Draft genome sequence data of the starch-utilizing yeast Saccharomycopsis fibuligera MBY1320 isolated from Nuruk.

Saccharomycopsis fibuligera MBY1320 was isolated from Nuruk, a traditional Korean starter for makgeolli (rice wine) production. This isolate has previously been reported to exhibit thermotolerance and starch-degrading activities. In this data description, we present the draft genome sequence of S. fibuligera MBY1320. The genome contained 19,138,941 bp in 16 contigs, and the internal transcribed spacer region of S. fibuligera MBY1320 rRNA gene showed the highest similarity with that of S. fibuligera NRRL Y-2388. The BioProject sequence has been deposited at DDBJ/EMBL/GenBank and Mendeley database. The GenBank accession numbers are PRJNA598085 for the BioProject data, SAMN13698230 for the BioSample data, and GCA_012062855 for the GenBank data.

Specifications Table

Value of the Data

The draft genome of S. fibuligera MBY1320, isolated from Nuruk, will facilitate the analysis of the strain genetic information. Thus, this data could improve our understanding of starch-utilizing yeast.

Data from the S. fibuligera MBY1320 strain will be useful for further study of starch metabolism in yeast.

Data on the genome sequence of MBY1320 could be used to search and characterize biotechnologically-relevant enzymes and gene clusters in the future.

Data Description

The starch-degrading yeast S. fibuligera is used in food fermentation and uses rice and cassava [1] as substrates. S. fibuligera produces both α-amylase and glucoamylase for starch-degradation [2,5]. Glucoamylase is also an essential enzyme in the food and fermentation industries. The S. fibuligera MBY1320 strain was isolated from Nuruk, a traditional Korean rice wine fermentation starter, showed high glucoamylase activity and thermotolerance [3].

Fig. 1 shows a phylogenetic tree comparing the internal transcribed spacer(ITS) region for S. fibuligera MBY1320 and other yeasts. The ITS of S. fibuligera MBY1320 (GenBank accession number MT944985) showed the highest similarity with that of S. fibuligera NRRL Y-2388.

Fig. 1

Phylogenetic tree showing the Saccharomycopsis fibuligera ITS region compared with that of other yeasts. The tree was constructed using the neighbor-joining method. The numbers on the nodes correspond to the percentages, with which clusters appeared during the 1000 pseudoreplicate bootstrap tests. The bars denote the relative branch lengths. The ITS region was identified by GenBank accession numbers (shown in parentheses).

Table 1 summarizes the main features for the draft genome sequence of S. fibuligera MBY1320. The assembled draft genome contained 19,138,941 bp distributed across 16 contigs, with a GC content of 38.2%. The longest contig had a length of 3974,907 bp, while the N50 contig was 2645,300 bp long. MAKER [4] predicted 2844 protein-coding genes that contained 524 hypothetical protein candidates. The predicted genes were annotated at 97% based on BLASTp similarity searches against an nr database selection. The data includes auxotrophic markers, such as the phosphoribosyl anthranilate isomerase gene (TRP1) [6] as well as the β-isopropyl malate dehydrogenase gene (LEU2) [7]. The data can be used to construct a host-vector tool for establishing an auxotrophic transformation system using the S. fibuligera MBY1320 strain. This draft genome sequence of S. fibuligera MBY1320 represents a new genomic information source that can provide valuable information for starch-related applications.

Table 1

Features of the draft genome of S. fibuligera MBY1320.

Attribute	S. fibuligera MBY1320
	Value
Total length (bp)	19,138,941
Number of contigs	16
N50	2645,300
Number of predicted genes	2844
GC content (%)	38.2

Experimental Design, Materials and Methods

Strain S. fibuligera MBY1320 was isolated from Nuruk, and was grown in YEPD liquid medium for 24 h at 30 °C. According to the manufacturer's instructions, genetic DNA was extracted using G-DEXTMIIc Genomic DNA Extraction Kit (iNtRON, Korea).

Sequences obtained by BLAST searching against the GenBank database were manually aligned with the ITS sequence of S. fibuligera MBY1320 using CLUSTAL_W. The phylogenetic tree was constructed with the neighbor-joining method in MEGA7.0.26.

The genome of S. fibuligera MBY1320 was sequenced using PacBio RSII (Pacific Biosciences, USA). The reads were assembled de novo into 16 contigs using HGAP2. The open reading frames were predicted using MAKER(http://www.yandell-lab.org/software/maker) [4] and subsequently annotated by SNAP(http://korflab.ucdavis.edu/software). Search of putative genes were conducted with BLASTP in NR database.

Ethics Statement

Not applicable.

CRediT Author Statement

Eun-Hee Park: Writing – Original draft; Writing – Revier & Edting; Visualization; Data curation; Myoung-Dong Kim: Concptualization, Supervision, Funding acquisition.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this article.

Subject	Biology
Specific subject area	Microbiology, Genomics, Biotechnology
Type of data	Table
How data were acquired	The draft genome sequence was determined using a Pac-Bio RSII instrument
Data format	Raw, analyzed and deposited
Parameters for data collection	Isolation of S. fibuligera MBY1320 from Nuruk, a traditional Korean starter for makgeolli (rice wine) fermentation. Genomic DNA extraction and sequencing procedures were used.
Description of data collection	Genomic DNA was isolated from a pure culture of the S. fibuligera MBY1320 strain
Data source location	Institution: Kangwon National UniversityCity/Town/Region: Chuncheon, Kangwon-do, Republic of KoreaLatitude and longitude: 37°87′ N, 127°74′ E.
Data accessibility	The draft genome sequence of S. fibuligera MBY1320 is available at DDBJ/EMBL/GenBank under the accession no. GCA_012062855. The BioSample, BioProject, and assembly/WGS accession numbers are SAMN13698230, PRJNA598085(https://www.ncbi.nlm.nih.gov/bioproject/PRJNA598085), and WXEZ01, respectively.All sequence files can be accessed at Mendeley Data (https://data.mendeley.com/datasets/vmr97×5mr7).
Related research article	D. H. Choi, E. H. Park, M. D. Kim, Characterization of starch-utilizing yeast Saccharomycopsis fibuligera isolated from nuruk, Microbiol. Biotechnol. Lett. 42(2014), 407–412. DOI: 10.4014/kjmb.1409.09006 [3].