SCIE4002 Bioinformatics and Data Analysis for Genomics

Your projects will continue the theme of chloroplast genomes, genes and RNAs that we've been focusing on in this course. In addition to the practical advantages of dealing with small genomes in a teaching class like this, chloroplast genomes are fascinating in their own right. Chloroplasts are being increasingly used as biotech factories for production of valuable compounds and proteins and are a primary target for the new science of synthetic biology. Understanding the natural diversity of chloroplast genes and their evolution is essential background to this work. We will give each group some unlabelled DNA sequence reads from total plant DNA and some RNA-seq data. Each project will have 4 main parts.

1. Your initial task will be to attempt to assemble the chloroplast genome. The task will be complicated by the fact that you will be given unpublished data, so there will be nothing publicly available that is completely identical to what you are studying. This of course leaves the path open for you to make some novel discoveries.

2. Next you will need to put your sequence in a phylogenetic context, by finding out what it is related to, and if possible, identify the source organism. The plants we have chosen are all Western Australian plants, and all have some special interest, so once you have figured out what you might have, you can try and find a ‘story’ behind the plant - it will make your presentation more fun to put together and more interesting to listen to.

3. The next step is to annotate the genome, identifying which genes are present in your assembly. You may find that some genes that are normally present in chloroplast genomes are missing from your genome. You will need to figure out if that’s because your assembly is incomplete, or whether this is a sign of a real biological difference. 4. The final step is to analyse the RNA-seq data; your task will be to discover which chloroplast genes are expressed and at what levels.

All these steps will involve similar analyses to those you carried out in the practicals, so you should be well-prepared. In addition to following this basic outline, we are likely to be impressed by groups that branch out to analyse some particularly interesting feature of their data, so don’t be afraid to explore. At different steps in your analysis you are encouraged to show off your data-wrangling skills by number crunching and plotting any quantitative values you come across in your research. Creative use of these skills will boost your marks in the assessment.