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Genome Announc. 2017 April; 5(14): e00064-17.
Published online 2017 April 6. doi:  10.1128/genomeA.00064-17
PMCID: PMC5383881

Genome Sequences of Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 Isolated from Fermented Masau Fruits in Zimbabwe

ABSTRACT

Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 have been isolated from the microbiota of fermented masau fruits. C. fabianii and P. kudriavzevii especially harbor promising features for biotechnology and food applications. Here, we present the draft annotated genome sequences of these isolates.

GENOME ANNOUNCEMENT

Cyberlindnera fabianii 65 [previously known as Lindnera fabianii, Hansenula fabianii, and Pichia fabianii (1, 2)], Pichia kudriavzevii 129 [previously known as Issatchenkia orientalis (2)], and Saccharomyces cerevisiae 131 have been isolated from the microbiota of fermented masau fruits (Ziziphus mauritiana) in Zimbabwe (3, 4).

All three species are found regularly in (fermented) food products (3, 5,14) but also occasionally in clinical sources (15,17). Nevertheless, P. kudriavzevii and S. cerevisiae were given the status of generally recognized as safe by the Food and Drug Administration (FDA) (18). C. fabianii 65 and P. kudriavzevii 129 especially harbor promising features for food fermentation applications, such as the production of extended aroma profiles (19). To further explore these features, the draft genomes of these wild isolates were investigated and annotated.

DNA was sequenced using Illumina MiSeq paired-end (2 × 251 bp) sequencing technology, with total depths of coverage of 83.3× (C. fabianii 65), 83.3× (P. kudriavzevii 129), and 100× (S. cerevisiae 131) based on a 12-Mb genome size. Moreover, PacBio sequencing was performed with total depths of coverage of 36.6× (C. fabianii 65), 32.1× (P. kudriavzevii 129), and 22.2× (S. cerevisiae 131). We performed hybrid assemblies using DBG2OLC with Illumina and PacBio data (20). PBJelly (21) was used for further scaffolding. The final assemblies were polished with Sparc (PacBio) (22) and Pilon (Illumina) (23). MAKER2 (24) was used to annotate the genomes using protein homology evidence from all available fungi in the Swiss-Prot database (25). De novo gene predictors Augustus (26) and SNAP (27) were trained using Pichia stipitis genome sequence data for C. fabianii 65 and P. kudriavzevii 129 and Saccharomyces cerevisiae for S. cerevisiae 131. Functional annotation was performed using BLASTp (28) against Swiss-Prot (25). Protein domains and gene ontology terms were assigned using InterProScan (29). BUSCO (30) analysis showed that more than 90% of the core fungal genes are present in all three assemblies (Table 1). The G+C percentage of C. fabianii 65 is 44.4% but is lower for P. kudriavzevii 129 (38.5%) and S. cerevisiae 131 (38.1%). Other assembly and annotation statistics are listed in Table 1.

TABLE 1
Assembly characteristics of three fungal genome sequences

The genome sequences and gene annotations can now be used to develop novel molecular tools to unravel the full metabolic repertoire of the two nonconventional yeasts compared to S. cerevisiae 131. Additionally, links between phenotypes and genotypes, as well as comparative genomic studies among the three species, will reveal opportunities for industrial applications of C. fabianii 65 and P. kudriavzevii 129.

Accession number(s).

The annotated genome sequences are deposited at DDBJ/EMBL/Genbank under the accession numbers listed in Table 1.

ACKNOWLEDGMENTS

This research was financially supported by the Graduate School VLAG (Wageningen University & Research, Wageningen, The Netherlands) and Heineken Supply Chain BV (Zoeterwoude, The Netherlands).

Footnotes

Citation van Rijswijck IMH, Derks MFL, Abee T, de Ridder D, Smid EJ. 2017. Genome sequences of Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 isolated from fermented masau fruits in Zimbabwe. Genome Announc 5:e00064-17. https://doi.org/10.1128/genomeA.00064-17.

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