3.6 Cross-species co-expression gene groups
To capture similar or contrasting patterns of expression between the two
species, we searched for co-expression patterns in orthologous gene
groups. Analysis with Clust revealed the presence of 8 gene
groups/clusters (Figure S9). We have focused on just three of these
because their patterns appear biologically relevant. Gene cluster C1
contained 150 orthogroups that had the same expression pattern between
the two species and were up-regulated with increasing temperature
(Figure 6). Five KEGG pathways were significantly enriched in the C1
group (p<0.05, FDR=0.05), including genes belonging to core
metabolic pathways (KEGG pathway: 01100). Two clusters (C6 and C7)
contained genes with opposing patterns of expression in the two species.
In cluster C6, genes from the heat-tolerant B.calyciflorus s.s.
had low expression at control conditions, were up-regulated at mild
heat, and down-regulated again under high heat. In contrast, forB. fernandoi , genes in C6 had higher expression under control
conditions, were down-regulated at mild heat and up-regulated again at
high heat. The longevity regulating pathway (KEGG pathway: 04212) was
significantly enriched in C6 cluster (p<0.05, FDR=0.05). In
cluster C7, for B. calyciflorus s.s. gene expression was high
under control and mild heat conditions and down-regulated at high heat.
However, for the heat-sensitive B. fernandoi , gene expression was
low for control and mild heat conditions and up-regulated under high
heat. In this cluster, a total number of 12 pathways were significantly
enriched (p<0.05, FDR=0.05), among which pathways involved in
signal transduction, nervous and endocrine systems, and replication and
repair.
DISCUSSION
We combined life history and expression data to test variation in
temperature-dependent responses between heat-tolerant and heat-sensitive
species (Paraskevopoulou et al., 2018) from the recently resolvedB. calyciflorus species complex (Papakostas et al., 2016). We
observed a transcriptomic response that was largely consistent with
phenotypic data from life history experiments. This has revealed both
shared and species-specific patterns in gene expression in response to
heat, and identified key functional pathways associated with temperate
adaptation in these species. This demonstrates the power of testing the
transcriptomic response of an organism to an environmental stressor by
combining transcriptome with phenotypic data (DeBiasse & Kelly, 2016).