Brief Communications Arising | Published:

Venkatesh et al. reply

Nature volume 511, pages E9E10 (10 July 2014) | Download Citation

Abstract

Replying to J. M. Dijkstra Nature 511, 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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    TH2 and Treg candidate genes in elephant shark. Nature 511, (2014)

  2. 2.

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

  3. 3.

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

  4. 4.

    , , , & Comprehensive clarification of two paralogous interleukin 4/13 loci in teleost fish. Immunogenetics 60, 383–397 (2008)

  5. 5.

    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)

  6. 6.

    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)

  7. 7.

    , & Comparative genomics reveals key gain-of-function events in Foxp3 during regulatory T cell evolution. Front. Immunol. 3, 113 (2012)

  8. 8.

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

  9. 9.

    , , , & 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)

Download references

Author information

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, Maryland 21201, 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, Missouri 63108, USA

    • Wesley C. Warren

Authors

  1. Search for Byrappa Venkatesh in:

  2. Search for Alison P. Lee in:

  3. Search for Jeremy B. Swann in:

  4. Search for Yuko Ohta in:

  5. Search for Martin F. Flajnik in:

  6. Search for Masanori Kasahara in:

  7. Search for Thomas Boehm in:

  8. Search for Wesley C. Warren in:

Corresponding authors

Correspondence to Byrappa Venkatesh or Wesley C. Warren.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/nature13447

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.

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