Genome sequence data of Saccharomyces cerevisiae CBS 493.94

Abstract

Whole genome sequencing (WGS) and data concerning identity and safety for Saccharomyces cerevisiae CBS 493.94 are reported. This strain was isolated from a British brewery in 1958 and deposited at the CBS culture collection Westerdijk Fungal Biodiversity Institute under the accession number CBS 493.94. The long-reads sequencing data, obtained via PacBio Sequel, and short-reads data, via Illumina NovaSeq 6000, were deposited at NCBI under accession number PRJNA1044661. The hybrid assembly was made publicly available via Zenodo and NCBI. For strain identification, data from 18S rRNA, ANI dendrogram and Core Genome single nucleotide polymorphism (SNP) Tree showed that the present isolate belongs to the genus Saccharomyces, species cerevisiae. The potential genes of concern, e.g. antimycotic resestance genes, were not detected. This strain is commonly used as a feed additive for animal health improvement and the present data summarise the unambiguous identity and strain's FKS1 gene does not code for any amino acid variants of concern.

Specifications Table

Subject	Microbiology
Specific subject area	Microbial genomics
Data format	Raw reads: NCBI BioProject number PRJNA1044661 and Zenodo (https://doi.org/10.5281/zenodo.10083536) Analysed: The genome assembly was deposited in Zenodo (https://doi.org/10.5281/zenodo.10209995) and NCBI (JBCEXF000000000) AGUSTUS coding sequences results were deposited in Zenodo (https://doi.org/10.5281/zenodo.10260328).
Type of data	Raw reads and assembled data from the Saccharomyces cerevisiae CBS 493.94 genome sequencing Table Figure
Data collection	DNA extraction Whole genome sequencing via Pacific Biosciences (PacBio) Sequel, using SMRT Cell, Illumina NovaSeq 6000
Data source location	Institution: Alltech Inc. City/Town/Region: Nicholasville, Kentucky Country: USA
Data accessibility	Repository name: NCBI BioProjects database Data identification number: PRJNA1044661 Direct URL to data: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1044661 Repository name: Zenodo Data identification number: 10.5281/zenodo.10209995 Direct URL to data: https://doi.org/10.5281/zenodo.10209995
Related research article	Not applicable

1. Value of the Data

• •Live yeast cells are commonly used as probiotic feed additives in animal nutrition aimed at performance and health improvement.
• •Although S. cerevisiae is a Qualified Presumptive Safe (QPS) species in the European Union, the unambiguous strain identity and safety of each strain should be demonstrated via Next Generation Sequencing (NGS) Technologies, being required for feed additives entry in a food supply chain. The present data reports the CBS 493.94 strain identity and safety-related information.
• •The dataset reported herein could be valuable information to different research and regulatory sectors.

2. Background

S. cerevisiae is commonly used as a feed additive for animal zootechnical performance improvement [1]. This species is considered a QPS species for humans, animals, and the environment [2]. However, all strains introduced in the food chain should be analysed via NGS for their identity and safety-related traits. For this purpose, we herein report the WGS data, strain taxonomical identity, and a search for genes of concern for CBS94.93 strain, commonly used as a feed additive.

3. Data Description

The WGS of long- and short-reads were obtained via PacBio and Illumina platforms. The raw reads were deposited to the NCBI BioProjects database under identification number PRJNA1044661 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1044661). After assembly, the WGS for CBS 493.94 was composed of 32 contigs. The total length of contigs reached a value of 11,635,572 bp, the mean contig length was 363,611.62, and the N50 value was 676,443 (Table 1).

Table 1.

Assembly results for S. cerevisiae CBS 493.94.

Assembly Statistics
Total length (bp)	Number of Contigs (bp)	Mean Contig Length (bp)	Longest Contig (bp)	Shortest Contig (bp)	N50
11,635,572	32	363,612	1,471,023	2511	676,443

bp=base pairs.

Benchmarking Universal Single-Copy Orthologs (BUSCO) was used to assess the genome assembly completeness and quality of the genome [3]. Results show that more than 90 % completely match to BUSCO gene set from core universal fungal orthologs (Fig. 1) and S. cerevisiae S288C orthologs (Fig. 2).

Fig. 1.

BUSCO analysis results for S. cerevisiae CBS 493.94 against universal fungal orthologs.

Fig. 2.

BUSCO analysis results for S. cerevisiae CBS 493.94 against saccharomycetes_odb10 orthologs.

The expected genome length for the strain S. cerevisiae S288C [4] is 12,157,105, being the total length of the S. cerevisiae CBS 493.94 contigs obtained within +/− 20 % of the expected genome size (11.6 Mb).

Taxonomic strain identification was performed using a comprehensive BLAST analysis. Furthermore, the average nucleotide identity (ANI) and single nucleotide polymorphism (SNP) approaches were used to compare CBS 493.94 strain with sequences of different publicly available strains classified as S. cerevisiae spp.

Concerning the BLAST analysis, identity percentages, referred to 18S rRNA, reached 100 % in the top 5 results, shown in Table 2.

Table 2.

Identification of S. cerevisiae CBS 493.94 by 18S rRNA gene.

Description	Max score	Total score	Query cover	E value	% identity	Accession length (bp)	Accession
S. cerevisiae strain NCIM3186 chromosome XII sequence	3321	6642	1	0	100	1,078,087	CP011821.1
S. cerevisiae YJM693 chromosome XII sequence	3321	534,700	1	0	100	2,458,844	CP006458.1
S. cerevisiae YJM1433 chromosome XII sequence	3321	342,100	1	0	100	1,874,567	CP006416.1
S. cerevisiae YJM1383 chromosome XII sequence	3321	318,900	1	0	100	1,869,821	CP006402.1
S. cerevisiae YJM1355 chromosome XII sequence	3321	425,100	1	0	100	2,249,646	CP006399.1

The publicly available S. cerevisiae spp. data used for the ANI and SNP comparison is shown in Table 3.

Table 3.

Reference genomes used for identification of S. cerevisiae CBS 493.94.

Reference Genome Sequences
GCA_000146045_2_Saccharomyces_cerevisiae_S288C_strain
GCA_001051215_1_Saccharomyces_cerevisiae_strain_ySR127
GCA_003086655_1_Saccharomyces_cerevisiae_strain_BY4742
GCA_003709285_1_Saccharomyces_cerevisiae_strain_KSD
GCA_004014915_1_Saccharomyces_cerevisiae_strain_Makgeolli
GCA_004328465_1_Saccharomyces_cerevisiae_strain_ySR128
GCA_018219195_1_Saccharomyces_cerevisiae_strain_IMF17
GCA_021172205_1_Saccharomyces_cerevisiae_strain_S288C
GCA_022695735_1_Saccharomyces_cerevisiae_strain_UWOPS83
GCA_023508825_1_Saccharomyces_cerevisiae_strain_CICC
GCA_024732265_1_Saccharomyces_cerevisiae_strain_PY0001
GCA_024972935_1_Saccharomyces_cerevisiae_strain_L261col5
GCA_024972955_1_Saccharomyces_cerevisiae_strain_L261
GCA_030607045_1_Saccharomyces_cerevisiae_strain_2
GCA_903819125_2_Saccharomyces_cerevisiae_strain_HN1
GCA_903819135_2_Saccharomyces_cerevisiae_strain_Y55
GCA_903819145_2_Saccharomyces_cerevisiae_strain_BJ4
GCA_903819155_2_Saccharomyces_cerevisiae_strain_HLJ1
GCA_903819175_2_Saccharomyces_cerevisiae_strain_SX2
GCA_903819185_2_Saccharomyces_cerevisiae_strain_JXXY16
GCA_903819195_2_Saccharomyces_cerevisiae_strain_XXYS1
GCA_903819205_2_Saccharomyces_cerevisiae_strain_EM14S01
GCF_000146045_2_Saccharomyces_cerevisiae_S288C.fasta

The achieved identity percentage when the sample isolate was compared with these sequences was above 98 % (Fig. 3). As a phylogenetic tree is recommended, a SNP tree was generated. A core genome alignment percentage of 82.2 % between the Saccharomyces genome sequences was achieved, with S. cerevisiae 2-105 the taxonomically closest strain (Fig. 4). Furthermore, SNP distance matrix results are shown in Annex 1 (Zenodo repository: https://zenodo.org/records/10262057).

Fig. 3.

Average Nucleotide Identity (ANI) dendrogram of S. cerevisiae CBS 493.94.

Fig. 4.

SNP Tree for S. cerevisiae CBS 493.94 based on Core Genome Phylogeny using Harvest.

The potential presence of antimycotic resistance was assessed via the Mycotic Antifungal Resistance Database (MARDy) [5]. The former database reports that antimycotic resistance is conferred by amino acid substitutions in FKS1 gene that are present in isolates, demonstrating the corresponding MIC breakpoint for arborcandin C and caspofungin (according to the CLSI Subcommittee for Antifungal Testing). These amino acid substitutions were not found in the genome assembly. AGUSTUS coding sequences results are available in Annex 2 and Annex 3, deposited at Zenodo repository (https://doi.org/10.5281/zenodo.10260328).

4. Experimental Design, Materials and Methods

4.1. DNA extraction

A freeze-dried pure culture was obtained from the CBS culture collection Westerdijk Fungal Biodiversity Institute (Utrecht,The Netherlands), grown in liquid nutrient media for 48 h at 30 °C, and the DNA was extracted. Methodology details relating to the strain growth and DNA extraction are covered by the intellectual property rights of Baseclear B.V (Leiden, The Netherlands). In brief, a fresh CBS 493.94 cell suspension was used for the DNA extraction using the Quick-DNA Fungal/Bacterial Miniprep kit (Zymo Research, USA) according to manufacturer's instructions; and the lysis was performed in combination with zymolyase (Zymo Research, USA; 5 units/μl final concentration).

4.2. Sequencing strategy, quality control and assembly

DNA from S. cerevisiae CBS 493.94 was used to create a 10-kb single-plex sequencing library sequenced on a SMRT Cell on the PacBio Sequel instrument that generated 7 Gb sequenced bases and 860,922 number of reads. For shot-reads Nextera XT sequencing library (Illumina) was used on the NovaSeq 6000 instrument that generated 4.96 Gb sequenced bases and 16,822,463 number of reads of paired-end 150 nucleotides.

Raw paired end reads were trimmed and processed using BBDuk, version 39.01 (BBMap – Bushnell B. – sourceforge.net/projects/bbmap/) with a read quality trimming parameter of 22. The parameters used were minlen=36, qtrim=rl, and trimq=22. The parameter “qtrim=rl” allows trimming on both ends of the reads; “minlen” establishes reads shorter than after trimmings were discarded; and regions with average quality below “trimq” value were trimmed. 94.37 % of reads were retained after trimming. PacBio CLR reads do not have a PHRED score associated. Illumina reads were used for post assembly polishing of PacBio long reads assembly to correct for errors in long reads assembly.

De novo assembly was performed with Flye 2.9.1-b1780, and the parameters used were “flye –pacbio-raw $fastq -o flye_out –threads 32″. Pilon [6], version 1.24 with default parameters, was the tool used to correct errors from PacBio assembly. Assembly statistics were checked using assemblystats.

BUSCO v5.4.4 was run with default parameters by running the genome assembly against: (1) the core universal fungal orthologs, and (2) against saccharomycetes_odb10 ortholog sets.

4.3. Taxonomical identification

Barrnap version 0.9 And Web Blastn for 18S rRNA were used for gene extraction and sequence identification, respectively. To ensure the accuracy of this prediction and verify its identity, the extracted sequence was subjected to a comprehensive BLAST analysis. BLAST nucleotide database with default parameters was used to perform the analysis against known S. cerevisiae 18S rRNA sequences.

Furthermore, an average nucleotide identity (ANI) approach using MUMmer 3.0 and dRep version 3.4.2 with default parameters was performed [7]. Comparative measurements between two genome sequences, called Overall Genome Relatedness Indices (OGRI), were developed, and proposed to provide a cut-off or define boundaries between species [8]. Among them, average nucleotide identity (ANI) is the most widely used, with a proposed species boundary cut-off of 95–96 % [9].

The isolate was assessed and compared with different whole sequences of strains classified as S. cerevisiae spp. publicly available sequences in NCBI [2]. Data from comparison sequences is shown in Table 3. The achieved identity percentage when the sample isolate was compared with these sequences was all above 98 % (Fig. 3).

The phylogenetic tree is recommended, particularly for taxa with a high identity level between related species [10]. An SNP tree was also made based on core genome phylogeny using Harvest (parsnp-1.7.4) with default parameters [11].

4.4. Identification of genes of potential concern

MARDy VERSION 1.1DB:1.3WS (BETA) was used to identify antimycotic resistance genes. Genes prediction of the identified coding sequences was performed using AUGUSTUS [12] (Model: S. cerevisiae), version 3.3.3, with default parameters.

Limitations

Not applicable.

Ethics Statement

The authors have read and follow the ethical requirements for publication in Data in Brief and confirming that the current work does not involve human subjects, animal experiments, or any data collected from social media platforms.

CRediT Author Statement

Ivana Nikodinoska: Conceptualisation, Writing - Original Draft, Data Curation Colm Moran: Conceptualisation, Writing - Review & Editing, Funding, Project administration.

Data Availability

• Saccharomyces cerevisiae strain CBS 493.94, whole genome shotgun sequencing project (Original data) (NCBI Bioproject Genbank).

• Whole genome sequencing data for Saccharomyces cerevisiae CBS 493.94 (Original data) (Zenodo).