Conclusion

From the Monthong and Musang king differential expression analysis, it is clear that there exists different adaptations that differentiate the species on at least the level of the fruit arils tissue. This can be seen by the clustering of Monthong fruit arils in the PCA plot, and also on the larger spread of p-values in the volcano plot, indicating that more genes are differentially expressed between species, than what is the case of the within species volcano plot (intraspecies). One potential adaptation that distinguishes Monthong from Musang king is the upregulation of HSP101 for this cultivar, which could be seen in the heat map. This upregulationon could imply that Monthong is a more heat-resistant cultivar than Musang king, since HSP101 can work as a repair mechanism and re-fold proteins that have been unfolded by heat stress. In conclusion: it seems like overexpression of HSP101 (named ClpA ClpB family in the heatmap) is an adaptation for the Monthong cultivar that makes it more heat resistant and the fact that the gene is involved in the longevity regulating pathway implies that this could be an adaptation that allows for the plant to grow in a warmer environment than the Musang king cultivar.

When looking at the within species comparison done for Musang King, it seems like root, leaf and stem are tissues that share the most similarites, while fruit arils distinguishes itself in the expression level of its genes. This could imply that fruit arils is a very differentiated tissue type. This claim is strengthened by the heat map which shows that for the 10 most differntially expressed genes, we have that genes that are overexpressed in fruit arils are underexpressed in the other tissues, and vice versa.

However in general, one can conclude that in general the expression levels are more similar between the tissues within a species, than when you compare the same tissue but from another cultivar. This can be seen by the volcano plots where you can see a lower spread of p-values in the volcano plot for the within species comparison.