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Abstract

Replying to J. M. Dijkstra Nature511,http://dx.doi.org/10.1038/nature13446(2014)

In the accompanying Comment1, Dijkstra has identified gene models potentially encoding cytokines in regions of the Callorhinchus milii genome, whose syntenic counterparts in teleost and tetrapod genomes harbour interleukin genes. These genes were not predicted by our assembly and annotation pipeline2. TBLASTN searches of the genome assembly and RNA-sequencing (RNA-seq) transcriptomes from 10 tissues (including thymus and spleen) of the elephant shark, and RNA-seq transcriptomes from the thymus and spleen of nurse shark using human and teleost fish interleukins as query sequences, were also unable to pick up these genes; although we readily detected other cytokine genes in the same family (for example, interleukin-7 (IL-7) and IL-15). Below are our comments on the candidate genes identified by Dijkstra.

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Figure 1: Primordial nature of IL-4 and IL-13 candidates predicted in C. milii.

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References

  1. Dijkstra, J. M. TH2 and Treg candidate genes in elephant shark. Nature 511, http://dx.doi.org/10.1038/nature13446 (2014)

    Article  ADS  CAS  Google Scholar 

  2. Venkatesh, B. et al. Elephant shark genome provides unique insights into gnathostome evolution. Nature 505, 174–179 (2014)

    Article  ADS  CAS  Google Scholar 

  3. Liu, M. & Grigoriev, A. Protein domains correlate strongly with exons in multiple eukaryotic genomes–evidence of exon shuffling? Trends Genet. 20, 399–403 (2004)

    Article  Google Scholar 

  4. Ohtani, M., Hayashi, N., Hashimoto, K., Nakanishi, T. & Dijkstra, J. M. Comprehensive clarification of two paralogous interleukin 4/13 loci in teleost fish. Immunogenetics 60, 383–397 (2008)

    Article  CAS  Google Scholar 

  5. Takizawa, F. et al. Constitutive high expression of interleukin-4/13A and GATA-3 in gill and skin of salmonid fishes suggests that these tissues form Th2-skewed immune environments. Mol. Immunol. 48, 1360–1368 (2011)

    Article  CAS  Google Scholar 

  6. Dijkstra, J. M. et al. Identification of a gene for an ancient cytokine, interleukin 15-like, in mammals; interleukins 2 and 15 co-evolved with this third family member, all sharing binding motifs for IL-15Rα. Immunogenetics 66, 93–103 (2014)

    Article  CAS  Google Scholar 

  7. Andersen, K. G., Nissen, J. K. & Betz, A. G. Comparative genomics reveals key gain-of-function events in Foxp3 during regulatory T cell evolution. Front. Immunol. 3, 113 (2012)

    Article  CAS  Google Scholar 

  8. Van Laethem, F. et al. Lck availability during thymic selection determines the recognition specificity of the T cell repertoire. Cell 154, 1326–1341 (2013)

    Article  CAS  Google Scholar 

  9. Dijkstra, J. M., Grimholt, U., Leong, J., Koop, B. F. & Hashimoto, K. Comprehensive analysis of MHC class II genes in teleost fish genomes reveals dispensability of the peptide-loading DM system in a large part of vertebrates. BMC Evol. Biol. 13, 260 (2013)

    Article  Google Scholar 

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Authors and Affiliations

  1. Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.,

    Byrappa Venkatesh & Alison P. Lee

  2. Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228.,

    Byrappa Venkatesh

  3. Department of Developmental Immunology, Max-Planck-Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany,

    Jeremy B. Swann & Thomas Boehm

  4. Department of Microbiology and Immunology, University of Maryland, Baltimore, 21201, Maryland, USA

    Yuko Ohta & Martin F. Flajnik

  5. Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan,

    Masanori Kasahara

  6. The Genome Institute at Washington University, St. Louis, 63108, Missouri, USA

    Wesley C. Warren

Authors
  1. Byrappa Venkatesh
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  2. Alison P. Lee
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  3. Jeremy B. Swann
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  4. Yuko Ohta
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  5. Martin F. Flajnik
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  6. Masanori Kasahara
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  7. Thomas Boehm
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  8. Wesley C. Warren
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Corresponding authors

Correspondence to Byrappa Venkatesh or Wesley C. Warren.

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Venkatesh, B., Lee, A., Swann, J. et al. Venkatesh et al. reply. Nature 511, E9–E10 (2014). https://doi.org/10.1038/nature13447

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