Epsilon Archive for Student Projects

Abstract

Genomic resources, in terms of biological sequence information are valuable tools for
yeast biotechnology since they can be utilized to guide decision in regards to genetic
engineering of potent strains. Oleaginous yeasts are organisms of particular interest for
fuel production, food, and feed industries since they are characterized by special
metabolic adaptations that allow them to accumulate more than 20% of their total dry
biomass in the form of fatty acids. Some of the most important and popular oleaginous
yeast strains belong to the Rhodotorula genus that also has unique carotenoid metabolism
properties. Since genomic resources are of great importance for lab engineering of those
strains, efforts to sequence and produce genomic assemblies have been ongoing during
the last years. Though, the produced assemblies display variation in number pseudochromosomes
and are characterized by uncertainty on whether contiguity is close to the
maximum. In this study, a selection of 23 whole-genome assemblies for Rhodotorula
strains belonging to four species is in regard to alignment-free genetic distances and
genome-wide homology before applying meta-scaffolding: an iterative reference-guided
scaffolding procedure to improve their contiguity. Moreover, comparative genomics
analyses were performed to provide a view on syntenic, and consequently evolutionary
relationships between the studied strains. All assemblies appeared improved in terms of
contiguity statistics after scaffolding, while the synteny analyses revealed varying levels
of homology and conservation in terms of sequence similarity but also gene-block
collinearity. Lastly, when focusing on a known hybrid and its parental strains, gene-order
synteny managed to uncover the origin of the hybrids at the chromosome level.