The SuperGenome, a new concept for comparative genomics and beyond
- Kay Nieselt (Universität Tübingen, Tübingen, Germany)
Abstract
Next-generation deep-sequencing (NGS) has been revolutionizing eukaryotic and prokaryotic genome analyses. The technology can be used to address a wide variety of questions, such as the evolution of species by comparison of their genomes. When genomes are compared based on genomic positions typically a specific reference genome is assigned which acts as the coordinate system for the comparison. However, rearrangements and insertions or deletions lead to substantial architectural variations between genomes and therefore genomic regions, that cannot be aligned to the reference, are lost.
We have proposed the SuperGenome as a solution, which establishes a general global coordinate system for multiply aligned genomes. This enables the consistent placement of genome annotations in the presence of insertions, deletions, and rearrangements.
In my talk I will first formally introduce the SuperGenome concept and then turn to various applications. One is GenomeRing, a visualisation of a multiple genome alignment based on the SuperGenome. With GenomeRing, we won the most creative algorithm award at Illumina's iDEA challenge 2011. The second one explains how the SuperGenome can be used as a general support for genome annotation pipelines. In particular, I will point out how the Pan-genome, i.e., the full complement of genes in a species, can be nicely derived from the SuperGenome.
Finally I will show how the SuperGenome can also be used for comparative transcriptomic analyses, notably how we have used the SuperGenome for the cross-genome prediction of transcription start sites from RNA-seq data [2]. I will end my talk by pointing out open questions that we hope to be able to solve in future research work.
References:
[1] Herbig A., Jäger G., Battke F. and Nieselt K. (2012), "GenomeRing: alignment visualization based on SuperGenome coordinates", Bioinformatics. Vol. 28(12), pp. i7-i15, doi:10.1093/bioinformatics/bts217.
[2] Dugar G., Herbig A., Förstner K., Heidrich N., Reinhardt R., Nieselt K. and Sharma C. (2013), "High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates", PLoS Genet 9(5):e1003495.
