From the Calsbeek Lab’s own Deb Goedert:
I received the EEES course award to attend the High Throughput Sequencing of Non-model Organisms course offered at Nord University in Bodo, Norway. High throughput sequencing (HTS) is any genomic sequencing method that generates a large number of sequenced base pairs, such as next or third generation DNA sequencing. These methods are the state of the art in evolutionary biology, allowing researchers to answer innumerable difficult questions in studies of genomics of adaptation. Due to many developments in the technology, these methods are becoming more financially accessible to researchers, so much that HTS is expected to substitute the more traditional methods for identification of SNPs and microsatellites. This is particularly relevant for non-model organisms, like the wood frogs, since the knowledge of their genome is much deficient. Therefore, understanding and developing the required skills for HTS techniques was a great and invaluable opportunity for my development as an evolutionary biologist.
The Nord University campus in Bodo has a strong research group in the area of genomics, focusing on both the development of new methods and in the use of these methods to test hypotheses in evolutionary biology. I had the opportunity to interact with amazing researchers, lab technicians, post-docs and grad students, developing a network and support group that were essential to get me up to speed during the course – since I was the only student not coming from a “DNA lab” – but that will also be of exceptional value when I need to work on my PhD data.
Over the course of 11 days (May 31st to June 10th, 2016), we had lectures, lab practical and bioinformatics sections. In the lectures, we covered the theoretical foundations of the methods, had invited talks about research using all the different methods we talked about, talks about the technology we were using in the lab section of the course (Ion Torrent sequencer and Illumina), and we were asked to give two presentations: the first being about our own projects, and the second about a paper using the methods we were interested in. During the lab section, we were able to sequence our own samples, preparing them to go into the sequencer ourselves, which included everything from DNA extraction, DNA quantification, fragment size analyses, library preparation (i.e. adding barcode and adapters to the DNA fragments for future identification of fragments), PCR, and fragment size selection. Once the sequencing was finished, we moved on to the bioinformatics practices. We were able to look at our own data set and learn basic tools for big data analyses, which allowed us to check the quality of our sequence, trim low quality reads as well as barcodes and adapters, etc. Finally, we were able to, at least partially, map our sequences. For the wood frog data I obtained, I was able to partially match some of the resultant sequences to mitochondrial DNA sequences of wood frogs published in BLAST, as well as a few important and highly conserved oncogenes from other species of frogs – not too bad for a frog without a reference genome!
DNA fragment distribution of wood frog obtained from the sample
Most importantly, difficulties that I will face during the analyses for my PhD project became evident during this course, and I was able to discuss possibilities of techniques that will most likely allow me to succeed considering specificities of my project and organism of study, as well as expected budget. This experience was, to me, one of the most incredible experiences I have had in a course, considering how much I was able to learn in such a short period of time: from a clueless field biologist with no experience in the area, to someone having a pretty decent idea of what I need to do for my project – what a journey! I cannot thank enough the organizers, invited speakers and lab technicians for how much effort and dedication they put into it. I am very thankful for the opportunity to participate in this course, due to the course award I received, and I hope other students can have an opportunity like that too.
HTS of non-model organisms 2016 course participants and faculty wait for the sequencer to run in big style.