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.
Bibliographical noteFunding Information:
Pierre Boudinot is gratefully acknowledged for his contribution to the phylogenetic tree of the cyprinid family. LD gratefully acknowledges Wageningen Institute of Animal Sciences (WIAS) for a research fellowship supporting this work. JP and GFW gratefully acknowledge that research leading to this review was funded by the Netherlands Organisation for Scientific Research and São Paulo Research Foundation, Brazil (FAPESP) as part of the Joint Research Projects BioBased Economy NWO-FAPESP Programme (Project number 729.004.002). GFW and LD were supported, in part, by the European Commission under the Work Programme 2012 of the Seventh Framework Programme for Research and Technological Development of the European Union (Grant Agreement 311993 TARGETFISH).
© 2017 The Authors
- Whole genome duplication