1
|
Flageul A, Lucas P, Hirchaud E, Touzain F, Blanchard Y, Eterradossi N, Brown P, Grasland B. Viral variant visualizer (VVV): A novel bioinformatic tool for rapid and simple visualization of viral genetic diversity. Virus Res 2020; 291:198201. [PMID: 33080244 DOI: 10.1016/j.virusres.2020.198201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/13/2020] [Accepted: 10/15/2020] [Indexed: 12/15/2022]
Abstract
Here a bioinformatic pipeline VVV has been developed to analyse viral populations in a given sample from Next Generation Sequencing (NGS) data. To date, handling large amounts of data from NGS requires the expertise of bioinformaticians, both for data processing and result analysis. Consequently, VVV was designed to help non-bioinformaticians to perform these tasks. By providing only the NGS data file, the developed pipeline generated consensus sequences and determined the composition of the viral population for an avian Metapneumovirus (AMPV) and three different animal coronaviruses (Porcine Epidemic Diarrhea Virus (PEDV), Turkey Coronavirus (TCoV) and Infectious Bronchitis Virus (IBV)). In all cases, the pipeline produced viral consensus genomes corresponding to known consensus sequence and made it possible to highlight the presence of viral genetic variants through a single graphic representation. The method was validated by comparing the viral populations of an AMPV field sample, and of a copy of this virus produced from a DNA clone. VVV demonstrated that the cloned virus population was homogeneous (as designed) at position 2934 where the wild-type virus demonstrated two variant populations at a ratio of almost 50:50. A total of 18, 10, 3 and 28, viral genetic variants were detected for AMPV, PEDV, TCoV and IBV respectively. The simplicity of this pipeline makes the study of viral genetic variants more accessible to a wide variety of biologists, which should ultimately increase the rate of understanding of the mechanisms of viral genetic evolution.
Collapse
Affiliation(s)
- Alexandre Flageul
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Virology, Immunology and Parasitology in Poultry and Rabbit (VIPAC) Unit, Université Bretagne Loire (UBL), France
| | - Pierrick Lucas
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES), Laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, France
| | - Edouard Hirchaud
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES), Laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, France
| | - Fabrice Touzain
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES), Laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, France
| | - Yannick Blanchard
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES), Laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, France
| | - Nicolas Eterradossi
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Virology, Immunology and Parasitology in Poultry and Rabbit (VIPAC) Unit, Université Bretagne Loire (UBL), France
| | - Paul Brown
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Virology, Immunology and Parasitology in Poultry and Rabbit (VIPAC) Unit, Université Bretagne Loire (UBL), France
| | - Béatrice Grasland
- Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Virology, Immunology and Parasitology in Poultry and Rabbit (VIPAC) Unit, Université Bretagne Loire (UBL), France.
| |
Collapse
|
2
|
Yang H, Jaime M, Polihronakis M, Kanegawa K, Markow T, Kaneshiro K, Oliver B. Re-annotation of eight Drosophila genomes. Life Sci Alliance 2018; 1:e201800156. [PMID: 30599046 PMCID: PMC6305970 DOI: 10.26508/lsa.201800156] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 12/11/2022] Open
Abstract
The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated evolutionary studies on the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation. We then applied this to the other species to add more than 10000 transcript models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This re-annotation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms, and suggests a strategy for annotating the many forthcoming genomes covering the tree of life.
Collapse
Affiliation(s)
- Haiwang Yang
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maria Jaime
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maxi Polihronakis
- Drosophila Species Stock Center, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelvin Kanegawa
- Hawaiian Drosophila Research Stock Center, Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Therese Markow
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Irapuato, Guanajuato, Mexico.,Drosophila Species Stock Center, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kenneth Kaneshiro
- Hawaiian Drosophila Research Stock Center, Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
3
|
Peters NT, Rohrbach JA, Zalewski BA, Byrkett CM, Vaughn JC. RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. RNA (NEW YORK, N.Y.) 2003; 9:698-710. [PMID: 12756328 PMCID: PMC1370437 DOI: 10.1261/rna.2120703] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2002] [Accepted: 03/06/2003] [Indexed: 05/19/2023]
Abstract
We have previously described an example of extensively A-to-G edited cDNA derived from adult heads of the fruitfly Drosophila melanogaster. In that study, the source of the predicted antisense RNA pairing strand for template recognition by dADAR editase was not identified, and the biological significance of the observed hyperediting was not known. Here, we address each of these questions. 4f-rnp and sas-10 are closely adjacent X-linked genes located on opposite DNA strands that produce convergent transcripts. We show that developmentally regulated antisense sas-10 readthrough mRNA arises by activation of an upstream promoter P2 during the late embryo stage of fly development. The sas-10 readthrough transcripts pair with 4f-rnp mRNA to form double-stranded molecules, as indicated by A-to-G editing observed in both RNA strands. It would be predicted that perfect RNA duplexes would be targeted for modification/degradation by enzyme pathways that recognize double-stranded RNAs, leading to decline in 4f-rnp mRNA levels, and this is what we observe. The observation using quantitative RT-PCR that sas-10 readthrough and 4f-rnp transcript levels are inversely related suggests a role for the antisense RNA in posttranscriptional regulation of 4f-rnp gene expression during development. Potential molecular mechanisms that could lead to this result are discussed, one of which is targeted transcript degradation via the RNAi pathway. Insofar as the dADAR editase and RNAi pathways are known to be constitutive in this system, it is likely that control of antisense RNA transcription is the rate-limiting factor. The results provide insight into roles of naturally occurring antisense RNAs in regulation of eukaryotic gene expression.
Collapse
Affiliation(s)
- Nick T Peters
- Department of Zoology, Miami University, Oxford, Ohio 45056, USA
| | | | | | | | | |
Collapse
|
4
|
Matsumoto K, Yamamoto DS, Sumitani M, Lee JM, Hatakeyama M, Oishi K. Detection of a single copy gene on a mitotic metaphase chromosome by fluorescence in situ hybridization (FISH) in the sawfly, Athalia rosae (Hymenoptera). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2002; 49:34-40. [PMID: 11754092 DOI: 10.1002/arch.10005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mitotic metaphase chromosomes of Athalia rosae (Hymenoptera) haploid males were subjected to fluorescence in situ hybridization (FISH) analysis using an rDNA probe and two vitellogenin (Vg) cDNA probes (one representing the 5' half and the other the 3' half of the gene, each about 3 kb long, and together covering the entire coding region). The rDNA probe produced signals in four chromosomes, all in pericentromeric regions (haploid chromosome number = 8), and the Vg probes, either the combined probes or the 3' region alone, produced a twin signal in the middle of a chromosome arm of a single chromosome. Arch.
Collapse
Affiliation(s)
- Kouhei Matsumoto
- Division of Biology, Graduate School of Science and Technology, Kobe University, Nada, Kobe, Japan
| | | | | | | | | | | |
Collapse
|
5
|
Abstract
During the past year, the Drosophila genome has been sequenced. More than 60% of genes implicated in human disease have Drosophila orthologues. Developments in RNA-mediated interference and homologous recombination have made 'reverse genetics' feasible in Drosophila. Conventional Drosophila genetics is being used increasingly to place human disease genes of unknown function in the context of functional pathways.
Collapse
Affiliation(s)
- A Bernards
- Massachusetts General Hospital Cancer Center, Building 149, 13th Street, Charlestown, Massachusetts 02129, USA.
| | | |
Collapse
|
6
|
Kostrouchova M, Krause M, Kostrouch Z, Rall JE. Nuclear hormone receptor CHR3 is a critical regulator of all four larval molts of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A 2001; 98:7360-5. [PMID: 11416209 PMCID: PMC34673 DOI: 10.1073/pnas.131171898] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CHR3 (nhr-23, NF1F4), the homologue of Drosophila DHR3 and mammalian ROR/RZR/RevErbA nuclear hormone receptors, is important for proper epidermal development and molting in the nematode Caenorhabditis elegans. Disruption of CHR3 (nhr-23) function leads to developmental changes, including incomplete molting and a short, fat (dumpy) phenotype. Here, we studied the role of CHR3 during larval development by using expression assays and RNA-mediated interference. We show that the levels of expression of CHR3 (nhr-23) cycle during larval development and reduction of CHR3 function during each intermolt period result in defects at all subsequent molts. Assaying candidate gene expression in populations of animals treated with CHR3 (nhr-23) RNA-mediated interference has identified dpy-7 as a potential gene acting downstream of CHR3. These results define CHR3 as a critical regulator of all C. elegans molts and begin to define the molecular pathway for its function.
Collapse
Affiliation(s)
- M Kostrouchova
- Laboratory of Molecular Biology and Genetics, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 116 36 Prague, Czech Republic
| | | | | | | |
Collapse
|
7
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2447213 DOI: 10.1002/cfg.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|