Fig 1.
Placement of Hanseniaspora gamundiae sp. nov. within the genus Hanseniaspora based on the sequences of the ITS and the D1/D2 LSU regions of the gene encoding the rRNA, as well as the genes encoding actin and elongation factor-1α (EF-1α) proteins.
(A) A phylogenetic tree inferred using Maximum-Likelihood analysis based on the Nei-Tamura model in MEGA6 [39]. Bootstrap analysis was carried out with 1000 pseudoreplicates [40]; only values above 50% are shown. Wickerhamomyces anomalus was used as the outgroup. Bar, nucleotide substitutions per site. p, indicating percentage of substitutions between the two marked sequences for each of the four individual genes or p-distance. (B) Parsimony networks based on the ITS and D1/D2 LSU of the rRNA gene sequences of strains of H. gamundiae sp. nov. and its closest relative H. taiwanica. Each connecting line represents a single nucleotide substitution, and each small circle indicates a missing intermediate haplotype. The rectangle indicates the sequences identified as ancestral by the analysis. Analyses were performed using TCS 1.21 [42]. (C) A consensus network showing relationships between H. gamunidae and its closest relatives. H. mollemarum [6] is not included in phylogenetic analyses.
Table 1.
Comparative analysis of genomes, assemblies, and gene statistics for Hanseniaspora gamundiae sp. nov. and other Hanseniaspora species.
Table 2.
Genome statistics.
Fig 2.
Phylogenomic relationships of the nine Hanseniaspora strains based on an alignment-free matching algorithm with a nine bases DNA seed.
Saccharomyces cerevisiae and Kluyveromyces lactis were used as outgroups. Similarities among closely related genomes are presented as the Alignment-Free Distance Measure (Kr), Average Nucleotide Identity (ANI) and by estimating digital DNA-DNA Homology values (dDDH values).
Fig 3.
Schematic gene organization around the putative sulfite pump gene SSU1 (purple) in H. gamundiae sp. nov. and related species.
Green arrows indicate genes without synteny, while the color intensity of arrows from yellow (40–50% nucleotide similarity), to orange (80–90% similarity), to red (more than 90% similarity), indicate the level of conservation between orthologous genes. Gene sizes and distances are approximately to scale. Numbers in parentheses indicate scaffold number and location of genes in the assembled genome.
Fig 4.
Metabolic traits and genes for the assimilation of the carbon sources sucrose, raffinose, melibiose, galactose, lactose, trehalose, maltose, cellobiose, and glucono δ-lactone by Hanseniaspora species and Saccharomyce cerevisiae (S288c).
Numbered boxes indicate presence (1) or absence (0) of putative homologous genes determined by Reciprocal Best Hit (RBH) prediction algorithm. Physiological characteristics are from Kurtzman et al. [84], except for H. gamundiae.
Fig 5.
Hanseniapora gamundiae sp. nov. CRUB 1928T.
(a) Budding cells, YM broth, 25°C, 220 rpm, 2 days. (b) Sphaerical and warty ascospore, 5% malt extract agar after 21 days at 25°C. Scale bars, 10 μm.