During the Autumn semester we have sequenced and asssembled two genomes: one from a Neochlamydia and one from a Ralstonia.
We have first ran one Illumina lane for both genomes, then the students assembled these reads using a variety of protocols (promised, we’ll blog this in more detail next year). We also had a PacBio run which was very helpful in assembling, as well as an Optical Map of restriction sites, to scaffold the contigs.
The students then performed PCRs to close the gaps between contigs, based on primers which they designed.
In the end, we have the following assemblies, good enough for annotation:
Neochlamydia: 4 large gaps left, estimated total size 3.07 Mb;
Ralstonia: three chromosomes:
- 3.65 Mb, 28 contigs mapped
- 1.80 Mb 20 contigs mapped
- 0.52 Mb 4 contigs mapped
Honesty forces us to say that many a contig remained unmapped… 🙁
When the new master program Molecular Life Sciences was launched in 2010 in the University of Lausanne, it contained a very unusual course. One made possible by the progress of technology, the concentration of competences in Lausanne, and the daring of a small team of instructors: the “Sequence a genome” class.
The principle is simple: a few bacterial species whose genome is unknown, and which are studied in Lausanne laboratories, are provided to the students. The class isolates and prepares the DNA, and sends it to the sequencing facility. A few weeks later (which are used to learn about modern computing systems), the class recovers the raw DNA read files, and spends the autumn semester assembling them into an actual genome sequence. There are always some gaps, so the spring semester starts with a few extra PCR experiments to close them. Then the students divide the genome into sets of interest, according to the known biology of the species (e.g., heavy metal resistance) or to unexpected features of the genome (e.g., a very large plasmid). They annotate these sets, which means that they identify the relevant genes and provide the best guess of their function. Finally, the full information is gathered into a paper, which is submitted for publication, co-authored by all the class!
A unique feature of this course is the work on an actual research project, for which the results are totally unknown at the start of every year, and for which the methods are continuously evolving: the teachers and the students must stay at the forefront of the latest experimental and computational expertise. In the end, the students have produced new knowledge, and have learned to work with cutting-edge sequencing and bioinformatics technologies.
As far as the Lausanne team knows, they were the first in the world to propose such a course. The course received a collective Excellence in teaching award from the Faculty of Biology and Medicine in 2012.
We are now going to add a new feature to this class: blogging the progress of the sequencing, assembly and annotation of the genomes, with the students. Stay tuned!