New DNA sequencing technologies and bioinformatics sequence analysis algorithms are able to produce high-quality chromosome-level assemblies of large genomes. However, many research communities still rely on ‘Version 1.0’ draft assemblies that are fragmented, incomplete, and lack chromosomal location data. In a study published in the journal BMC Biology, the SIB Group of Robert Waterhouse (University of Lausanne) demonstrates how genome-comparison-based evolutionary approaches can be used to help such draft assemblies along the journey towards becoming ‘finished’ reference genomes.
Exploiting conserved gene arrangements
Although genomic rearrangement events lead to the shuffling of genome contents over time, regions with conserved orders and orientations in multiple species can be identified. These are known as synteny blocks, where equivalent genes in different species (orthologs) have maintained their local genomic neighbourhoods. Draft genomes are made up of genomic regions assembled into scaffolds of different lengths, but their relative orders and orientations along chromosomes is usually unknown. The SIB Researchers hypothesised that conserved synteny blocks could be used as the basis for an evolutionarily guided approach to ordering and orienting scaffolds to improve currently fragmented draft assemblies. “The logic is fairly simple,” explains lead investigator Robert Waterhouse, SIB Group Leader at the University of Lausanne’s Department of Ecology and Evolution, “when genes located at scaffold extremities in one species have orthologues from many other species that are maintained as genomic neighbours, then evolution is suggesting we can stitch those scaffolds together to reunite these pairs of genes”.
Waterhouse R et al. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biology 2019.