3.3 Cross-temperature differential gene expression
We first examined the expression data for temperature-dependent
responses in each species by a two-dimensional plot of the first two
principal components of a PCA. This analysis showed
temperature-dependent separation of replicates for the heat-tolerant,B. calyciflorus s.s. This separation was less clear for the
heat-sensitive species, in which replicates from 20 oC
and 23 oC clustered together, while all samples
treated at 26 °C formed a separate cluster (Figure S2). Overall, we
found a greater number of differentially expressed genes (DEGs) in the
heat-tolerant species than the heat-sensitive. In both species we
captured a greater number of DEGs in pairwise comparison controlvs. high heat (Figure 3A, 3B). However, in the heat-tolerant
species, we captured a greater number of genes differentially expressed
between control and mild heat (1268) than between mild and high heat
(64). In contrast, in the heat-sensitive we found the opposite pattern
(Figure 3A, 3B).
We focused on pairwise comparison mild vs. high heat in both
species as we had evidence from population growth rate data that there
is a strong effect of temperature in this transition. In B.
calyciflorus s.s., among the 64 genes differentially expressed between
mild (26 oC) and high (32 oC) heat,
were genes encoding for RNA polymerases, histone proteins and
transferases. The above genes showed different temperature induction
with genes encoding for RNA polymerases and N-acetyltranferases being
up-regulated at high heat. Genes encoding for histones such as H2B
family were either up- or down- regulated at high heat (Figure S3A). In
heat-sensitive B. fernandoi , among the 310 differentially
expressed between mild (23 oC) and high (26oC) heat, we found genes encoding for several histone
methyltranferase proteins such as H3K4, H3K79, H4K20. All above genes
were up-regulated with heat (Figure S3B).
We further focused on genes that are differentially expressed in all the
three pairwise comparisons. These genes are of high importance as they
are the most responsive to temperature presenting either up- or
down-regulation along with temperature increase. In the heat tolerantB calyciflorus s.s., there were 23 genes differentially expressed
in all pairwise comparisons. Among these, genes encoding for ribosomal
proteins and glutathione S-transferase were up-regulated at lower
temperatures, while proteases related genes were up-regulated at higher
temperatures (Figure S4A). In the heat-sensitive B. fernandoi,there were two genes that were differentially expressed in all pairwise
comparisons. These genes encode for E3 ubiquitin-ligase and a mediator
of RNA polymerase were up-regulated at higher temperatures (Figure S4B).