In the project section of my blog, I will describe each week what I did on my traineeship. I will also post about my experiences about my workplace EMBL-EBI, located on the Wellcome Trust Genome Campus in Hinxton.
My first post is a report about what I exacly did my first week at EMBL-EBI. My task this week was developing a synteny map where the chromosomes of AcoCah and Mus musculus are compared (two rodent species).
In order to understand the following post, it is necessary to know the meaning of some bioinformatic words:
- Synteny: Describing the conservation of the order of blocks of genes between two sets of chromosomes (in this case two different Rodent Species) that are being compared with each other.
- Scaffolds: Blocks of genes that can be assembled into chromosomes. In this study only scaffolds of at least 2 million base pairs are taken into account during synteny mapping.
- Karyotype: A karyotype is an image of the chromosomes (also called karyogram). The chromosomes show a band pattern depending on the used probes.
- FISH: Abbreviation of Fluorescence In Situ Hybridization: Technique that results in the obtaining of a karyogram. By using multiple probes with different colours/identifiers, it is possible to differentiate the different chromosomes from each other and to detect the various scaffolds that are present in the chromosomes.
Since I did not perform any of the actual wet lab work myself, I will shortly describe the methods used to obtain the AcoCah data. This data is required for the creation of the synteny map between Mus musculus (MMU) and AcoCah. Genome wide sequencing was performed using PacBio’s SMRT (single molecule real time sequencing) platform in order to obtain the entire sequenced genome of AcoCah.
An entire high throughput sequencing pipeline has to be followed first, before the data is ready to be used for the comparison. After the data has been released for usage, the creation of a synteny map can start. I first perform a blastn alignment between the obtained AcoCah genome and the MMU reference genome. In this way matching regions between both Rodent species can be found. Next I run the synteny python script that results in a scalable vector graphics (.svg) file consisting of sorted AcoCah scaffolds that can be aligned with the Mus musculus reference genome.
The sorted scaffolds can now be mapped on the chromosomes of AcoCah. The creation of the synteny map requires a combination of methods. One of the methods is using the karyogram that has been obtained with a special form of cross-species FISH. I also use a previously created synteny map where AcoRus is compared with MMU. Since both Aco species are closely related to each other, both syntenies are very similar. This similarity can be used to solve sections of uncertainty.
An (easy) example of this mapping can be found below:
1. We try to identify the band pattern of chromosome 14, present in the karyogram (left). We found a matching pattern in the right figure. To determine the exact matching section, we use the synteny map of AcoRus (not shown here),
2. The syntony python script creates .svg files like the one that is shown here. The red bars represent our area of interest. We see that four scaffolds (pseudohap44, 217, 247 and 249) are present in this region.
3. This image shows the result of our mapping. The four scaffolds found earlier are placed in the short arm of chromosome 7 of AcoCah. This way we can conclude that, after many years of evolution, a section of chromosome 14 of MMU is located in chromosome 7 of AcoCah.