Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq

Luke T. Dunning, Alice B. Dennis, Duckchul Park, Brent J. Sinclair, Richard D. Newcomb, Thomas R. Buckley

Research output: Contribution to journalArticlepeer-review

Abstract

The endemic New Zealand alpine stick insect Micrarchus nov. sp. 2 regularly experiences sub-zero temperatures in the wild. 454-based RNA-Seq was used to generate a de novo transcriptome and differentiate between treatments to investigate the genetic basis of cold tolerance. Non cold-treated individuals were compared to those exposed to 0 C for 1 h followed by a 1 h recovery period at 20 C. We aligned 607,410 Roche 454 reads, generating a transcriptome of 5235 contigs. Differential expression analysis ranked candidate cold responsive genes for qPCR validation by P-value. The top nine up-regulated candidates, together with eight a priori targets identified from previous studies, had their relative expression quantified using qPCR. Three candidate cold responsive genes from the RNA-Seq data were verified as significantly up-regulated, annotated as: prolyl 4-hydroxylase subunit alpha-1 (P4HA1), staphylococcal nuclease domain-containing protein 1 (snd1) and cuticular protein analogous to peritrophins 3-D2 (Cpap3-d2). All three are novel candidate genes, illustrating the varied response to low temperature across insects.

Original languageEnglish
Pages (from-to)24-31
Number of pages8
JournalComparative Biochemistry and Physiology. Part D: Genomics and Proteomics
Volume8
Issue number1
DOIs
Publication statusPublished - 2013
Externally publishedYes

Keywords

  • Cold-shock
  • Phasmatodea
  • Stick insect
  • Transcriptome

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