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Seasonally Induced Hepatotranscriptomic Changes in the Freeze Tolerant North American Wood Frog Rana sylvatica
Author(s) -
Kiss Andor,
Posner Mason,
Mock Thomas
Publication year - 2015
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.29.1_supplement.981.2
Subject(s) - transcriptome , biology , de novo transcriptome assembly , sequence assembly , rna seq , illumina dye sequencing , kegg , contig , deep sequencing , gene , genetics , evolutionary biology , gene expression , genome
The North American wood frog Rana sylvatica uses an overwintering strategy that includes metabolic depression and freeze tolerance. Summer‐acclimated wood frogs will not survive freeze events, suggesting that there is a seasonally induced acclimation. Previous hepatoproteome analysis indicated a shift in metabolism in summer vs winter acclimated animals. The current study evaluated the differential expression between seasonally acclimated wood frogs. Using frogs just thawed and four weeks post‐thaw, we isolated hepatic total RNA, verifying integrity by RIN蠅8. Total RNA (3 frogs, each in duplicate) were used to construct Illumina TruSeq RNA v2 libraries. All twelve samples were sequenced (100 bp PE) on an Illumina HiSeq2000. FASTQ files were processed by SICKLE and AlienTrimmer. De novo transcriptome assembly was performed in CLC Genomics Workbench 7.5. The assembled wood frog transcriptome generated 44,023 contigs, which were annotated (BlastX, GO, IPS, EC, KEGG) via Blast2GO. The annotated transcriptome served as the reference for RNA‐Seq based differential gene expression (DGE) using bROC. DGE analysis identified 1090 candidate cDNAs exhibiting significant (CONF >0.95) expression differences between just thawed and four week post‐thawed frogs. We are currently sequencing the wood frog genome using the ' m oleculo ' approach (Illumina) to aid in identification of novel DGE cDNAs. Pathways analysis, in addition to comparisons to other freeze‐tolerant animals, are being analysed for similarity of differential gene expression during seasonal acclimation.