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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(3): 328-331

https://doi.org/10.48022/mbl.2307.07002

Received: July 12, 2023; Revised: September 20, 2023; Accepted: September 21, 2023

Draft Genome Sequence of the Neodothiora populina-Like Yeast Strain JAF-11, Which Produces the Biosurfactant myo-Inositol Lipids

Jeong-Seon Kim1†, Parthiban Subramanian2†, Seunghwan Kim1, Jun Heo1, Bong-Sik Yun3, and Yiseul Kim1*

1Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
2National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
3Department of Biotechnology, College of Environmental and Bioresource Sciences, Jeonbuk National University, Wanju 54596, Republic of Korea

Correspondence to :
Yiseul Kim,        dew@korea.kr

†These authors contributed equally to this work and are listed alphabetically.

Abstract

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Genomic information of biotechnologically and industrially important microorganisms provides the basis for understanding their metabolic potential. Here, we report the draft genome sequence of the Neodothiora populina-like yeast strain JAF-11 capable of producing biosurfactant myo-inositol lipids. The draft genome contained genes associated with secondary metabolite biosynthesis, including transport and metabolism of lipids, which are a major component of fungal surfactants. Identification of myo-inositol and acyl chain synthesis genes in the draft genome corresponded to the specific biosurfactant produced by strain JAF-11. Further experimental studies could help to elucidate the genes responsible for the production of biosurfactant by strain JAF-11.

Keywords: Yeast, Neodothiora, biosurfactant, genome

Body

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With the growing interest in the development of microbial surfactants, strain JAF-11 was isolated and screened for its biosurfactant producing ability [1]. Initial analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region of strain JAF-11 exhibited similarities less than the thresholds, representing a novel yeast species most closely related to Neodothiora populina CPC 39399T in the family Dothioraceae. This strain JAF-11 was shown to produce a novel biosurfactant of myo-inositol lipid type, which is known as a common and essential polyol found in yeast cells. This compound has a similar chemical structure to a previously reported yeast-derived surfactant, pullusurfactan E [2]. In order to gain a better understanding of the biosurfactant-producing yeast, strain JAF-11 was subject to genome sequencing. Here, we report the genomic information of the Neodothiora populina-like yeast strain JAF-11, isolated from flower of Prunus mume Sieb. et Zucc. in the Republic of Korea.

The genome of strain JAF-11 was sequenced using a combination of Oxford Nanopore MinION (Oxford Nanopore Technologies, UK) and Illumina HiSeq X-ten (Illumina, USA) platforms by Seeders Inc. (Republic of Korea). De novo genome assembly based on high-quality reads of Nanopore and Illumina data was constructed using HASLR 0.8a1 [3]. Unless otherwise specified, all further analyses were carried out on the Galaxy Web server (https://usegalaxy.org). Completeness assessment of genome assembly was examined using BUSCO 4.1.4 [4]. Repetitive elements were investigated using Repeat-Masker 4.1.5 followed by gene prediction using AUGUSTUS 3.4.0 with Neurospora crassa as a model for training [5]. Subsequently, the functional annotation of the data from AUGUSTUS was carried out using eggNOG-mapper 2 [6]. During mapping, the query genome was screened for Clusters of Orthologous Genes (COGs), Gene Ontology (GO terms), Carbohydrate-Active enZYmes (CAZy), and Pfam. The genome was also queried at the main pathway databases, including KEGG and PANTHER using KOBAS 2.0 to study functional metabolism genes [7]. Secondary metabolite production by strain JAF-11 was analyzed using fungal version of antiSMASH 6.1.1 (https://fungismash.secondarymetabolites.org/#!/start). The genome of strain JAF-11 has been deposited in GenBank with the accession number of JASVWA000000000.

The genome assembly was 27.2 Mbp in size with 14 scaffolds, N50 value of 2.2 Mbp, and a GC content of 50.8%. The largest scaffold was 2.61 Mbp and the shortest was 0.53 Mbp long. Completeness of the genome assembly was 94.3%, showing the following profile C:94.3% [S: 94.0%, D: 0.3%], F: 1.9%, M: 3.8%, n: 3786 when dothideomycetes_odb10 dataset was used as reference. Analysis of repetitive elements exhibited very few repeat elements in the genome (0.72%). Gene prediction using AUGUSTUS indicated the presence of 10,883 genes, of which 7,398 were selected by eggNOG-mapper for scanning. For quality assessment of gene prediction, annotations of strain JAF-11 based on AUGUSTUS and Maker were compared using the genome annotation statistics tool available at the Galaxy server [8]. A comparison of the annotations using the different tools are provided in Table 1.

Table 1 . Comparison of gene prediction using the different programs.

AttributeAUGUSTUS 3.4.0Maker 2.31.11
Number of genes predicted10,8838,997
Number of transcripts predicted10,8838,997
Mean gene locus size (first to last exon)1,752.71708.6
Mean exon size304.6507.6
Mean number of distinct exons per gene3.022.8
Number of distinct exons32,90625,263
Number of single-exon genes2,252 (20.7%)2,196 (24.4%)
Number of multi-exon genes8,330 (76.5%)6,801 (75.6%)
Number of selected queries by EggNOG-mapper7,398 (68%)7,708 (85%)
Pfam hits*6,6746,946
Pfam domains10,48410,830
GO hits*3,6183,774
EC hits*1,8131,855
CAZy hits*141149

*Number of predicted genes containing at least one Pfam domain, one GO term, one enzyme, and one CAZy hit.

Functional annotation revealed about 24% of genes (1,762 genes) having unknown function. Genes with known functions were mainly associated with secondary metabolites biosynthesis, including transport and catabolism (369 genes), translation, ribosomal structure, and biogenesis (336 genes), signal transduction mechanisms (250 genes), and lipid transport and metabolism (236 genes) (Fig. 1). Lipids are known as a major component of fungal surfactants [9] and observation of a large number of genes belonging to the COG category of lipid transport and metabolism is in line with the biosurfactant producing ability of strain JAF-11. KEGG analysis showed presence of metabolic pathways of inositol phosphate as well as sphingolipid. We found five contigs with high similarity to genes coding for inositol monophosphatase family proteins, which convert 1D-myo-inositol 3-phosphate to myo-inositol. In addition, a contig was found exhibiting high similarity to genes coding for Saccharomyces cerevisiae inositol phospholipid synthesis and fat storage-inducing transmembrane protein Scs3p [10].

Figure 1.Functional COG classification of the genome of the Neodothiora populina-like yeast strain JAF-11.

Furthermore, Pfam search led to identification of 22 Glycosyl transferase family genes, which help in elongation of complex oligosaccharides and putative acyltransferase family genes. Three of these acyltransferases also showed similarity to ketoacyl-synt domain of β-ketoacyl synthases, previously reported to be involved in fatty acid synthesis [11]. Identification of three acyl chains in the structure of the biosurfactant molecule [1] and our observation of these acyltransferases could be hypothesized to have played a role in formation of the acyl moieties. Investigation of the effect of acyltransferases activity on the incorporation of the acyl moieties may yield further insights into their metabolic potential.

Lastly, although there is currently no threshold of average nucleotide identity (ANI) used for yeast species demarcation, calculation of ANI was performed between strain JAF-11 and Delphinella strobiligena CBS 735.71T (78.0%), which is the only genome available from the phylogenetic tree [1] and from the family Dothioraceae. Beside the phylogenetic assessment, additional analysis including phenotypic characterization could help provide genomic insights for accurate species identification.

Acknowledgment

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This study (Project No. 015675) was carried out with the support of National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea.

References

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