General thoughts & discussion

When starting with this project, I believed that it would be quite easy to find out which genes that were upregulated and how the expression level differed between tissue types. However, it was a bit hard to interpret the results from the differential expression analyses. Even now, after finishing this project I am quite uncertain if my conclusions are correct or not.

When looking at the PCA plot from the DESeq2 differential expression analysis, the arils are pretty far away from each other which means that the genes in those samples differ in expression level. Since all the arils are pretty far away from one another, the conclusion is that maybe taste and smell differ from sample to sample as well as the ripeness of the samples.

I think that the assembled genome has some bias; when producing the heatmap from the DESeq2 differential expression analysis it showed a gene that had a very varied expression level in a transcriptomic read, but it only had one more read count than the other transcriptomic reads when checking the output from HTseq. I feel like that gene was not very varied in expression level compared with the other ones. As I mentioned above, this is probably due to some bias in the assembled genome.

For several of the genes in the heatmap no results showed up when looking up if the genes had functions. This could be due to the fact that these genes are only hypothetical since these analyses are based on a novel genome and has not been annotated before. Nevertheless, since the expression level is quite varied for these compared with the others, an assumption is that they have an important function in the fruit.

I only obtained results about the functions of two genes that were upregulated, since the other ones had not been previously annotated so no data existed for them. The function of one gene in the durian fruit is that it works as a transcription factor, and the function of the other gene is that it creates methionine. I think that the gene that have the function as a transcription factor is related to the ripening of the fruit, since Tean Teh, Lim, Han Yong et al. mention it in the article The draft genome of tropical fruit durian (Durio zibethinus). Therefore, I also think that the gene is related to the odor and taste of the fruit since that changes according to the fruits life cycle. I think that the other gene that creates methionine is associated with producing volatile sulfur compounds which are associated with the fruits odor, since Tean Teh, Lim, Han Yong et al. mention it in the article The draft genome of tropical fruit durian (Durio zibethinus). Moreover, methionine regeneration is also associated with the ethylene biosynthesis which is associated with the ripening of the fruit.