Lexi & Laura
-tRNAs, rRNAs, and other nontranslated RNAs (number, type, etc.): Both the strawberry and the grape papers identified the number of tRNA genes found. The strawberry paper identified some rRNA genes but noted that they “found no full-length copies of large cytoplasmic rRNAs.” The grape paper does not mention rRNA, though it is possible this data exists in the supplemental data.
We can use our annotation services to identify tRNAs and rRNAs. We can compare the numbers we calculate with the numbers of tRNA and rRNA genes in grape, strawberry and other plants.
-MYB TFs: We can identify these TFs by using BLAST for Arabidopsis. We can compare these to those present in strawberry using the strawberry genome browser or another method. Myb TFs were not discussed in the grape paper but we may be able to identify them through the grape genome. We can note any distinctions between blueberry and its relatives.
-pH: What makes the blueberry basic? We know anthocyanins are pH dependent and can serve as an indicator of pH, but what actually creates that pH? We need to do research to determine what can change pH in fruits and then search for those factors within the blueberry genome.
-pectin: how much is in blueberries as compared to other fruits? How is it beneficial? Is there a specific gene for pectin? Can we find it?
-cranberry genome (if it has been sequenced)
-Determine RBS for blueberries: Is it the same for every gene? Use this to find areas of DNA where genes may be located.
-Create a map similar to Figure 1 of strawberry paper