3.1 Extensive species differences in gene expression
The cichlid genome has over 25000 protein-coding genes (Conte et al., 2019). Of these, 17525 were expressed in focal tissues, and 5318 were differentially expressed (DE) between our two species, across both foraging conditions, with 2667 upregulated in MZ (relative to TRC - red in Figure 2A) and 2651 upregulated in TRC (relative to MZ - blue in Figure 2A) (Table 1). Cluster analysis using the top 500 most differentially expressed genes (DEGs) illustrates a clear separation of species (Figure 2B), but differences between foraging environments are less apparent. While MZ shows some separation by environment, TRC does not (more on this below).
Gene ontology (GO) analyses were performed on DEGs, using the annotated MZ genome (ensembl.org), to determine what biological processes were enriched (Figure 2C). Whereas processes related to cell cycle regulation were among the most enriched in MZ, a diversity of other processes were enriched in TRC. These data suggest that there may be divergent modes of bone growth operating in these species at the time when tissues were collected.