At long last, our genome project is truly underway – the sequencing has been done so now begins the process of assembly!
Getting to this point, we ran into an unexpected series of setbacks with DNA quality control. A major issue lay in quantifying the DNA for sequencing from very tiny bees. We used a Nanodrop spectrophotometer, which fooled us several times into thinking we had more DNA than we actually did. It turns out that the total DNA from a tiny sweat bee like Lasioglossum laevissimum, when eluted in a reasonable liquid volume, is at a concentration well below accurate levels of measurement for our instruments. This explains why some people refer to Nanodrops as expensive random number generators. We actually found the Nanodrop to be quite accurate in measuring relatively high DNA concentrations from big bees. A second set of problems arose with DNA quality – low quality DNA might not produce sufficient or high enough quality DNA libraries. After several apparently unsuccessful attempts to solve this problem, we instead decided to ignore it! Lo and behold, we got all the libraries we originally planned for.
So now we have billions of sequences to assemble. We will be learning a lot of new skills soon. Once we have more or less figured out how to do this, we hope to use this genome assembly and annotation project not only for our research, but also to teach bioinformatics skills to undergrad and grad students to widen their technical experience. This should be fun!