Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods

Background Lake Baikal is one of the oldest freshwater lakes and has constituted a stable environment for millions of years, in stark contrast to small, transient bodies of water in its immediate vicinity. A highly diverse endemic endemic amphipod fauna is found in one, but not the other habitat. We ask here whether differences in stress response can explain the immiscibility barrier between Lake Baikal and non-Baikal faunas. To this end, we conducted exposure experiments to increased temperature and the toxic heavy metal cadmium as stressors. Results Here we obtained high-quality de novo transcriptome assemblies, covering mutiple conditions, of three amphipod species, and compared their transcriptomic stress responses. Two of these species, Eulimnogammarus verrucosus and E. cyaneus, are endemic to Lake Baikal, while the Holarctic Gammarus lacustris is a potential invader. Conclusions Both Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions. Electronic supplementary material The online version of this article (10.1186/s12864-019-6024-3) contains supplementary material, which is available to authorized users.


Assembly statistics
: characteristics of the assembly. Shown are technical characteristics of the complete and reduced transcriptome assemblies according to TransRate [42]. The explanation of the terms can be found at http: Mapping rate Figure S1: The percent of mapped reads was calculated by mapping raw reads of each species to each of the assemblies with salmon [47] and extracting the mapping rate from salmon output. Each box plot summarizes ca. 60 values.

Text S1: Checks for mislabeled samples
To check for consistency of samples and variability between replicates, we used the transcript abundance data generated by mapping of all samples to one transcriptome assembly to perform principal component analysis (PCA).
Two first principal components showed a clear distinction between the species. Moreover, while PC1 differentiates between Eulimnogammarus and Gammarus, PC2 differentiates between E. verrucosus and E. cyaneus.
However, several samples were located not in the expected places on the plot (an example is show below). A possible explanation could be that two samples have been swapped during library preparation, and one was a mixture of material in between the two species.
An example PCA plot of control and LT10 exposure samples showing the problematic samples. Other samples not shown on this plot were correctly attributed to the species.
To checke for potential wrong assignment of the sample to species, we analyzed 18S rRNA sequences as a phylogenetic marker. The 18S sequences of these species are known (Qiu, Y., Smith, J.E., Sherbakov, D.Y. and Kamaltynov, R.M., unpublished).
Here are the data for a subset of samples (including the most "interesing" ones). The vertical scale shows number of reads with the corresponding species-specific 18S sequence in the reads: Indeed, we found two samples that have been most probably swapped and one more sample that potentially contained mixed materials of two different species. Two swapped samples were renamed, while the mixed sample was removed from further analysis. Thus, we renamed Ecy10LT3_3 and Gla10LT3_4 and excluded EveB24_2_6 and GlaB24_1 from the analysis.   Figure 4D) with the sequence from A. tomentosa. Note the absolute conservation of the cystein residues. The remaining panels feature the abundance of different transcripts encoding all MT-like transcripts in different conditions. TPM, transcript for million counts. The labels of the horizontal axis are the same as in Figure S2. C E K C S S E C K C S N K E E C S K N C K K P C S C C P --C E N C K G S C D C S S V D A C A T N C D T P C S C C P T E C E N C K G S C D C S S V D A C A T N C D T P C S C C P T E 60