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Friedrich M. Close to complete conservation of the brachyceran opsin repertoire in the stalk-eyed fly Teleopsis dalmanni. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:469-473. [PMID: 37814507 DOI: 10.1002/jez.b.23220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/02/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023]
Abstract
Due to the unique morphology of their adult visual system, stalk-eyed flies represent an important model of exaggerated trait evolution through sexual selection. Early physiological measurements indicated wavelength sensitivity peaks in the ultraviolet (360 nm), blue (450), blue-green (490 nm), and red (>550 nm) ranges in the compound eye retina of the stalk-eyed fly Teleopsis dalmanni, consistent with the trichromatic color and broad range motion detection vision system of brachyceran Diptera. A previous study of dipteran opsin gene diversification, however, detected only homologs of members of the long wavelength range sensitive opsin subfamilies Rh2 and Rh6 in T. dalmanni. Here, I report findings from analyzing the most recent T. dalmanni genome assembly, which revealed the conservation of most brachyceran opsin homologs except for the UV wavelength range-sensitive homolog Rh4. These results and other examples highlight the caution that needs to be applied to gene loss conclusions.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
- Department of Ophthalmological, School of Medicine, Visual, and Anatomical Sciences, Wayne State University, Detroit, Michigan, USA
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2
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Zhang Q, Zhou Q, Han S, Li Y, Wang Y, He H. The genome of sheep ked (Melophagus ovinus) reveals potential mechanisms underlying reproduction and narrower ecological niches. BMC Genomics 2023; 24:54. [PMID: 36717784 PMCID: PMC9887928 DOI: 10.1186/s12864-023-09155-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Melophagus ovinus is considered to be of great veterinary health significance. However, little is known about the information on genetic mechanisms of the specific biological characteristics and novel methods for controlling M. ovinus. RESULTS In total, the de novo genome assembly of M. ovinus was 188.421 Mb in size (330 scaffolds, N50 Length: 10.666 Mb), with a mean GC content of 27.74%. A total of 13,372 protein-coding genes were functionally annotated. Phylogenetic analysis indicated that the diversification of M. ovinus and Glossina fuscipes took place 72.76 Mya within the Late Cretaceous. Gene family expansion and contraction analysis revealed that M. ovinus has 65 rapidly-evolving families (26 expansion and 39 contractions) mainly involved DNA metabolic activity, transposases activity, odorant receptor 59a/67d-like, IMD domain-containing protein, and cuticle protein, etc. The universal and tightly conserved list of milk protein orthologues has been assembled from the genome of M. ovinus. Contractions and losses of sensory receptors and vision-associated Rhodopsin genes were significant in M. ovinus, which indicate that the M. ovinus has narrower ecological niches. CONCLUSIONS We sequenced, assembled, and annotated the whole genome sequence of M. ovinus, and launches into the preliminary genetic mechanisms analysis of the adaptive evolution characteristics of M. ovinus. These resources will provide insights to understand the biological underpinnings of this parasite and the disease control strategies.
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Affiliation(s)
- Qingxun Zhang
- grid.458458.00000 0004 1792 6416National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.418265.c0000 0004 0403 1840Beijing Milu Ecological Research Center, Beijing, 100076 China
| | - Qingsong Zhou
- grid.458458.00000 0004 1792 6416Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shuyi Han
- grid.458458.00000 0004 1792 6416National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ying Li
- grid.262246.60000 0004 1765 430XState Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China
| | - Ye Wang
- grid.458458.00000 0004 1792 6416National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongxuan He
- grid.458458.00000 0004 1792 6416National Research Center for Wildlife-Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
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3
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Asgari D, Saski CA, Meisel RP, Nayduch D. Constitutively-expressed and induced immune effectors in the house fly (Musca domestica) and the transcription factors that may regulate them. INSECT MOLECULAR BIOLOGY 2022; 31:782-797. [PMID: 35875866 DOI: 10.1111/imb.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Insects possess both infection-induced and constitutively expressed innate immune defences. Some effectors, such as lysozymes and antimicrobial peptides (AMPs), are constitutively expressed in flies, but expression patterns vary across tissues and species. The house fly (Musca domestica L.) has an impressive immune repertoire, with more effector genes than any other flies. We used RNA-seq to explore both constitutive and induced expression of immune effectors in flies. House flies were fed either Pseudomonas aeruginosa or Escherichia coli, or sterile control broth, and gene expression in the gut and carcass was analysed 4 h post-feeding. Flies fed either bacterium did not induce AMP expression, but some lysozyme and AMP genes were constitutively expressed. Prior transcriptome data from flies injected with bacteria also were analysed, and these constitutively expressed genes differed from those induced by bacterial injection. Binding sites for the transcription factor Myc were enriched upstream of constitutively expressed AMP genes, while upstream regions of induced AMPs were enriched for NF-κB binding sites resembling those of the Imd-responsive transcription factor Relish. Therefore, we identified at least two expression repertoires for AMPs in the house fly: constitutively expressed genes that may be regulated by Myc, and induced AMPs likely regulated by Relish.
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Affiliation(s)
- Danial Asgari
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, USA
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Dana Nayduch
- Arthropod-Borne Animal Diseases Research Unit, United States Department of Agriculture, Agricultural Research Service, Manhattan, Kansas, USA
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4
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Meng F, Han H, Wang M, Jiang Y, Pi Z, Qu Y, Liu Z, Cai J. Characterized Gene Repertoires and Functional Gene Reference for Forensic Entomology: Genomic and Developmental Transcriptomic Analysis of Aldrichina grahami (Diptera: Calliphoridae). JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:810-819. [PMID: 35139213 DOI: 10.1093/jme/tjac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Indexed: 06/14/2023]
Abstract
Many flies of Diptera are common entomological evidence employed in forensic investigation. Exploring the existence of inter- and intra-species genomic differences of forensically relevant insects is of great importance. Aldrichina grahami is a common blow fly species of forensic importance. The present study characterized the gene repertoires of A. grahami, and provides insights into issues related to forensic entomology, such as necrophagous behavior, gene family features, and developmental patterns. Gene families were clustered and classified according to their function in different aspects of the necrophagous lifestyle, generating several gene repertoires. The genes under positive selection pressure and evolutionary changes were screen and identified. Moreover, genes that exhibited potential prediction value in the post mortem interval (PMI) estimation and development of immature stages were subjected to analysis based on the developmental transcriptome. Related insect species were compared at the genomic level to reveal the genes associated with necrophagous behaviors. The expression of selected genes in separated repositories was verified using qPCR. This work was conducted using a high-quality chromosome-level genome assembly of A. grahami and its developmental transcriptome. The findings will facilitate future research on A. grahami and the other forensically important species.
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Affiliation(s)
- Fanming Meng
- School of Basic Medicine, Central South University, Changsha, China
| | - Han Han
- School of Basic Medicine, Central South University, Changsha, China
| | - Mo Wang
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Yangshuai Jiang
- School of Basic Medicine, Central South University, Changsha, China
| | - Zhiyun Pi
- School of Basic Medicine, Central South University, Changsha, China
| | - Yihong Qu
- School of Basic Medicine, Central South University, Changsha, China
| | - Zhuoying Liu
- School of Basic Medicine, Central South University, Changsha, China
| | - Jifeng Cai
- School of Basic Medicine, Central South University, Changsha, China
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5
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Shah JS, Buckmeier BG, Griffith W, Olafson PU, Perez de Leon AA, Renthal R. Odorant-binding protein from the stable fly (Stomoxys calcitrans) has a high-histidine N-terminal extension that binds transition metals. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 141:103707. [PMID: 34979251 DOI: 10.1016/j.ibmb.2021.103707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
The role of odorant- and pheromone-binding proteins (OBPs) in olfactory function is not fully understood. We found an OBP sequence from the stable fly, Stomoxys calcitrans, ScalOBP60, that has a 25 amino acid N-terminal extension with a high content of histidine and acidic amino acids, suggesting a possible metal binding activity. A search of public databases revealed a large number of other fly OBPs with histidine-rich N-terminal extensions, as well as beetle, wasp and ant OBPs with histidine-rich C-terminal extensions. We recombinantly expressed ScalOBP60, as well as a truncated sequence which lacks the histidine-rich N-terminal region, tScalOBP60. Using fluorescence quenching and electrospray quadrupole time-of-flight mass spectrometry (ESI-QTOF), we detected two different types of metal-binding sites. Divalent copper, nickel and zinc bind to the N-terminal histidine-rich region, and divalent copper binds to an internal sequence position. Comparison of the ESI-QTOF spectra of ScalOBP60 and tScalOBP60 showed that the histidine-rich sequence is structurally disordered, but it becomes more ordered in the presence of divalent metal. When copper is bound to the internal site, binding of a hydrophobic ligand to ScalOBP60 is inhibited. The internal and N-terminal metal sites interact allosterically, possibly through a conformational equilibrium, suggesting a mechanism for metal regulation of ligand binding to ScalOBP60. Based on our studies of ScalOBP60, we propose several possible olfactory and non-olfactory functions for this OBP.
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Affiliation(s)
- Jaee Shailesh Shah
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | | | - Wendell Griffith
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Pia Untalan Olafson
- USDA-ARS, Knipling-Bushland U.S. Livestock Insects Research Lab, Kerrville, TX, 78028, USA
| | | | - Robert Renthal
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA; Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX, 78249, USA.
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6
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Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, Davis P, De Silva NH, Diamantakis S, Dyer S, Elser J, Filippi CV, Gall A, Grigoriadis D, Guijarro-Clarke C, Gupta P, Hammond-Kosack KE, Howe KL, Jaiswal P, Kaikala V, Kumar V, Kumari S, Langridge N, Le T, Luypaert M, Maslen GL, Maurel T, Moore B, Muffato M, Mushtaq A, Naamati G, Naithani S, Olson A, Parker A, Paulini M, Pedro H, Perry E, Preece J, Quinton-Tulloch M, Rodgers F, Rosello M, Ruffier M, Seager J, Sitnik V, Szpak M, Tate J, Tello-Ruiz MK, Trevanion SJ, Urban M, Ware D, Wei S, Williams G, Winterbottom A, Zarowiecki M, Finn RD, Flicek P. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Res 2021; 50:D996-D1003. [PMID: 34791415 PMCID: PMC8728113 DOI: 10.1093/nar/gkab1007] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 11/28/2022] Open
Abstract
Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.
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Affiliation(s)
- Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ridwan M Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Barba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lahcen I Campbell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Carbajo Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Mikkel Christensen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alayne Cuzick
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Luca Da Rin Fioretto
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nishadi H De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Carla V Filippi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dionysios Grigoriadis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cristina Guijarro-Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Kim E Hammond-Kosack
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Vinay Kaikala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Nick Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gareth L Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helder Pedro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Faye Rodgers
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Seager
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Vasily Sitnik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Martin Urban
- Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Gary Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magdalena Zarowiecki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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7
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Davis RJ, Belikoff EJ, Dickey AN, Scholl EH, Benoit JB, Scott MJ. Genome and transcriptome sequencing of the green bottle fly, Lucilia sericata, reveals underlying factors of sheep flystrike and maggot debridement therapy. Genomics 2021; 113:3978-3988. [PMID: 34619342 DOI: 10.1016/j.ygeno.2021.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/03/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
The common green bottle blow fly Lucilia sericata (family, Calliphoridae) is widely used for maggot debridement therapy, which involves the application of sterile maggots to wounds. The larval excretions and secretions are important for consuming necrotic tissue and inhibiting bacterial growth in wounds of patients. Lucilia sericata is also of importance as a pest of sheep and in forensic studies to estimate a postmortem interval. Here we report the assembly of a 565.3 Mb genome from long read PacBio DNA sequencing of genomic DNA. The genome contains 14,704 predicted protein coding genes and 1709 non-coding genes. Targeted annotation and transcriptional analyses identified genes that are highly expressed in the larval salivary glands (secretions) and Malpighian tubules (excretions) under normal growth conditions and following heat stress. The genomic resources will underpin future genetic studies and in development of engineered strains for genetic control of L. sericata and for biotechnology-enhanced maggot therapy.
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Affiliation(s)
- Rebecca J Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA.
| | - Esther J Belikoff
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA.
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Campus Box 7566, Raleigh, NC 27695-7566, USA.
| | - Elizabeth H Scholl
- Bioinformatics Research Center, North Carolina State University, Campus Box 7566, Raleigh, NC 27695-7566, USA.
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211, USA.
| | - Maxwell J Scott
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA.
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8
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Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze SH, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. BMC Biol 2021; 19:150. [PMID: 34325695 PMCID: PMC8320157 DOI: 10.1186/s12915-021-01098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Pia U Olafson
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California - Davis, Davis, CA, USA
| | - Greta Buckmeier
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Xiaoting Chen
- The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Craig J Coates
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - Megan Davis
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Justin Dykema
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Scott J Emrich
- Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Evan N Jansen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel Lawson
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Gareth L Maslen
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dana Nayduch
- Arthropod-borne Animal Diseases Research Unit, USDA-ARS, Manhattan, KS, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kennan J Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Tyler J Raszick
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - José M C Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Timothy B Sackton
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Perot Saelao
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Sonja L Swiger
- Department of Entomology, Texas A&M AgriLife Research and Extension Center, Stephenville, TX, USA
| | - Sing-Hoi Sze
- Department of Computer Science & Engineering, Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX, USA
| | - Aaron M Tarone
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - David B Taylor
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, USA
| | - Wesley C Warren
- University of Missouri, Bond Life Sciences Center, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,College of Medicine, Ohio State University, Columbus, OH, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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9
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Yang Y, Ye X, Dang C, Cao Y, Hong R, Sun YH, Xiao S, Mei Y, Xu L, Fang Q, Xiao H, Li F, Ye G. Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation. BMC Biol 2021; 19:145. [PMID: 34315471 PMCID: PMC8314478 DOI: 10.1186/s12915-021-01081-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Background Hymenoptera comprise extremely diverse insect species with extensive variation in their life histories. The Dryinidae, a family of solitary wasps of Hymenoptera, have evolved innovations that allow them to hunt using venom and a pair of chelae developed from the fore legs that can grasp prey. Dryinidae larvae are also parasitoids of Auchenorrhyncha, a group including common pests such as planthoppers and leafhoppers. Both of these traits make them effective and valuable for pest control, but little is yet known about the genetic basis of its dual adaptation to parasitism and predation. Results We sequenced and assembled a high-quality genome of the dryinid wasp Gonatopus flavifemur, which at 636.5 Mb is larger than most hymenopterans. The expansion of transposable elements, especially DNA transposons, is a major contributor to the genome size enlargement. Our genome-wide screens reveal a number of positively selected genes and rapidly evolving proteins involved in energy production and motor activity, which may contribute to the predatory adaptation of dryinid wasp. We further show that three female-biased, reproductive-associated yellow genes, in response to the prey feeding behavior, are significantly elevated in adult females, which may facilitate the egg production. Venom is a powerful weapon for dryinid wasp during parasitism and predation. We therefore analyze the transcriptomes of venom glands and describe specific expansions in venom Idgf-like genes and neprilysin-like genes. Furthermore, we find the LWS2-opsin gene is exclusively expressed in male G. flavifemur, which may contribute to partner searching and mating. Conclusions Our results provide new insights into the genome evolution, predatory adaptation, venom evolution, and sex-biased genes in G. flavifemur, and present genomic resources for future in-depth comparative analyses of hymenopterans that may benefit pest control. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01081-6.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Cong Dang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yunshen Cao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Rui Hong
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Shan Xiao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Le Xu
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Huamei Xiao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.,Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, College of Life Sciences and Resource Environment, Yichun University, Yichun, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
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