Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Brief Communications Arising
  • Published:

Venkatesh et al. reply

Nature volume 511, pages E9–E10 (2014)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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

Similar content being viewed by others

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 

Download references

Author information

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
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alison P. Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jeremy B. Swann
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuko Ohta
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Martin F. Flajnik
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Masanori Kasahara
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Thomas Boehm
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Wesley C. Warren
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Byrappa Venkatesh or Wesley C. Warren.

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature13447

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing