305801, India
| | - Richard J Stancliffe
- Argelander-Institut für Astronomie, Universität Bonn, Auf dem Hügel 71, 53121, Bonn, Germany
- Present address: E. A. Milne Centre for Astrophysics, Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, UK
| | - Olivia Tidswell
- Department of Biochemistry and Genomics Aotearoa, University of Otago, Dunedin, 9054, New Zealand
- Present address: Department of Zoology, University of Cambridge, Cambridge, CB2 3DT, UK
| | - Lucila Traverso
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Maurijn van der Zee
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Séverine Viala
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, École Normale Supérieure de Lyon, 46 Allée d'Italie, 69364, Lyon, France
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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Jackson C, van Staaden M. Characterization of locomotor response to psychostimulants in the parthenogenetic marbled crayfish (Procambarus fallax forma virginalis): A promising model for studying the neural and molecular mechanisms of drug addiction. Behav Brain Res 2019; 361:131-138. [PMID: 30550950 DOI: 10.1016/j.bbr.2018.12.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 11/17/2022]
Abstract
Although scientific research using mammalian models has made great strides in uncovering the enigmatic neural and molecular mechanisms orchestrating the state of drug addiction, a complete understanding has thus far eluded researchers. The complexity of the task has led to the use of invertebrate model systems to complement the research of drug-induced reward in mammalian systems. Invertebrates, such as crayfish, offer excellent model systems to help reveal the underlying mechanisms of drug addiction as they retain the ancestral neural reward circuit that is evolutionarily conserved across taxa, and they possess relatively few, large neurons, laid out in an accessible, modularly organized nervous system. Crayfish offer the benefits of delineated developmental life stages, a large body size suitable for a variety of experimental methods, and stereotyped behaviors. Unique among crayfish is the parthenogenetic marbled crayfish (Procambarus fallax forma virginalis), a species of asexually reproducing, genetically identical clones. With the benefits of reduced individual variation, high fecundity, and easy lab husbandry, the marbled crayfish would make a particularly powerful addition to the animal model repertoire. Here we characterize the locomotor response of juvenile P. f. f. virginalis exposed to the psychostimulant, d-amphetamine sulfate. Custom video-tracking software was used to record the movement patterns of juveniles exposed to water infused with varying concentrations of d-amphetamine sulfate. ANOVA demonstrated that crayfish locomotion was significantly impacted by drug concentration. These psychostimulant effects provide the foundation of P. f. f. virginalis as a model for parsing the neural and molecular mechanisms of drug addiction.
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Affiliation(s)
- Cedric Jackson
- J.P. Scott Center for Neuroscience, Mind & Behavior, and Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Moira van Staaden
- J.P. Scott Center for Neuroscience, Mind & Behavior, and Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.
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de Souza CL, Dos Santos-Pinto JRA, Esteves FG, Perez-Riverol A, Fernandes LGR, de Lima Zollner R, Palma MS. Revisiting Polybia paulista wasp venom using shotgun proteomics - Insights into the N-linked glycosylated venom proteins. J Proteomics 2019; 200:60-73. [PMID: 30905720 DOI: 10.1016/j.jprot.2019.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022]
Abstract
The partial proteome of Polybia paulista wasp venom was previously reported elsewhere using a gel-dependent approach and resulted in the identification of a limited number of venom toxins. Here, we reinvestigated the P. paulista venom using a gel-free shotgun proteomic approach; the highly dynamic range of this approach facilitated the detection and identification of 1673 proteins, of which 23 venom proteins presented N-linked glycosylation as a posttranslational modification. Three different molecular forms of PLA1 were identified as allergenic proteins, and two of these forms were modified by N-linked glycosylation. This study reveals an extensive repertoire of hitherto undescribed proteins that were classified into the following six different functional groups: (i) typical venom proteins; (ii) proteins related to the folding/conformation and PTMs of toxins; (iii) proteins that protect toxins from oxidative stress; (iv) proteins involved in chemical communication; (v) housekeeping proteins; and (vi) uncharacterized proteins. It was possible to identify venom toxin-like proteins that are commonly reported in other animal venoms, including arthropods such as spiders and scorpions. Thus, the findings reported here may contribute to improving our understanding of the composition of P. paulista venom, its envenoming mechanism and the pathologies experienced by the victim after the wasp stinging accident. BIOLOGICAL SIGNIFICANCE: The present study significantly expanded the number of proteins identified in P. paulista venom, contributing to improvements in our understanding of the envenoming mechanism produced by sting accidents caused by this wasp. For example, novel wasp venom neurotoxins have been identified, but no studies have assessed the presence of this type of toxin in social wasp venoms. In addition, 23 N-linked glycosylated venom proteins were identified in the P. paulista venom proteome, and some of these proteins might be relevant allergens that are immunoreactive to human IgE.
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Affiliation(s)
- Caroline Lacerra de Souza
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil
| | - José Roberto Aparecido Dos Santos-Pinto
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil.
| | - Franciele Grego Esteves
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil
| | - Amilcar Perez-Riverol
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil
| | - Luís Gustavo Romani Fernandes
- Laboratory of Translational Immunology, Faculty of Medicine, University of Campinas (UNICAMP), Cidade Universitária "Zeferino Vaz", Campinas, SP 13083887, Brazil
| | - Ricardo de Lima Zollner
- Laboratory of Translational Immunology, Faculty of Medicine, University of Campinas (UNICAMP), Cidade Universitária "Zeferino Vaz", Campinas, SP 13083887, Brazil
| | - Mario Sergio Palma
- Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, SP 13500, Brazil.
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Falcon T, Pinheiro DG, Ferreira-Caliman MJ, Turatti ICC, de Abreu FCP, Galaschi-Teixeira JS, Martins JR, Elias-Neto M, Soares MPM, Laure MB, Figueiredo VLC, Lopes NP, Simões ZLP, Garófalo CA, Bitondi MMG. Exploring integument transcriptomes, cuticle ultrastructure, and cuticular hydrocarbons profiles in eusocial and solitary bee species displaying heterochronic adult cuticle maturation. PLoS One 2019; 14:e0213796. [PMID: 30870522 PMCID: PMC6417726 DOI: 10.1371/journal.pone.0213796] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/28/2019] [Indexed: 12/26/2022] Open
Abstract
Differences in the timing of exoskeleton melanization and sclerotization are evident when comparing eusocial and solitary bees. This cuticular maturation heterochrony may be associated with life style, considering that eusocial bees remain protected inside the nest for many days after emergence, while the solitary bees immediately start outside activities. To address this issue, we characterized gene expression using large-scale RNA sequencing (RNA-seq), and quantified cuticular hydrocarbon (CHC) through gas chromatography-mass spectrometry in comparative studies of the integument (cuticle plus its underlying epidermis) of two eusocial and a solitary bee species. In addition, we used transmission electron microscopy (TEM) for studying the developing cuticle of these and other three bee species also differing in life style. We found 13,200, 55,209 and 30,161 transcript types in the integument of the eusocial Apis mellifera and Frieseomelitta varia, and the solitary Centris analis, respectively. In general, structural cuticle proteins and chitin-related genes were upregulated in pharate-adults and newly-emerged bees whereas transcripts for odorant binding proteins, cytochrome P450 and antioxidant proteins were overrepresented in foragers. Consistent with our hypothesis, a distance correlation analysis based on the differentially expressed genes suggested delayed cuticle maturation in A. mellifera in comparison to the solitary bee. However, this was not confirmed in the comparison with F. varia. The expression profiles of 27 of 119 genes displaying functional attributes related to cuticle formation/differentiation were positively correlated between A. mellifera and F. varia, and negatively or non-correlated with C. analis, suggesting roles in cuticular maturation heterochrony. However, we also found transcript profiles positively correlated between each one of the eusocial species and C. analis. Gene co-expression networks greatly differed between the bee species, but we identified common gene interactions exclusively between the eusocial species. Except for F. varia, the TEM analysis is consistent with cuticle development timing adapted to the social or solitary life style. In support to our hypothesis, the absolute quantities of n-alkanes and unsaturated CHCs were significantly higher in foragers than in the earlier developmental phases of the eusocial bees, but did not discriminate newly-emerged from foragers in C. analis. By highlighting differences in integument gene expression, cuticle ultrastructure, and CHC profiles between eusocial and solitary bees, our data provided insights into the process of heterochronic cuticle maturation associated to the way of life.
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Affiliation(s)
- Tiago Falcon
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Núcleo de Bioinformática, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Brazil
| | - Maria Juliana Ferreira-Caliman
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Izabel C. C. Turatti
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Fabiano C. Pinto de Abreu
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Juliana S. Galaschi-Teixeira
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Juliana R. Martins
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Moysés Elias-Neto
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Michelle P. M. Soares
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Marcela B. Laure
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vera L. C. Figueiredo
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Norberto Peporine Lopes
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Zilá L. P. Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Carlos A. Garófalo
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Márcia M. G. Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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Beer K, Kolbe E, Kahana NB, Yayon N, Weiss R, Menegazzi P, Bloch G, Helfrich-Förster C. Pigment-Dispersing Factor-expressing neurons convey circadian information in the honey bee brain. Open Biol 2019; 8:rsob.170224. [PMID: 29321240 PMCID: PMC5795053 DOI: 10.1098/rsob.170224] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/07/2017] [Indexed: 11/12/2022] Open
Abstract
Pigment-Dispersing Factor (PDF) is an important neuropeptide in the brain circadian network of Drosophila and other insects, but its role in bees in which the circadian clock influences complex behaviour is not well understood. We combined high-resolution neuroanatomical characterizations, quantification of PDF levels over the day and brain injections of synthetic PDF peptide to study the role of PDF in the honey bee Apis mellifera We show that PDF co-localizes with the clock protein Period (PER) in a cluster of laterally located neurons and that the widespread arborizations of these PER/PDF neurons are in close vicinity to other PER-positive cells (neurons and glia). PDF-immunostaining intensity oscillates in a diurnal and circadian manner with possible influences for age or worker task on synchrony of oscillations in different brain areas. Finally, PDF injection into the area between optic lobes and the central brain at the end of the subjective day produced a consistent trend of phase-delayed circadian rhythms in locomotor activity. Altogether, these results are consistent with the hypothesis that PDF is a neuromodulator that conveys circadian information from pacemaker cells to brain centres involved in diverse functions including locomotion, time memory and sun-compass orientation.
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Affiliation(s)
- Katharina Beer
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Esther Kolbe
- Institute of Zoology, University of Regensburg, Universitätsstraße 31, 93040 Regensburg, Germany
| | - Noa B Kahana
- Department of Ecology, Evolution, and Behaviour, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nadav Yayon
- Department of Ecology, Evolution, and Behaviour, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ron Weiss
- Department of Ecology, Evolution, and Behaviour, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Pamela Menegazzi
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Guy Bloch
- Department of Ecology, Evolution, and Behaviour, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Charlotte Helfrich-Förster
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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236
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Scheffzek K, Shivalingaiah G. Ras-Specific GTPase-Activating Proteins-Structures, Mechanisms, and Interactions. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031500. [PMID: 30104198 DOI: 10.1101/cshperspect.a031500] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ras-specific GTPase-activating proteins (RasGAPs) down-regulate the biological activity of Ras proteins by accelerating their intrinsic rate of GTP hydrolysis, basically by a transition state stabilizing mechanism. Oncogenic Ras is commonly not sensitive to RasGAPs caused by interference of mutants with the electronic or steric requirements of the transition state, resulting in up-regulation of activated Ras in respective cells. RasGAPs are modular proteins containing a helical catalytic RasGAP module surrounded by smaller domains that are frequently involved in the subcellular localization or contributing to regulatory features of their host proteins. In this review, we summarize current knowledge about RasGAP structure, mechanism, regulation, and dual-substrate specificity and discuss in some detail neurofibromin, one of the most important negative Ras regulators in cellular growth control and neuronal function.
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Affiliation(s)
- Klaus Scheffzek
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
| | - Giridhar Shivalingaiah
- Division of Biological Chemistry (Biocenter), Medical University of Innsbruck, A-6020 Innsbruck, Austria
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Nikolić TV, Kojić D, Orčić S, Vukašinović EL, Blagojević DP, Purać J. Laboratory bioassays on the response of honey bee (Apis mellifera L.) glutathione S-transferase and acetylcholinesterase to the oral exposure to copper, cadmium, and lead. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:6890-6897. [PMID: 30635884 DOI: 10.1007/s11356-018-3950-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
In the present study, the influence of cadmium, copper, and lead on two enzymes often used as biomarkers in toxicological analysis was investigated. Bees were fed with 1 M sucrose solution containing 10-fold serial dilutions of CuCl2 (1000 mg L-1, 100 mg L-1, and 10 mg L-1), CdCl2 (0.1 mg L-1, 0.01 mg L-1, and 0.001 mg L-1), or PbCl2 (10 mg L-1, 1 mg L-1, and 0.1 mg L-1) during 48 h. Our results showed that the total glutathione S-transferase activity was not changed under the influence of cadmium and lead, and it was decreased with the highest concentration of copper. The level of gene expression of the three analyzed classes of glutathione S-transferase was significantly increased with increasing concentrations of copper and cadmium. Lead did not cause significant changes in glutathione S-transferase activity and gene expression, while it showed biphasic effect on acetylcholinesterase activity: lower concentration of lead, 0.1 mg L-1 inhibited and higher dose, 10 mg L-1 induced acetylcholinesterase activity in honey bees. Furthermore, our results showed a significant decrease of the acetylcholinesterase activity in honey bees treated with 0.001 and 0.01 mg L-1 CdCl2. Our results indicate the influence of cadmium, copper, and lead on GST and AChE in the honey bees. These results form the basis for future research on the impact of metallic trace element pollution on honey bees.
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Affiliation(s)
- Tatjana V Nikolić
- Department of Biology and Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Republic of Serbia.
| | - Danijela Kojić
- Department of Biology and Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Republic of Serbia
| | - Snežana Orčić
- Department of Biology and Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Republic of Serbia
| | - Elvira L Vukašinović
- Department of Biology and Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Republic of Serbia
| | - Duško P Blagojević
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11000, Republic of Serbia
| | - Jelena Purać
- Department of Biology and Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, Novi Sad, 21000, Republic of Serbia
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238
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Tupec M, Buček A, Janoušek V, Vogel H, Prchalová D, Kindl J, Pavlíčková T, Wenzelová P, Jahn U, Valterová I, Pichová I. Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera. eLife 2019; 8:e39231. [PMID: 30714899 PMCID: PMC6361591 DOI: 10.7554/elife.39231] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022] Open
Abstract
Fatty acyl reductases (FARs) are involved in the biosynthesis of fatty alcohols that serve a range of biological roles. Insects typically harbor numerous FAR gene family members. While some FARs are involved in pheromone biosynthesis, the biological significance of the large number of FARs in insect genomes remains unclear. Using bumble bee (Bombini) FAR expression analysis and functional characterization, hymenopteran FAR gene tree reconstruction, and inspection of transposable elements (TEs) in the genomic environment of FARs, we uncovered a massive expansion of the FAR gene family in Hymenoptera, presumably facilitated by TEs. The expansion occurred in the common ancestor of bumble bees and stingless bees (Meliponini). We found that bumble bee FARs from the expanded FAR-A ortholog group contribute to the species-specific pheromone composition. Our results indicate that expansion and functional diversification of the FAR gene family played a key role in the evolution of pheromone communication in Hymenoptera.
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Affiliation(s)
- Michal Tupec
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Aleš Buček
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
- Okinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Václav Janoušek
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Heiko Vogel
- Department of EntomologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Darina Prchalová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Jiří Kindl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Tereza Pavlíčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Petra Wenzelová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Irena Valterová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
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239
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Dogantzis KA, Zayed A. Recent advances in population and quantitative genomics of honey bees. CURRENT OPINION IN INSECT SCIENCE 2019; 31:93-98. [PMID: 31109680 DOI: 10.1016/j.cois.2018.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/09/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
The increase in the availability of individual Apis mellifera genomes has resulted in significant progress toward understanding the evolution and adaptation of the honey bee. These efforts have identified new subspecies, evolutionary lineages, and a significant number of genes involved with adaptations and colony-level quantitative traits. Many studies have also developed genetic assays that are being used to monitor the movement and admixture of honey bee populations. These resources are valuable for conservation and breeding programs that seek to improve the economic value of colonies or preserve locally adapted populations and subspecies. This review provides a brief discussion on how population and quantitative genomic studies has improved our understanding of the honey bee.
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Affiliation(s)
- Kathleen A Dogantzis
- Department of Biology, York University, 4700 Keele St., Toronto, Ontario, Canada
| | - Amro Zayed
- Department of Biology, York University, 4700 Keele St., Toronto, Ontario, Canada.
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240
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Mello TRP, Aleixo AC, Pinheiro DG, Nunes FMF, Cristino AS, Bitondi MMG, Barchuk AR, Simões ZLP. Hormonal control and target genes of ftz-f1 expression in the honeybee Apis mellifera: a positive loop linking juvenile hormone, ftz-f1, and vitellogenin. INSECT MOLECULAR BIOLOGY 2019; 28:145-159. [PMID: 30270498 DOI: 10.1111/imb.12541] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ftz-f1 is an orphan member of the nuclear hormone receptor superfamily. A 20-hydroxyecdysone pulse allows ftz-f1 gene expression, which then regulates the activity of downstream genes involved in major developmental progression events. In honeybees, the expression of genes like vitellogenin (vg), prophenoloxidase and juvenile hormone-esterase during late pharate-adult development is known to be hormonally controlled in both queens and workers by increasing juvenile hormone (JH) titres in the presence of declining levels of ecdysteroids. Since Ftz-f1 is known for mediating intracellular JH signalling, we hypothesized that ftz-f1 could mediate JH action during the pharate-adult development of honeybees, thus controlling the expression of these genes. Here, we show that ftz-f1 has caste-specific transcription profiles during this developmental period, with a peak coinciding with the increase in JH titre, and that its expression is upregulated by JH and downregulated by ecdysteroids. RNAi-mediated knock down of ftz-f1 showed that the expression of genes essential for adult development (e.g. vg and cuticular genes) depends on ftz-f1 expression. Finally, a double-repressor hypothesis-inspired vg gene knock-down experiment suggests the existence of a positive molecular loop between JH, ftz-f1 and vg.
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Affiliation(s)
- T R P Mello
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - A C Aleixo
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - D G Pinheiro
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - F M F Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - A S Cristino
- Translational Research Institute, The University of Queensland Diamantina Institute, Brisbane, Australia
| | - M M G Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - A R Barchuk
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - Z L P Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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241
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Sommerlandt FMJ, Brockmann A, Rössler W, Spaethe J. Immediate early genes in social insects: a tool to identify brain regions involved in complex behaviors and molecular processes underlying neuroplasticity. Cell Mol Life Sci 2019; 76:637-651. [PMID: 30349993 PMCID: PMC6514070 DOI: 10.1007/s00018-018-2948-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/25/2018] [Accepted: 10/15/2018] [Indexed: 01/31/2023]
Abstract
Social insects show complex behaviors and master cognitive tasks. The underlying neuronal mechanisms, however, are in most cases only poorly understood due to challenges in monitoring brain activity in freely moving animals. Immediate early genes (IEGs) that get rapidly and transiently expressed following neuronal stimulation provide a powerful tool for detecting behavior-related neuronal activity in vertebrates. In social insects, like honey bees, and in insects in general, this approach is not yet routinely established, even though these genes are highly conserved. First studies revealed a vast potential of using IEGs as neuronal activity markers to analyze the localization, function, and plasticity of neuronal circuits underlying complex social behaviors. We summarize the current knowledge on IEGs in social insects and provide ideas for future research directions.
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Affiliation(s)
- Frank M J Sommerlandt
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Axel Brockmann
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India
| | - Wolfgang Rössler
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Johannes Spaethe
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
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242
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Quan Q, Hu X, Pan B, Zeng B, Wu N, Fang G, Cao Y, Chen X, Li X, Huang Y, Zhan S. Draft genome of the cotton aphid Aphis gossypii. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 105:25-32. [PMID: 30590189 DOI: 10.1016/j.ibmb.2018.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 12/03/2018] [Accepted: 12/14/2018] [Indexed: 05/15/2023]
Abstract
The cotton aphid Aphis gossypii Glover is a worldwide agricultural pest that feeds on cotton, melon, and other landscape plants, causing a high level of economic loss. In addition to the common characteristics shared with other aphids, Ap. gossypii has evolved multiple biotypes that present substantial differences in host adaption. These intriguing biological features are of interest from both a fundamental and applied perspective. However, the molecular studies of Ap. gossypii have been restrained by the lack of a reference genome. Furthermore, in order to establish a platform for the development of novel and sustainable control methods, it is necessary to generate genomic resources for Ap. gossypii. Here, we present a 294 Mb draft genome sequence of Ap. gossypii, which consists of 4,724 scaffolds with an N50 size of 438 kb. Compared to other aphid species with published genomes, Ap. gossypii presents the most compact genome size. A total of 14,694 protein-coding genes were predicted and annotated in the consensus gene set, 98.03% of CEGMA genes and 93.5% of BUSCO genes were captured respectively. Genome-wide selection analyses revealed that significantly evolving pathways in the genus Aphis are related to biological processes of detoxification, steroid biosynthesis, and ethylbenzene degradation. The acquisition of the genome of Ap. gossypii makes it possible to understand the molecular mechanism of intricate biological traits of this species, and will further facilitate the study of aphid evolution.
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Affiliation(s)
- Qingmei Quan
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiao Hu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bohu Pan
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baosheng Zeng
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ningning Wu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gangqi Fang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanghui Cao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; Plant Science Research Center, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Shuai Zhan
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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243
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Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol 2019; 19:11. [PMID: 30626321 PMCID: PMC6327564 DOI: 10.1186/s12862-018-1324-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. RESULTS Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6% in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58% in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. CONCLUSION While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire.
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Affiliation(s)
- Malte Petersen
- University of Bonn, Bonn, Germany
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt, 60325 Germany
| | - David Armisén
- Université 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, Lyon, 69364 France
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Abderrahman Khila
- Université 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, Lyon, 69364 France
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, Freiburg (Brsg.), 79104 Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
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244
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Arvidson R, Kaiser M, Lee SS, Urenda JP, Dail C, Mohammed H, Nolan C, Pan S, Stajich JE, Libersat F, Adams ME. Parasitoid Jewel Wasp Mounts Multipronged Neurochemical Attack to Hijack a Host Brain. Mol Cell Proteomics 2019; 18:99-114. [PMID: 30293061 PMCID: PMC6317478 DOI: 10.1074/mcp.ra118.000908] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/26/2018] [Indexed: 11/06/2022] Open
Abstract
The parasitoid emerald jewel wasp Ampulex compressa induces a compliant state of hypokinesia in its host, the American cockroach Periplaneta americana through direct envenomation of the central nervous system (CNS). To elucidate the biochemical strategy underlying venom-induced hypokinesia, we subjected the venom apparatus and milked venom to RNAseq and proteomics analyses to construct a comprehensive "venome," consisting of 264 proteins. Abundant in the venome are enzymes endogenous to the host brain, including M13 family metalloproteases, phospholipases, adenosine deaminase, hyaluronidase, and neuropeptide precursors. The amphipathic, alpha-helical ampulexins are among the most abundant venom components. Also prominent are members of the Toll/NF-κB signaling pathway, including proteases Persephone, Snake, Easter, and the Toll receptor ligand Spätzle. We find evidence that venom components are processed following envenomation. The acidic (pH∼4) venom contains unprocessed neuropeptide tachykinin and corazonin precursors and is conspicuously devoid of the corresponding processed, biologically active peptides. Neutralization of venom leads to appearance of mature tachykinin and corazonin, suggesting that the wasp employs precursors as a prolonged time-release strategy within the host brain post-envenomation. Injection of fully processed tachykinin into host cephalic ganglia elicits short-term hypokinesia. Ion channel modifiers and cytolytic toxins are absent in A. compressa venom, which appears to hijack control of the host brain by introducing a "storm" of its own neurochemicals. Our findings deepen understanding of the chemical warfare underlying host-parasitoid interactions and in particular neuromodulatory mechanisms that enable manipulation of host behavior to suit the nutritional needs of opportunistic parasitoid progeny.
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Affiliation(s)
- Ryan Arvidson
- From the ‡Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, California 92521;; ¶Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521
| | - Maayan Kaiser
- §Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Sang Soo Lee
- ¶Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521;; ‖Graduate Program in Neuroscience, University of California, Riverside, California 92521
| | - Jean-Paul Urenda
- ¶Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521
| | - Christopher Dail
- ¶Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521
| | - Haroun Mohammed
- ¶Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521
| | - Cebrina Nolan
- **Department of Entomology, University of California, Riverside, California 92521
| | - Songqin Pan
- ‡‡Institute for Integrated Genome Biology, University of California, Riverside, California 92521
| | - Jason E Stajich
- §§Department of Microbiology & Plant Pathology, University of California, Riverside, California 92521
| | - Frederic Libersat
- §Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Michael E Adams
- From the ‡Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, California 92521;; ¶Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521;; ‖Graduate Program in Neuroscience, University of California, Riverside, California 92521;; **Department of Entomology, University of California, Riverside, California 92521;; ‡‡Institute for Integrated Genome Biology, University of California, Riverside, California 92521;; ¶Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521;.
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245
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Shullia NI, Raffiudin R, Juliandi B. The Phosphofructokinase and Pyruvate Kinase Genes in Apis andreniformis and Apis cerana indica: Exon Intron Organisation and Evolution. Trop Life Sci Res 2019; 30:89-107. [PMID: 30847035 PMCID: PMC6396890 DOI: 10.21315/tlsr2019.30.1.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Genes related to carbohydrate metabolism have evolved rapidly in eusocial bees, including honey bees. However, the characterisation of carbohydrate metabolism genes has not been reported in Apis andreniformis or Apis cerana indica. This study aimed to characterise phosphofructokinase (PFK) and pyruvate kinase (PK) genes in these honey bee species and to analyse the evolution of the genus Apis using these genes. This study found the first data regarding A. andreniformis PFK and PK-like nucleotide sequences. A BLAST-n algorithm-based search showed that A. andreniformis and A. c. indica PFK and PK genes were homologous with those of Apis florea and Apis cerana cerana from Korea, respectively. Multiple alignments of PFKs from five Apis species showed many exon gains and losses, but only one among the PKs. Thus, the exon-intron organisation of the PK genes may be more conserved compare with that of the PFKs. Another evolutionary pattern indicated that more nucleotide substitutions occurred in Apis' PK than PFK genes. Deduced PFK amino acid sequences revealed a PFK consensus pattern of 19 amino acids, while the deduced PK amino acid sequences were predicted to have barrel and alpha/beta domains. Based on these two metabolism-related genes, The Neighbour-joining and Maximum likelihood phylogenetic trees are congruent and revealed that the A. andreniformis and A. florea group were in the basal position. Apis mellifera, A. cerana, and Apis dorsata formed a monophyletic clade, although the positions of A. mellifera and A. dorsata were different in the nucleotide- and amino acid-based phylogenetic trees.
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Affiliation(s)
- Nurul I. Shullia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia
| | - Rika Raffiudin
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia
| | - Berry Juliandi
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor 16680, Indonesia
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246
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Blaz J, Barrera-Redondo J, Vázquez-Rosas-Landa M, Canedo-Téxon A, Aguirre von Wobeser E, Carrillo D, Stouthamer R, Eskalen A, Villafán E, Alonso-Sánchez A, Lamelas A, Ibarra-Juarez LA, Pérez-Torres CA, Ibarra-Laclette E. Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. Life (Basel) 2018; 9:E2. [PMID: 30583535 PMCID: PMC6463014 DOI: 10.3390/life9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/08/2018] [Accepted: 12/20/2018] [Indexed: 01/03/2023] Open
Abstract
Mutualistic symbiosis and eusociality have developed through gradual evolutionary processes at different times in specific lineages. Like some species of termites and ants, ambrosia beetles have independently evolved a mutualistic nutritional symbiosis with fungi, which has been associated with the evolution of complex social behaviors in some members of this group. We sequenced the transcriptomes of two ambrosia complexes (Euwallacea sp. near fornicatus⁻Fusarium euwallaceae and Xyleborus glabratus⁻Raffaelea lauricola) to find evolutionary signatures associated with mutualism and behavior evolution. We identified signatures of positive selection in genes related to nutrient homeostasis; regulation of gene expression; development and function of the nervous system, which may be involved in diet specialization; behavioral changes; and social evolution in this lineage. Finally, we found convergent changes in evolutionary rates of proteins across lineages with phylogenetically independent origins of sociality and mutualism, suggesting a constrained evolution of conserved genes in social species, and an evolutionary rate acceleration related to changes in selective pressures in mutualistic lineages.
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Affiliation(s)
- Jazmín Blaz
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Josué Barrera-Redondo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04500, Mexico.
| | | | - Anahí Canedo-Téxon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | | | - Daniel Carrillo
- Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Richard Stouthamer
- Department of Plant Pathology, University of California⁻Riverside, Riverside, CA 92521, USA.
| | - Akif Eskalen
- Department of Plant Pathology, University of California, Davis, CA 95616-8751, USA.
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Luis Arturo Ibarra-Juarez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
- Cátedras CONACyT/Instituto de Ecología A.C., Xalapa, Veracruz 91070, Mexico.
| | - Claudia Anahí Pérez-Torres
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
- Cátedras CONACyT/Instituto de Ecología A.C., Xalapa, Veracruz 91070, Mexico.
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
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247
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Liu Y, Zhao X, Huang J, Chen M, An J. Structural Insights into the Preferential Binding of PGRP-SAs from Bumblebees and Honeybees to Dap-Type Peptidoglycans Rather than Lys-Type Peptidoglycans. THE JOURNAL OF IMMUNOLOGY 2018; 202:249-259. [DOI: 10.4049/jimmunol.1800439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/28/2018] [Indexed: 11/19/2022]
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248
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Dong X, Chaisiri K, Xia D, Armstrong SD, Fang Y, Donnelly MJ, Kadowaki T, McGarry JW, Darby AC, Makepeace BL. Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism. Gigascience 2018; 7:5160133. [PMID: 30445460 PMCID: PMC6275457 DOI: 10.1093/gigascience/giy127] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
Background Trombidid mites have a unique life cycle in which only the larval stage is ectoparasitic. In the superfamily Trombiculoidea ("chiggers"), the larvae feed preferentially on vertebrates, including humans. Species in the genus Leptotrombidium are vectors of a potentially fatal bacterial infection, scrub typhus, that affects 1 million people annually. Moreover, chiggers can cause pruritic dermatitis (trombiculiasis) in humans and domesticated animals. In the Trombidioidea (velvet mites), the larvae feed on other arthropods and are potential biological control agents for agricultural pests. Here, we present the first trombidid mites genomes, obtained both for a chigger, Leptotrombidium deliense, and for a velvet mite, Dinothrombium tinctorium. Results Sequencing was performed using Illumina technology. A 180 Mb draft assembly for D. tinctorium was generated from two paired-end and one mate-pair library using a single adult specimen. For L. deliense, a lower-coverage draft assembly (117 Mb) was obtained using pooled, engorged larvae with a single paired-end library. Remarkably, both genomes exhibited evidence of ancient lateral gene transfer from soil-derived bacteria or fungi. The transferred genes confer functions that are rare in animals, including terpene and carotenoid synthesis. Thirty-seven allergenic protein families were predicted in the L. deliense genome, of which nine were unique. Preliminary proteomic analyses identified several of these putative allergens in larvae. Conclusions Trombidid mite genomes appear to be more dynamic than those of other acariform mites. A priority for future research is to determine the biological function of terpene synthesis in this taxon and its potential for exploitation in disease control.
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Affiliation(s)
- Xiaofeng Dong
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.,Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China.,School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China.,Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom
| | - Kittipong Chaisiri
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom.,Faculty of Tropical Medicine, Mahidol University, Ratchathewi Bangkok 10400, Thailand
| | - Dong Xia
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom.,The Royal Veterinary College, London NW1 0TU, United Kingdom
| | - Stuart D Armstrong
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom
| | - Yongxiang Fang
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - John W McGarry
- Institute of Veterinary Science, University of Liverpool, Liverpool L3 5RP, United Kingdom
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Benjamin L Makepeace
- Institute of Infection & Global Health, University of Liverpool, L3 5RF, United Kingdom
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249
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Evans JD, McKenna D, Scully E, Cook SC, Dainat B, Egekwu N, Grubbs N, Lopez D, Lorenzen MD, Reyna SM, Rinkevich FD, Neumann P, Huang Q. Genome of the small hive beetle (Aethina tumida, Coleoptera: Nitidulidae), a worldwide parasite of social bee colonies, provides insights into detoxification and herbivory. Gigascience 2018; 7:5232982. [PMID: 30535280 PMCID: PMC6302959 DOI: 10.1093/gigascience/giy138] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/08/2018] [Indexed: 12/11/2022] Open
Abstract
Background The small hive beetle (Aethina tumida; ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, facilitating its spread and increasing its impact on honey bees and other pollinators. We have sequenced and annotated the ATUMI genome, providing the first genomic resources for this species and for the Nitidulidae, a beetle family that is closely related to the extraordinarily species-rich clade of beetles known as the Phytophaga. ATUMI thus provides a contrasting view as a neighbor for one of the most successful known animal groups. Results We present a robust genome assembly and a gene set possessing 97.5% of the core proteins known from the holometabolous insects. The ATUMI genome encodes fewer enzymes for plant digestion than the genomes of wood-feeding beetles but nonetheless shows signs of broad metabolic plasticity. Gustatory receptors are few in number compared to other beetles, especially receptors with known sensitivity (in other beetles) to bitter substances. In contrast, several gene families implicated in detoxification of insecticides and adaptation to diverse dietary resources show increased copy numbers. The presence and diversity of homologs involved in detoxification differ substantially from the bee hosts of ATUMI. Conclusions Our results provide new insights into the genomic basis for local adaption and invasiveness in ATUMI and a blueprint for control strategies that target this pest without harming their honey bee hosts. A minimal set of gustatory receptors is consistent with the observation that, once a host colony is invaded, food resources are predictable. Unique detoxification pathways and pathway members can help identify which treatments might control this species even in the presence of honey bees, which are notoriously sensitive to pesticides.
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Affiliation(s)
- Jay D Evans
- USDA-ARS, Bee Research Laboratory, BARC-East Building 306, Beltsville, Maryland 20705, USA
| | - Duane McKenna
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152, USA
| | - Erin Scully
- USDA-ARS, Center for Grain and Animal Health, Stored Product Insect and Engineering Research Unit, Manhattan, KS 66502, USA
| | - Steven C Cook
- USDA-ARS, Bee Research Laboratory, BARC-East Building 306, Beltsville, Maryland 20705, USA
| | - Benjamin Dainat
- Agroscope, Swiss Bee Research Center, CH-3003 Bern, Switzerland
| | - Noble Egekwu
- USDA-ARS, Bee Research Laboratory, BARC-East Building 306, Beltsville, Maryland 20705, USA
| | - Nathaniel Grubbs
- Department of Entomology and Plant Pathology, North Carolina State University, 1566 Thomas Hall, Raleigh, NC 27695, USA
| | - Dawn Lopez
- USDA-ARS, Bee Research Laboratory, BARC-East Building 306, Beltsville, Maryland 20705, USA
| | - Marcé D Lorenzen
- Department of Entomology and Plant Pathology, North Carolina State University, 1566 Thomas Hall, Raleigh, NC 27695, USA
| | - Steven M Reyna
- Department of Entomology and Plant Pathology, North Carolina State University, 1566 Thomas Hall, Raleigh, NC 27695, USA
| | - Frank D Rinkevich
- USDA, Honey Bee Breeding, Genetics and Physiology Laboratory, 1157 Ben Hur Road, Baton Rouge, LA 70820, USA
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Schwarzenburgstrasse 161, CH-3097, Liebefeld, Switzerland
| | - Qiang Huang
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Schwarzenburgstrasse 161, CH-3097, Liebefeld, Switzerland.,Honey Bee Research Institute, Jiangxi Agricultural University, Zhimin Avenue 1101, 330045 Nanchang, China
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250
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Sapountzis P, Zhukova M, Shik JZ, Schiott M, Boomsma JJ. Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants. eLife 2018; 7:e39209. [PMID: 30454555 PMCID: PMC6245734 DOI: 10.7554/elife.39209] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/16/2018] [Indexed: 12/25/2022] Open
Abstract
Mollicutes, a widespread class of bacteria associated with animals and plants, were recently identified as abundant abdominal endosymbionts in healthy workers of attine fungus-farming leaf-cutting ants. We obtained draft genomes of the two most common strains harbored by Panamanian fungus-growing ants. Reconstructions of their functional significance showed that they are independently acquired symbionts, most likely to decompose excess arginine consistent with the farmed fungal cultivars providing this nitrogen-rich amino-acid in variable quantities. Across the attine lineages, the relative abundances of the two Mollicutes strains are associated with the substrate types that foraging workers offer to fungus gardens. One of the symbionts is specific to the leaf-cutting ants and has special genomic machinery to catabolize citrate/glucose into acetate, which appears to deliver direct metabolic energy to the ant workers. Unlike other Mollicutes associated with insect hosts, both attine ant strains have complete phage-defense systems, underlining that they are actively maintained as mutualistic symbionts.
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Affiliation(s)
- Panagiotis Sapountzis
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Mariya Zhukova
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jonathan Z Shik
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Morten Schiott
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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