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Chauviere L, Hoffbeck L, Shoaib M, Tessier F, Firat H, Satagopam V, Devaux Y. Firalink: A bioinformatics pipeline for long non-coding RNA data analysis. Noncoding RNA Res 2023; 8:602-604. [PMID: 37771472 PMCID: PMC10523182 DOI: 10.1016/j.ncrna.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
Summary The Firalink bioinformatics pipeline has been developed to analyse long non-coding RNA (lncRNA) data generated by targeted sequencing. This pipeline has been first implemented for use with the FIMICS panel containing 2906 lncRNAs useful for investigations in cardiovascular disease. It has been subsequently tested and validated using a panel of lncRNAs targeting brain disease. The pipeline can be adapted to other targeted sequencing panels or other transcriptomics data (e.g. whole transcriptome) through a change of the reference genome/panel. Therefore, Firalink can be applied to different lncRNA panels and transcriptomics data targeting multiple diseases. Availability and implementation The Firalink pipeline works on Linux and is freely available to non-commercial users at https://gitlab.lcsb.uni.lu/covirna/covirna-ext/covirna-firalink-pipeline. Access will be granted after contacting bioinformatics@firalis.com. The pipeline is implemented with the Nextflow workflow manager using Python and R scripts. It will remain available for at least two years following publication and will be regularly updated and upgraded. Supplementary information For an example of the application of the Firalink pipeline using the FIMICS panel, see www.covirna.eu.
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Affiliation(s)
| | | | - Muhammad Shoaib
- Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, University of Luxembourg, Belvaux, Luxembourg
| | | | | | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, University of Luxembourg, Belvaux, Luxembourg
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - COVIRNA consortium
- From Firalis SA, Huningue, France
- Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, University of Luxembourg, Belvaux, Luxembourg
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
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Boštjančić LL, Francesconi C, Rutz C, Hoffbeck L, Poidevin L, Kress A, Jussila J, Makkonen J, Feldmeyer B, Bálint M, Schwenk K, Lecompte O, Theissinger K. Host-pathogen coevolution drives innate immune response to Aphanomyces astaci infection in freshwater crayfish: transcriptomic evidence. BMC Genomics 2022; 23:600. [PMID: 35989333 PMCID: PMC9394032 DOI: 10.1186/s12864-022-08571-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/20/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND For over a century, scientists have studied host-pathogen interactions between the crayfish plague disease agent Aphanomyces astaci and freshwater crayfish. It has been hypothesised that North American crayfish hosts are disease-resistant due to the long-lasting coevolution with the pathogen. Similarly, the increasing number of latent infections reported in the historically sensitive European crayfish hosts seems to indicate that similar coevolutionary processes are occurring between European crayfish and A. astaci. Our current understanding of these host-pathogen interactions is largely focused on the innate immunity processes in the crayfish haemolymph and cuticle, but the molecular basis of the observed disease-resistance and susceptibility remain unclear. To understand how coevolution is shaping the host's molecular response to the pathogen, susceptible native European noble crayfish and invasive disease-resistant marbled crayfish were challenged with two A. astaci strains of different origin: a haplogroup A strain (introduced to Europe at least 50 years ago, low virulence) and a haplogroup B strain (signal crayfish in lake Tahoe, USA, high virulence). Here, we compare the gene expression profiles of the hepatopancreas, an integrated organ of crayfish immunity and metabolism. RESULTS We characterised several novel innate immune-related gene groups in both crayfish species. Across all challenge groups, we detected 412 differentially expressed genes (DEGs) in the noble crayfish, and 257 DEGs in the marbled crayfish. In the noble crayfish, a clear immune response was detected to the haplogroup B strain, but not to the haplogroup A strain. In contrast, in the marbled crayfish we detected an immune response to the haplogroup A strain, but not to the haplogroup B strain. CONCLUSIONS We highlight the hepatopancreas as an important hub for the synthesis of immune molecules in the response to A. astaci. A clear distinction between the innate immune response in the marbled crayfish and the noble crayfish is the capability of the marbled crayfish to mobilise a higher variety of innate immune response effectors. With this study we outline that the type and strength of the host immune response to the pathogen is strongly influenced by the coevolutionary history of the crayfish with specific A. astaci strains.
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Affiliation(s)
- Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Caterina Francesconi
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany.
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Lucien Hoffbeck
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Laetitia Poidevin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
| | - Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
- Present address: BioSafe - Biological Safety Solutions, Microkatu 1, 70210, Kuopio, Finland
| | - Barbara Feldmeyer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
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Boštjančić LL, Francesconi C, Rutz C, Hoffbeck L, Poidevin L, Kress A, Jussila J, Makkonen J, Feldmeyer B, Bálint M, Schwenk K, Lecompte O, Theissinger K. Dataset of the de novo assembly and annotation of the marbled crayfish and the noble crayfish hepatopancreas transcriptomes. BMC Res Notes 2022; 15:281. [PMID: 35989321 PMCID: PMC9394041 DOI: 10.1186/s13104-022-06137-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVES Crayfish plague disease, caused by the oomycete pathogen Aphanomyces astaci represents one of the greatest risks for the biodiversity of the freshwater crayfish. This data article covers the de novo transcriptome assembly and annotation data of the noble crayfish and the marbled crayfish challenged with Ap. astaci. Following the controlled infection experiment (Francesconi et al. in Front Ecol Evol, 2021, https://doi.org/10.3389/fevo.2021.647037 ), we conducted a differential gene expression analysis described in (Boštjančić et al. in BMC Genom, 2022, https://doi.org/10.1186/s12864-022-08571-z ) DATA DESCRIPTION: In total, 25 noble crayfish and 30 marbled crayfish were selected. Hepatopancreas tissue was isolated, followed by RNA sequencing using the Illumina NovaSeq 6000 platform. Raw data was checked for quality with FastQC, adapter and quality trimming were conducted using Trimmomatic followed by de novo assembly with Trinity. Assembly quality was assessed with BUSCO, at 93.30% and 93.98% completeness for the noble crayfish and the marbled crayfish, respectively. Transcripts were annotated using the Dammit! pipeline and assigned to KEGG pathways. Respective transcriptome and raw datasets may be reused as the reference transcriptome assemblies for future expression studies.
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Affiliation(s)
- Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Caterina Francesconi
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany.
| | - Christelle Rutz
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Lucien Hoffbeck
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Laetitia Poidevin
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Arnaud Kress
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
| | - Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
- BioSafe - Biological Safety Solutions, Microkatu 1, 70210, Kuopio, Finland
| | - Barbara Feldmeyer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
| | - Odile Lecompte
- Department of Computer ScienceUMR 7357Centre de Recherche en Biomédecine de Strasbourg, ICube, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
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