Genome Analysis of a Newly Discovered Yeast Species, Hanseniaspora menglaensis

Abstract

Annual surveys of Irish soil samples identified three isolates, CBS 16921 (UCD88), CBS 18246 (UCD443), and CBS 18247 (UCD483), of an apiculate yeast species within the Hanseniaspora genus. The internal transcribed spacer (ITS) and D1/D2 region of the large subunit (LSU) rRNA sequences showed that these are isolates of the recently described species Hanseniaspora menglaensis, first isolated from Southwest China. No genome sequence for H. menglaensis is currently available. The genome sequences of the three Irish isolates were determined using short-read (Illumina) sequencing, and the sequence of one isolate (CBS 16921) was assembled to chromosome level using long-read sequencing (Oxford Nanopore Technologies). Phylogenomic analysis shows that H. menglaensis belongs to the fast-evolving lineage (FEL) of Hanseniaspora. Only one MAT idiomorph (encoding MATα1) was identified in all three sequenced H. menglaensis isolates, consistent with one mating type of a heterothallic species. Genome comparisons showed that there has been a rearrangement near MATα of FEL species compared to isolates from the slowly evolving lineage (SEL).

Keywords: Illumina sequencing; MAT locus; chromosomes; fast-evolving lineage; genome assembly; heterothallic; nanopore sequencing; phylogenomics; sporulation; yeast mitochondrion.

Figure 1

Chromosome circle diagram of H. menglaensis CBS 16921 genome assembly. The central circle (blue) shows each chromosome, labelled by number 1 through 7 on the outermost ring. Chromosome sizes are shown in 300 kb intervals. The pink-to-red heatmap rings show the genotypes of well-supported SNPs in comparison to the reference genome, in the order CBS 16921, CBS 18246 and CBS 18247 (from inner to outer). “0/0” represents sites called as homozygous for the reference allele, “1/1” represents sites called as homozygous for an alternative allele, and “0/1” represents sites called as heterozygous. The black ring shows protein-coding sequences, the green ring shows tRNA genes, and the gold ring shows the rRNA array on chromosome 3.

Figure 2

Phylogenomic tree generated from 522 single-copy orthologs from 23 Hanseniaspora isolates and 4 outgroup species, S. cerevisiae, K. marxianus, W. anomalus and C. jadinii. Bootstraps lower than 100% are shown. The accession of the reference assembly or protein set used is shown in parentheses. The slow (SEL) and fast (FEL) evolving lineages are shown with blue and yellow boxes, respectively. The new species H. menglaensis is marked in bold text.

Figure 3

Identification of mating-type (MAT) loci. Mating loci were identified using BLAST analysis. Orthologous genes are indicated with shading in the background. MATa2 genes are colored in green and orthologs are indicated with green shading, whereas MATα1 genes are colored in pink and orthologs are indicated with pink shading. The accession numbers and locations of the MAT loci are indicated. MATa and MATα loci were identified in different assemblies of H. vinae TO2/19AF [56]. Some MAT loci are assembled into short contigs (e.g., H. nectarophila and H. hatyaiensis). The MATa loci of H. pseudoguilliermondii CBS8772 and H. opuntiae AWRI 357 are described in Saubin et al. [56]. There is a rearrangement around SUI1/MATα1 in FEL isolates, as previously described by Saubin et al. [56]. The three H. menglaensis isolates have identical MATα loci. Pairwise similarity with the reference H. menglaensis sequence varies for each gene: CWC25 (34–61.5%), GNEAS1 (35.4–67.4%), MATα1 (34.6–52.9%), SLA2 (10.8–76%), SUI1 (10.1–89.7%), VPS75 (41.1–77.3%) and YNL247W (63.5–80.7%). MATa2 was compared to H. valbyensis and ranges from 37.6 to 65.7% identity.

Figure 4

Formation of ascospores of Hanseniaspora menglaensis strains. (a) CBS 16921 ascospores (indicated with arrows) in asci; (b) CBS 18246 ascospore (indicated with arrow) in ascus; (c) CBS 18247 ascospores (indicated with arrows) in asci. Scale bar = 5 µm.