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Rozo-Lopez P, Brewer W, Käfer S, Martin MM, Parker BJ. Untangling an insect's virome from its endogenous viral elements. BMC Genomics 2023; 24:636. [PMID: 37875824 PMCID: PMC10594914 DOI: 10.1186/s12864-023-09737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery. METHODS In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome. RESULTS We found reads from two insect-specific viruses (a Flavivirus and an Ambidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the 'virome' of this insect can be attributed to EVEs in the host genome. CONCLUSION Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.
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Affiliation(s)
- Paula Rozo-Lopez
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
| | - William Brewer
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Simon Käfer
- Institut Für Biologie Und Umweltwissenschaften, Carl Von Ossietzky Universität Oldenburg, 26129, Oldenburg, Germany
| | - McKayla M Martin
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA
| | - Benjamin J Parker
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37916, USA.
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Vajen B, Hänselmann S, Lutterloh F, Käfer S, Espenkötter J, Beening A, Bogin J, Schlegelberger B, Göhring G. Classification of fluorescent R-Band metaphase chromosomes using a convolutional neural network is precise and fast in generating karyograms of hematologic neoplastic cells. Cancer Genet 2021; 260-261:23-29. [PMID: 34839233 DOI: 10.1016/j.cancergen.2021.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 11/02/2022]
Abstract
Karyotype analysis has a great impact on the diagnosis, treatment and prognosis in hematologic neoplasms. The identification and characterization of chromosomes is a challenging process and needs experienced personal. Artificial intelligence provides novel support tools. However, their safe and reliable application in diagnostics needs to be evaluated. Here, we present a novel laboratory approach to identify chromosomes in cancer cells using a convolutional neural network (CNN). The CNN identified the correct chromosome class for 98.8% of chromosomes, which led to a time saving of 42% for the karyotyping workflow. These results demonstrate that the CNN has potential application value in chromosome classification of hematologic neoplasms. This study contributes to the development of an automatic karyotyping platform.
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Affiliation(s)
- Beate Vajen
- Department of Human Genetics, Hannover Medical School, Hannover 30625, Germany.
| | - Siegfried Hänselmann
- MetaSystems Hard and Software GmbH, Robert-Bosch-Str. 6, Altlussheim 68804, Germany
| | | | - Simon Käfer
- Department of Human Genetics, Hannover Medical School, Hannover 30625, Germany
| | | | - Anna Beening
- Department of Human Genetics, Hannover Medical School, Hannover 30625, Germany
| | - Jochen Bogin
- MetaSystems Hard and Software GmbH, Robert-Bosch-Str. 6, Altlussheim 68804, Germany
| | | | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Hannover 30625, Germany
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Behrens YL, Göhring G, Bawadi R, Cöktü S, Reimer C, Hoffmann B, Sänger B, Käfer S, Thol F, Erlacher M, Niemeyer CM, Baumann I, Kalb R, Schindler D, Kratz CP. A novel classification of hematologic conditions in patients with Fanconi anemia. Haematologica 2021; 106:3000-3003. [PMID: 34196171 PMCID: PMC8561275 DOI: 10.3324/haematol.2021.279332] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - Randa Bawadi
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - Sümeyye Cöktü
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Christina Reimer
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Beatrice Hoffmann
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Birte Sänger
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Simon Käfer
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - Felicitas Thol
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Miriam Erlacher
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Germany and German Cancer Consortium (DKTK), Freiburg, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Germany and German Cancer Consortium (DKTK), Freiburg, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Reinhard Kalb
- Department of Human Genetics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Detlev Schindler
- Department of Human Genetics, University of Würzburg, Biocenter, Würzburg, Germany
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Keinert J, Käfer S, Mattes M. Evaluation of coherent and incoherent thermal neutron scattering cross-sections for polycrystalline bismuth / Evaluierung von Wirkungsquerschnitten für kohärente und inkohärente Streuung thermischer Neutronen in polykristallinem Wismut. KERNTECHNIK 2021. [DOI: 10.1515/kern-1992-570412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Paraskevopoulou S, Käfer S, Zirkel F, Donath A, Petersen M, Liu S, Zhou X, Drosten C, Misof B, Junglen S. Viromics of extant insect orders unveil the evolution of the flavi-like superfamily. Virus Evol 2021; 7:veab030. [PMID: 34026271 PMCID: PMC8129625 DOI: 10.1093/ve/veab030] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insects are the most diversified and species-rich group of animals and harbor an immense diversity of viruses. Several taxa in the flavi-like superfamily, such as the genus Flavivirus, are associated with insects; however, systematic studies on insect virus genetic diversity are lacking, limiting our understanding of the evolution of the flavi-like superfamily. Here, we examined the diversity of flavi-like viruses within the most complete and up-to-date insect transcriptome collection comprising 1,243 insect species by employing a Flaviviridae RdRp profile hidden Markov model search. We identified seventy-six viral sequences in sixty-one species belonging to seventeen insect, one entognathan, and one arachnidan orders. Phylogenetic analyses revealed that twenty-seven sequences fell within the Flaviviridae phylogeny but did not group with established genera. Despite the large diversity of insect hosts studied, we only detected one virus in a blood-feeding insect, which branched within the genus Flavivirus, indicating that this genus likely diversified only in hematophagous arthropods. Nine new jingmenviruses with novel host associations were identified. One of the jingmenviruses established a deep rooting lineage additional to the insect- and tick-associated clades. Segment co-segregation phylogenies support the separation of tick- and insect-associated groups within jingmenviruses, with evidence for segment reassortment. In addition, fourteen viruses grouped with unclassified flaviviruses encompassing genome length of up to 20 kb. Species-specific clades for Hymenopteran- and Orthopteran-associated viruses were identified. Forty-nine viruses populated three highly diversified clades in distant relationship to Tombusviridae, a plant-infecting virus family, suggesting the detection of three previously unknown insect-associated families that contributed to tombusvirus evolution.
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Affiliation(s)
- Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Simon Käfer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical Center, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Malte Petersen
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 17 Qinghua E Rd, Haidian District, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 17 Qinghua E Rd, Haidian District, Beijing, China
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), partner site Charité, Chariteplatz 1, 10117 Berlin, Germany
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), partner site Charité, Chariteplatz 1, 10117 Berlin, Germany
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Käfer S, Paraskevopoulou S, Zirkel F, Wieseke N, Donath A, Petersen M, Jones TC, Liu S, Zhou X, Middendorf M, Junglen S, Misof B, Drosten C. Re-assessing the diversity of negative strand RNA viruses in insects. PLoS Pathog 2019; 15:e1008224. [PMID: 31830128 PMCID: PMC6932829 DOI: 10.1371/journal.ppat.1008224] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 12/26/2019] [Accepted: 11/19/2019] [Indexed: 12/21/2022] Open
Abstract
The spectrum of viruses in insects is important for subjects as diverse as public health, veterinary medicine, food production, and biodiversity conservation. The traditional interest in vector-borne diseases of humans and livestock has drawn the attention of virus studies to hematophagous insect species. However, these represent only a tiny fraction of the broad diversity of Hexapoda, the most speciose group of animals. Here, we systematically probed the diversity of negative strand RNA viruses in the largest and most representative collection of insect transcriptomes from samples representing all 34 extant orders of Hexapoda and 3 orders of Entognatha, as well as outgroups, altogether representing 1243 species. Based on profile hidden Markov models we detected 488 viral RNA-directed RNA polymerase (RdRp) sequences with similarity to negative strand RNA viruses. These were identified in members of 324 arthropod species. Selection for length, quality, and uniqueness left 234 sequences for analyses, showing similarity to genomes of viruses classified in Bunyavirales (n = 86), Articulavirales (n = 54), and several orders within Haploviricotina (n = 94). Coding-complete genomes or nearly-complete subgenomic assemblies were obtained in 61 cases. Based on phylogenetic topology and the availability of coding-complete genomes we estimate that at least 20 novel viral genera in seven families need to be defined, only two of them monospecific. Seven additional viral clades emerge when adding sequences from the present study to formerly monospecific lineages, potentially requiring up to seven additional genera. One long sequence may indicate a novel family. For segmented viruses, cophylogenies between genome segments were generally improved by the inclusion of viruses from the present study, suggesting that in silico misassembly of segmented genomes is rare or absent. Contrary to previous assessments, significant virus-host codivergence was identified in major phylogenetic lineages based on two different approaches of codivergence analysis in a hypotheses testing framework. In spite of these additions to the known spectrum of viruses in insects, we caution that basing taxonomic decisions on genome information alone is challenging due to technical uncertainties, such as the inability to prove integrity of complete genome assemblies of segmented viruses.
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Affiliation(s)
- Simon Käfer
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Nicolas Wieseke
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Terry C. Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Shanlin Liu
- BGI-Shenzhen, China Beishan Industrial Zone, Shenzhen, Guangdong Province, China
| | - Xin Zhou
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Leipzig, Germany
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), associated partner site Charité, Berlin, Germany
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