Building genomic profiles for uncovering segmental homology in the twilight zone.

Abstract

The identification of homologous regions within and between genomes is an essential prerequisite for studying genome structure and evolution. Different methods already exist that allow detecting homologous regions in an automated manner. Those methods are either based on finding sequence similarities at the DNA level or on identifying chromosomal regions showing conservation of gene order and content. Especially the latter approach has proven useful for detecting homology between highly divergent chromosomal regions. However, until now, such map-based approaches required that candidate homologous regions show significant colinearity with other segments in order to be considered as being homologous. Here, we present a novel method that creates profiles combining the gene order and content information of multiple mutually homologous genomic segments. These profiles can be used to scan one or more genomes to detect segments that show significant colinearity with the entire profile but not necessarily with individual segments. When applying this new method to the combined genomes of Arabidopsis and rice, we find additional evidence for ancient duplication events in the rice genome.

Supplementary Data

Browse the multiplicons of the Arabidopsis and rice only datasets and of the combined Arabidopsis-rice dataset. Use the drop-down boxes to show only multiplicons of a given multiplication level (number of homologous segments in a multiplicon). For the combined dataset, you search can for multiplicons with a specific number of segments from one genome as well as on the overall multiplication level.