Research Article: Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina

Date Published: January 30, 2019

Publisher: Public Library of Science

Author(s): Neža Čadež, Nicolas Bellora, Ricardo Ulloa, Chris Todd Hittinger, Diego Libkind, Andrey M. Yurkov.

http://doi.org/10.1371/journal.pone.0210792

Abstract

A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, Kr, and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928T (ex-types: ZIM 2545T = NRRL Y-63793T = PYCC 7262T; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).

Partial Text

Since the introduction of DNA sequence analysis for species delineation, the number of newly described species of the yeast genera Hanseniaspora and Kloeckera (the allied anamorphic genus) has increased from seven to nineteen [1–6]. A similar number of newly described species can be observed for other yeast genera, mostly as an extensive database of barcode sequences of D1/D2 and internal transcribed spacer (ITS) regions provides data of all described species [7]. However, additional protein-coding genes have also been employed in yeast taxonomy to construct statistically well-supported phylogenetic trees that reflect the evolutionary relationships among species and genera [8–10]. With emergence of whole genome sequencing, reconstructions of more robust yeast phylogenies are now being recovered [11–14], from which a frame for new species definition is being built [15–21]. A shift from phenotype- to sequence-based taxonomy enables introduction of the new International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code; [22]) by which the teleomorphic genus Hanseniaspora has a priority over its anamorphic counterpart, Kloeckera, by the rules of nomenclature and the number of species assigned to each genus [23]. Accordingly, the three asexual species Kloeckera hatyaiensis, Kloeckera lindneri and Kloeckera taiwanica should be transferred to the genus Hanseniaspora (see Taxonomy).

 

Source:

http://doi.org/10.1371/journal.pone.0210792

 

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