The term inter-species hybridisation refers to the
crossing of two divergent organisms, leading to a situation
where the two parental genomes coexist in the same nuclear
compartment. In higher eukaryotes, this scenario often results
in incompatibilities and interference between the genetic
material of the two parents, generally detrimental for the
newly formed hybrid. However, hybridisation also represents
a major source of genomic diversity that can drive adaptation
to new niches. After a hybridisation event, the resulting
hybrids have a highly heterozygous genome which can, on
occasion, derive in extreme phenotypes beneficial for
adaptation to new niches or confer properties by new allele
combinations that are advantageous with respect to the
parentals [1].
In the yeast clade of Saccharomycotina,
hybridisation has been found to be a rather common
phenomenon with numerous hybrid lineages found in
industrial environments and many others isolated from clinical
settings posing a serious threat to human health [2].
Candida metapsilosis and Candida orthopsilosis are
two emergent fungal pathogens species that belong to the
Candida parapsilosis sensu lato species complex and have
been found to be of hybrid nature [3]. C. metapsilosis
descends from a single hybridisation event between unknown
parentals whereas for C. orthopsilosis, the isolates found to
date originate from one of four hybridisation events from the
same two parental lineages, of which only one has been
identified [4,5]. The vast majority of clinical isolates from
these two species are hybrids. Parental lineages are never or
very rarely isolated from clinical settings suggesting that the
pathogenic hybrids might have arisen from non-pathogenic
parentals. In other words, that hybridisation might enhance the
emergence of new hybrid lineages with an advantage to thrive
in new environments, such as in the human host.
This research aims to shed light into the genomic traits that shape yeast hybrids and their evolution. In
particular, we sought to understand what the environmental
source of these hybrids and their parental species could be,
and what are the genomic traits may have facilitated an
opportunistic pathogenic behaviour. To this end, we here
analyse the genomes of thirteen marine environmental strains
from C. orthopsilosis and C. metapsilosis. We show that the
majority of isolates (11 out of 13) are hybrids which expands
the map of ecological distributions where these yeasts can be
found to include aquatic environments. The fact that hybrids
are overrepresented over parental strains also suggests that
hybrids have an advantage over parental lineages not only in
the clinical settings but in some environmental niches too. We
hypothesize that the genomic features that make hybrids
highly competitive in certain (perhaps extreme) environments
might be also advantageous in other niches like the human
body. Consistent with this statement, our phylogenetic
reconstruction based on genome-wide polymorphisms shows
that the new environmental hybrids fall in (or close to)
previously defined clades that harbour clinical isolates.
Until now it has been a complex task to fully
characterise the genome of a hybrid cell when one or both of
the parentals remained unknown, and parameters like
divergence between parentals or percentage of each parental
haplotype in the hybrid have so far been based on estimations.
In this study we find that two of the marine C. orthopsilosis
isolates which have highly homozygous genomes represent a
long-sought parental lineage so far unidentified. Thus, using a
combination of short- and long-read sequencing technologies
we generated a genome assembly of the new parental strain
which opens a door for future research including the
generation of a phased genome with resolved haplotypes that
in turn, will lead to a better understanding of the hybrid
genomes and a more accurate view of genetic variants
