Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data

Alexandra Livernois; Kristine Hardy; Renae Domaschenz; Alexie Papanicolaou; Arthur Georges; Stephen D Sarre; Sudha Rao; Tariq Ezaz; Janine E Deakin

doi:10.1007/s00251-016-0922-1

Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data

Immunogenetics. 2016 Oct;68(9):719-31. doi: 10.1007/s00251-016-0922-1. Epub 2016 Jun 2.

Authors

Alexandra Livernois¹, Kristine Hardy², Renae Domaschenz³, Alexie Papanicolaou⁴, Arthur Georges¹, Stephen D Sarre¹, Sudha Rao², Tariq Ezaz¹, Janine E Deakin⁵

Affiliations

¹ Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia.
² Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, ACT, 2617, Australia.
³ John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
⁴ The Hawkesbury Institute for the Environment, University of Western Sydney, Penrith, NSW, 2751, Australia.
⁵ Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia. janine.deakin@canberra.edu.au.

PMID: 27255409
DOI: 10.1007/s00251-016-0922-1

Abstract

Interleukins are a group of cytokines with complex immunomodulatory functions that are important for regulating immunity in vertebrate species. Reptiles and mammals last shared a common ancestor more than 350 million years ago, so it is not surprising that low sequence identity has prevented divergent interleukin genes from being identified in the central bearded dragon lizard, Pogona vitticeps, in its genome assembly. To determine the complete nucleotide sequences of key interleukin genes, we constructed full-length transcripts, using the Trinity platform, from short paired-end read RNA sequences from stimulated spleen cells. De novo transcript reconstruction and analysis allowed us to identify interleukin genes that are missing from the published P. vitticeps assembly. Identification of key cytokines in P. vitticeps will provide insight into the essential molecular mechanisms and evolution of interleukin gene families and allow for characterization of the immune response in a lizard for comparison with mammals.

Keywords: Cytokine; De novo assembly; Interleukin; Pogona vitticeps.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Animals
Computational Biology / methods*
Gene Expression Profiling
High-Throughput Nucleotide Sequencing / methods*
Interleukins / genetics*
Lizards / genetics*
Sequence Analysis, RNA / methods*
Sequence Homology, Amino Acid
Software
Transcriptome / genetics*

Substances

Interleukins