Scientists Develop Algorithm to Compare Closely Related Plant Genomes

Scientists at the Max Planck Institute for Plant Breeding Research in Germany have developed a new algorithm for comparing closely related genomes, irrespective of their species. The algorithm efficiently identifies sequences in which the genomes differ. This also includes the mutation that makes a plant behave completely different.

The team developed a method that does not need reference sequences. Based on the simple theory that the DNA of the parental plant differs from the DNA of the mutants in the relevant mutation, the method therefore seeks to draw a direct comparison of these closely related genomes.

If the identical sequences are removed by an algorithm, this means that only those that differentiate the two genomes are left. These are analysed using so-called "k-mer", which are roughly thirty base pairs long fragments that can be counted and grouped very easily and efficiently. All identical k-mers, i.e. all identical DNA sequences, are grouped together in a stack. As fragments with the relevant mutation have a different sequence to the parental sequence, a new k-mer stack is opened for their specific sequence information. In the end, the new algorithm shows which new stacks have arisen from the comparison and the genes that they belong to.

For more information, see Max Planck Institute's news release at http://www.mpipz.mpg.de/441094/schneeberger. Access the study's full article at http://www.nature.com/nbt/journal/v31/n4/abs/nbt.2515.html.