Transcriptome sequencing of two Baikal (Eulimnogammarus verrucosus and E. cyaneus) and one Holarctic (Gammarus lacustris) amphipod species exposed to 1.5 and 12 degree Celsius

This project aims to find the molecular changes driving the cold stress response of freshwater amphipods with different overwintering strategies Overall design: After preacclimation at 6 degrees C for two weeks, three amphipod species were exposed to 1.5 and 12 degrees C for 30 days. At each temperature point, there were 4 replicates of each amphipod species analyzed. Animals were pooled; pools of E. verrucosus, E. cyaneus, and G. lacustris contained 3, 12-15, and 10-12 animals, respectively. De novo transcriptome assembly was performed using Trinity. Redundant transcripts were removed with cd-hit-est. Misassembled or incomplete contigs were filtered out with TransRate. Only transcripts with matches to metazoan sequences were retained. Transcript quantification was performed with salmon and further processed with the DESeq2 package for R.