Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes

  • Litman, G. W., Cannon, J. P. & Dishaw, L. J. Reconstructing immune phylogeny: New perspectives. Nat. Rev. Immunol. 5, 866–879 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Criscitiello, M. F. & de Figueiredo, P. Fifty shades of immune defense. Heitman J, editor. PLoS Pathog. 9, e1003110 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Flajnik, M. F. A cold-blooded view of adaptive immunity. Nat. Rev. Immunol. 18, 438–453 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Turvey, S. E. & Broide, D. H. Innate immunity. J. Allergy Clin. Immunol. 125, S24-32 (2010).

    Article 
    PubMed 

    Google Scholar
     

  • Maekawa, T., Kufer, T. A. & Schulze-Lefert, P. NLR functions in plant and animal immune systems: So far and yet so close. Nat. Immunol. 12, 817–826 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Meunier, E. & Broz, P. Evolutionary convergence and divergence in NLR function and structure. Trends Immunol. 38, 744–757 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kienes, I., Weidl, T., Mirza, N., Chamaillard, M. & Kufer, T. A. Role of NLRs in the regulation of type I interferon signaling, host defense and tolerance to inflammation. Int. J. Mol. Sci. (Multidisciplinary Digital Publishing Institute) 22, 1301 (2021).

    CAS 

    Google Scholar
     

  • Li, D. & Wu, M. Pattern recognition receptors in health and diseases. Signal Transduct. Target Ther. (Nature Publishing Group) 6, 1–24 (2021).


    Google Scholar
     

  • Howe, K. et al. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biol. 6, 160009 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jones, J. D. G., Vance, R. E. & Dangl, J. L. Intracellular innate immune surveillance devices in plants and animals. Science 354, aaf6395–aaf6395 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Tørresen, O. K. et al. Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics 19, 240 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brown, K. H. et al. Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. Proc. Natl. Acad. Sci. 109, 529–534 (2012).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Butler, M. G. et al. SNPfisher: Tools for probing genetic variation in laboratory-reared zebrafish. Development 142, 1542–1552 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McConnell, S. C. et al. Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution. Proc. Natl. Acad. Sci. 113, E5014–E5023 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McConnell, S. C., Restaino, A. C. & de Jong, J. L. O. Multiple divergent haplotypes express completely distinct sets of Class I MHC genes in zebrafish. Immunogenetics 66, 199–213 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • ZFIN. Genotype: AB [Internet]. Genotype AB. zfin.org/ZDB-GENO-960809-7. Accessed 1 Aug 2017 (2017).

  • Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246–251 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McLaren, W. et al. The Ensembl variant effect predictor. Genome Biol. 17, 122 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).

  • Pucker, B. et al. A de novo genome sequence assembly of the Arabidopsis thaliana accession Niederzenz-1 displays presence/absence variation and strong synteny. Vandepoele K, editor. PLoS ONE 11, e0164321 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wilson, C. A. et al. Wild sex in zebrafish: Loss of the natural sex determinant in domesticated strains. Genetics 198, 1291–1308 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: An R package for comparing biological themes among gene clusters. OMICS J Integr Biol. 16, 284–287 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. Gibas C, editor. PLoS ONE 6, e21800 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • The Wellcome Trust Case Control Consortium, Conrad, D.F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010).

  • Guryev, V. et al. Genetic variation in the zebrafish. Genome Res. 16, 491–497 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Patowary, A. et al. A sequence-based variation map of zebrafish. Zebrafish 10, 15–20 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • LaFave, M. C., Varshney, G. K., Vemulapalli, M., Mullikin, J. C. & Burgess, S. M. A defined zebrafish line for high-throughput genetics and genomics: NHGRI-1. Genetics 198, 167–170 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Read, A. C. et al. Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with nanopore sequencing. PLOS Genet. (Public Library of Science) 16, e1008571 (2010).

    Article 

    Google Scholar
     

  • Tørresen, O. K. et al. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res. 47, 10994–11006 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Q., Jiang, X.-M., & Shao, Z.-Q. Genome-wide analysis of NLR disease resistance genes in an updated reference genome of barley. Front. Genet. [Internet]. doi.org/10.3389/fgene.2021.694682 (2021). Accessed 24 Aug 2022.

  • Steuernagel, B. et al. The NLR-annotator tool enables annotation of the intracellular immune receptor Repertoire1 [OPEN]. Plant Physiol. 183, 468–482 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goritschnig, S., Steinbrenner, A. D., Grunwald, D. J. & Staskawicz, B. J. Structurally distinct Arabidopsis thaliana NLR immune receptors recognize tandem WY domains of an oomycete effector. New Phytol. 210, 984–996 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Prigozhin, D. M. & Krasileva, K. V. Analysis of intraspecies diversity reveals a subset of highly variable plant immune receptors and predicts their binding sites. Plant Cell 33, 998–1015 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Suurväli, J. et al. The laboratory domestication of zebrafish: From diverse populations to inbred substrains. Parsch J, editor. Mol. Biol. Evol. 37, 1056–1069 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Levraud, J.-P., Jouneau, L., Briolat, V., Laghi, V. & Boudinot, P. IFN-stimulated genes in zebrafish and humans define an ancient arsenal of antiviral immunity. J. Immunol. (American Association of Immunologists) 203, 3361–3373 (2019).

    CAS 

    Google Scholar
     

  • Niu, L., Luo, G., Liang, R., Qiu, C., Yang, J., Xie, L. et al. Negative regulator Nlrc3-like maintain the balanced innate immune response during mycobacterial infection in zebrafish. Front. Immunol. [Internet]. doi.org/10.3389/fimmu.2022.893611 (2022). Accessed 24 Aug 2022.

  • Balla, K. M., Rice, M. C., Gagnon, J. A. & Elde, N. C. Linking virus discovery to immune responses visualized during zebrafish infections. Curr. Biol. 30, 2092-2103.e5 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Morimoto, N., Kono, T., Sakai, M. & Hikima, J. Inflammasomes in teleosts: Structures and mechanisms that induce pyroptosis during bacterial infection. Int. J. Mol. Sci. (Multidisciplinary Digital Publishing Institute) 22, 4389 (2021).

    CAS 

    Google Scholar
     

  • Horton, R. et al. Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project. Immunogenetics 60, 1–18 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McLure, C. A. et al. Genomic evolution and polymorphism: Segmental duplications and haplotypes at 108 regions on 21 chromosomes. Genomics 102, 15–26 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Laing, K. J., Purcell, M. K., Winton, J. R. & Hansen, J. D. A genomic view of the NOD-like receptor family in teleost fish: Identification of a novel NLR subfamily in zebrafish. BMC Evol. Biol. 8, 42 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bryant, C. E. & Monie, T. P. Mice, men and the relatives: Cross-species studies underpin innate immunity. Open Biol. (Royal Society) 2, 120015 (2022).


    Google Scholar
     

  • Tan, M. et al. The whale shark genome reveals patterns of vertebrate gene family evolution. eLife (eLife Sciences Publications, Ltd) 10, e65394 (2021).

    CAS 

    Google Scholar
     

  • Hui, F. et al. Genome-wide identification and characterization of NLR genes in lamprey (Lethenteron reissneri) and their responses to lipopolysaccharide/poly(I:C) challenge. Mol. Immunol. 143, 122–134 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jin, X., Morro, B., Tørresen, O.K., Moiche, V., Solbakken, M.H., Jakobsen, K.S. et al. Innovation in nucleotide-binding oligomerization-like receptor and toll-like receptor sensing drives the major histocompatibility complex-II free Atlantic cod immune system. Front. Immunol. [Internet]. doi.org/10.3389/fimmu.2020.609456 (2020). Accessed 24 Aug 2022.

  • Smith, A. C. H. et al. High-throughput cell transplantation establishes that tumor-initiating cells are abundant in zebrafish T-cell acute lymphoblastic leukemia. Blood 115, 3296–3303 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mizgirev, I. & Revskoy, S. Generation of clonal zebrafish lines and transplantable hepatic tumors. Nat. Protoc. 5, 383–394 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guide for the Care and Use of Laboratory Animals, 8th edition. Washington (DC), National Research Council (US). Committee for the Update of the Guide for the Care and Use of Laboratory Animals. (National Academies Press (US), 2011).

  • Westerfield, M. The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish (Danio rerio) 4th edition (University of Oregon Press, Eugene, 2000).

  • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: Fast processing of NGS alignment formats. Bioinformatics 31, 2032–2034 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McKenna, A. et al. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cleary, J. G. et al. Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data. J. Comput. Biol. 21, 405–419 (2014).

    Article 
    MathSciNet 
    CAS 
    PubMed 

    Google Scholar
     

  • Cleary, J. G. et al. Comparing variant call files for performance benchmarking of next-generation sequencing variant calling pipelines [internet]. Bioinformatics doi.org/10.1101/023754 (2015).

    Article 

    Google Scholar
     

  • Yu, G., Wang, L.-G., Yan, G.-R. & He, Q.-Y. DOSE: An R/bioconductor package for disease ontology semantic and enrichment analysis. Bioinformatics 31, 608–609 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A. & Manke, T. deepTools: A flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pohl, A. & Beato, M. bwtool: A tool for bigWig files. Bioinformatics 30, 1618–1619 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dale, R. K., Pedersen, B. S. & Quinlan, A. R. Pybedtools: A flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 27, 3423–3424 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Quinlan, A. R. & Hall, I. M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weisenfeld, N. I. et al. Comprehensive variation discovery in single human genomes. Nat. Genet. 46, 1350–1355 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinform. Oxf. Engl. 31, 3210–3212 (2015).

    Article 

    Google Scholar
     

  • Read more here: Source link