title: Genomic and transcriptomic approaches to study immunology in cyprinids: What is next?
abstract: Accelerated by the introduction of Next-Generation Sequencing (NGS), a number of genomes of cyprinid fish species have been drafted, leading to a highly valuable collective resource of comparative genome information on cyprinids (Cyprinidae). In addition, NGS-based transcriptome analyses of different developmental stages, organs, or cell types, increasingly contribute to the understanding of complex physiological processes, including immune responses. Cyprinids are a highly interesting family because they comprise one of the most-diversified families of teleosts and because of their variation in ploidy level, with diploid, triploid, tetraploid, hexaploid and sometimes even octoploid species. The wealth of data obtained from NGS technologies provides both challenges and opportunities for immunological research, which will be discussed here. Correct interpretation of ploidy effects on immune responses requires knowledge of the degree of functional divergence between duplicated genes, which can differ even between closely-related cyprinid fish species. We summarize NGS-based progress in analysing immune responses and discuss the importance of respecting the presence of (multiple) duplicated gene sequences when performing transcriptome analyses for detailed understanding of complex physiological processes. Progressively, advances in NGS technology are providing workable methods to further elucidate the implications of gene duplication events and functional divergence of duplicates genes and proteins involved in immune responses in cyprinids. We conclude with discussing how future applications of NGS technologies and analysis methods could enhance immunological research and understanding.
authors.affiliation: Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands.
authors.forename: Jules
authors.initials: J
authors.lastname: Petit
authors.affiliation: Department of Animal Sciences, R. H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
authors.forename: Lior
authors.initials: L
authors.lastname: David
authors.affiliation: ZF-screens B.V., J.H, Oortweg 19, 2333 CH, Leiden, The Netherlands.
authors.forename: Ron
authors.initials: R
authors.lastname: Dirks
authors.affiliation: Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box 338, 6700 AH, Wageningen, The Netherlands. Electronic address: geert.wiegertjes@wur.nl.
authors.forename: Geert F
authors.initials: GF
authors.lastname: Wiegertjes
mesh_terms: D000486:Allergy and Immunology; D000818:Animals; D005075:Biological Evolution; D003530:Cyprinidae / Q000235:genetics* / Q000276:immunology*; D020440:Gene Duplication; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D007113:Immunity, Innate / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D011123:Polyploidy; D013045:Species Specificity; D059467:Transcriptome
keywords: Carp; Cyprinidae; Immunity; NGS; Polyploidy; Whole genome duplication