Transcriptome sequencing has revolutionized many fields of biology in the last 10 years. In particular it has enabled detailed research on non-model species and created the fields of ecological and evolutionary transcriptomics.

Research on species without a sequenced reference genome includes multiple challenges, for instance i) in assembling millions of short sequencing reads into full length transcripts, ii) distinguishing paralogs and orthologs and iii) identifying transcript variants. This project centers on the first of those challenges.

The raw material is Illumina sequenced transcriptome of variable timepoints, during early development of four arctic charr varieties (Aquaculture strain from Hólar in Hjaltadalur and small benthic, large benthic and pelagic charr from Þingvallavatn). Our aim is to assemble the transcriptome of Arctic charr from these samples. The transcriptome data will be used to identify putative candidate genes of ecological and morphological importance by comparing the differences in gene expression between these morphs. The sequencing data will also be used to survey for sequence variation, specifically differences in SNP frequency between these morphologies.