NEW YORK (GenomeWeb) – An apparent 100 million-year-old duplication of the yeast genome was actually due to an ancient interspecies hybridization event, according to a new phylogenetic analysis.
Using a large-scale phylogenetic approach, a pair of researchers from the Center for Genomic Regulation in Spain examined the evolutionary history of Saccharomyces cerevisiae genes and teased out when each duplication event occurred. However, the researchers found that many of the yeast genes defined as duplicated gene ohnologs actually diverged prior to when the whole-genome duplication event was expected to have taken place, as they reported today in PLOS Biology.
"When we first saw the results of our study, we thought there had been some kind of mistake," CRG's Toni Gabaldón said in a statement. "But once all the potential problems have been discarded, you begin to interpret the data objectively, without preconceived ideas, and to do real science. That's when we started to consider the different possible explanations and to work on a new idea."
Gabaldón and his colleague Marina Marcet-Houben analyzed 26 completely sequenced S. cerevisiae genomes and constructed a reference species phylogeny based on the alignment concatenation of 56 common single-copy orthologs. Using the phylomeDB pipeline, they reconstructed the evolutionary history of every protein encoded in the S. cerevisiae genome.
Such gene family trees, they noted, can be used to uncover and gauge the timing of duplication events.
The largest duplication peak Gabaldón and Marcet-Houben found could be traced to the branch that preceded the divergence of Saccharomyces from Kluyveromyces, Lachancea, and Eremothecium.
This KLE peak, as they dubbed it, was more apparent in the duplications leading to conserved pairs of whole-genome duplication (WGD) ohnologs, suggesting that the duplication is related to the observed WGD paralogous blocks but also that the genes in those blocks diverged at different times.
After a series of experiments using other methodologies and exploring alternative explanations, the duo concluded that the majority of genes thought to be ohnologs, actually diverged prior to the suspected timing of the WGD event.
An alternative explanation, the pair noted, could be an ancient interspecies hybridization event. Such an occurrence could lead to the phylogenetic pattern seen as duplications map to the common ancestor of the two hybridizing species, they said.
To examine this idea, they studied the duplication densities of S. pastorianus, which is the result of a recent hybridization of S. cerevisiae and S. eubayanus. This analysis uncovered an apparent duplication peak at the common ancestor of S. cerevisiae and S. eubayanus, but not at the time of the hybridization event when the doubling was known to have occurred.
This, they noted, suggests the ancient doubling in the S. cerevisiae lineage could be due to hybridization between two lineages that diverged just after the observed peak, though before the post-WGD species diverged.
There are, Gabaldón and Marcet-Houben said, two possible hybridization scenarios that could have occurred. In one, two diploid cells from two distinct species could have formed an allotetraploid, and recombination and gene loss then led to an effective doubling of the genome. Another possibility is that two haploid cells from different species formed an allodiploid that then underwent autopolyploidization to re-enable meiotic recombination.
"Interspecies hybridization brings together different physiological properties and isolates sexually the newly formed lineage, hence providing an initial selective advantage to explain observed WGDs in eukaryotes," the duo noted in their paper. "Considering the widespread presence of hybrids among current species, this scenario should also be considered when interpreting ancient polyploidies."