Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

Abstract

In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype, and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users, and discusses some of the challenges facing the genome-based systematics of yeasts.

Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments

“…3 and 81.1; and (3) between closely related species and varieties, values were between 83.2 and 91.8. In view of these results, we support the proposal of Libkind et al (2020b) and Lachance et al (2020) that OGRI values, preferably the ANI, should accompany any formal yeast species description.…”

What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes

“…The present analysis was limited by the number of strains’ genomes that contained all the analyzed genes. rRNA markers are not always present or well-assembled [ 38 , 40 , 41 ]; however, a more extensive analyses of these markers will be necessary to confirm the preliminary findings of the current study.…”

The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

“…Whole-genome sequencing is rapidly becoming commonplace and can contribute greatly to a sound species recognition (James et al 2020;Libkind et al 2020). In addition to enlightening the evolution and genetics of the phenotype of the novel species, whole-genome data can provide a robust phylogeny, which can be of great utility not only to situate the species hierarchically, but also if the PSC is to be applied.…”

“…In addition to enlightening the evolution and genetics of the phenotype of the novel species, whole-genome data can provide a robust phylogeny, which can be of great utility not only to situate the species hierarchically, but also if the PSC is to be applied. Overall genome similarity metrics are useful in the application of the genetic species concept (GSC, Libkind et al 2020). This will, however, require empirical validation.…”