Differential expression of miRNAs during diapause
We began by looking at global patterns of miRNA expression in order to
gain an overview of temporal changes across diapause. General expression
patterns observed via multidimensional scaling (MDS) showed that direct
developing individuals have a linear development pattern largely moving
along dimension 2 in both head and abdomen tissue. Diapause individuals
have a divergent development that moves along dimension 1 reaching a
maximal divergence at day 114-144, after which miRNA expression
converges with the developmental trajectory of the direct developing
individuals at diapause day 155 and direct day 3 (Figure 2).
Continuing with our global perspective, differential expression analysis
found that there were 117 DE miRNAs between all comparisons in the head
tissue, and 49 in abdomen tissue (Table S4). In order to identify
clusters of similarly expressed miRNA during the course of diapause
development, differentially expressed miRNAs among timepoints of
diapause were used as input for a cluster analysis. The optimal number
of clusters for each of the analyses was 7 for the head tissue (Figure
3) and 5 for the abdomen tissue (Figure 4). When DE miRNAs were filtered
to fit a membership of > 0.8 to one of the clusters, the
number of DE miRNAs were reduced to 83 in the head, and 25 in the
abdomen. Of these filtered DEGs, 19 were in both head and abdomen
samples.