High-Quality Draft Genome Sequence and Annotation of the Basidiomycete Yeast Sporisorium graminicola CBS10092, a Producer of Mannosylerythritol Lipids

The basidiomycete Sporisorium graminicola (formally Pseudozyma graminicola) strain CBS10092 was originally isolated from an herbaceous plant in Russia. It is a known producer of mannosylerythritol lipids (MELs), the main component being MEL-C. Here, we present the 19.9-Mb draft genome sequence, which comprises 6,602 genes, including those encoding the MEL biosynthetic pathway.

ABSTRACT

The basidiomycete Sporisorium graminicola (formally Pseudozyma graminicola) strain CBS10092 was originally isolated from an herbaceous plant in Russia. It is a known producer of mannosylerythritol lipids (MELs), the main component being MEL-C. Here, we present the 19.9-Mb draft genome sequence, which comprises 6,602 genes, including those encoding the MEL biosynthetic pathway.

ANNOUNCEMENT

Sporisorium graminicola is a basidiomycete belonging to the Ustilaginomycetes (1). Members of this group, which includes the plant pathogen Ustilago maydis, produce a range of secondary metabolites with a wide range of potential industrial applications (2). Among these, biosurfactants are attracting particular attention as “green” alternatives to current commercial products (3–5). The principal biosurfactants produced by the Ustilaginomycetes group are the mannosylerythritol lipids (MELs), and S. graminicola has been reported to primarily produce MEL-C (6). Therefore, this strain has a potential application in the industrial production of MELs. However, little is known about this particular species. Here, we report the draft genome sequence of S. graminicola strain CBS10092, which was originally isolated from Plenum pratense in the Moscow region of Russia (1).

S. graminicola CBS10092 was grown in yeast extract peptone sucrose light (YEPSL) medium (7) for 48 h at 30°C in an orbital incubator (120 rpm). The harvested cells were homogenized using liquid nitrogen, and DNA was extracted by implementing the cetyltrimethylammonium bromide (CTAB) chloroform-isoamyl alcohol protocol (8). Genome sequencing was performed using the PacBio Sequel platform to generate 50× coverage with a total of 293,670 reads, which had an average read length of 13,690 bp. De novo assembly was performed with Hierarchical Genome Assembly Process (HGAP) version 3.2 (9), and contigs were ordered relative to the U. maydis genome as a reference using Mauve version 2.4.0 (10). This resulted in a chromosome-level genome assembly of 19.57 Mb, distributed in 22 contigs. The longest contig, at 2.35 Mb, was chromosome length. The assembly N₅₀ value was 823,447 bp with a GC content of 56.75%.

Cells for RNA extraction were grown in a 5-liter fermenter containing 1 liter of medium (11) supplemented with 20 g/liter of glucose and enriched with fatty acid at a feed rate of 0.67 g/liter/h from 24 to 120 h. Cells were harvested by centrifugation and washed twice with phosphate-buffered saline (PBS). RNA was extracted using the RNeasy midi kit (Qiagen, Hilden, Germany) according to the manufacture’s protocol. To aid gene calling, strand-specific transcriptome sequencing (RNA-Seq) libraries were made from total RNA, using NEBNext poly(A) selection and Ultra directional RNA library preparation kits (New England BioLabs, Ipswich, MA, USA), and sequenced using the Illumina HiSeq 4000 platform. Illumina adapter sequences were removed from the FastQ files using Cutadapt version 1.2.1 (12). These were then trimmed using Sickle version 1.200 (13) with a minimum window score of 20. The Braker2 pipeline (14) was used to call genes and found a total of 7,190 transcripts, assigned to 6,602 genes.

Using the available annotation of U. maydis (15) and other related fungi (16–18), we annotated the S. graminicola genome and identified the MEL biosynthetic gene cluster. The in silico translation of the five genes from this cluster, mac2, emt1, mac1, mmf1, and mat1, shared 65%, 80.45%, 67.79%, 73.76%, and 56% identity, respectively, to the corresponding genes in U. maydis, and 76.64%, 56.49%, 61.96%, 74.28%, and 51.13% identity, respectively, to the corresponding genes in Moesziomyces aphidis DSM 70725. The S. graminicola sequence and annotation will aid in the utilization of this strain for future industrial exploitation.

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number SRRM00000000. The version described in this paper is the first version, SRRM01000000 (as 22 contigs). All sequence data for RNA-Seq experiments used for annotation purposes have been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (accession numbers SRR8919640 to SRR8919655). The raw reads for the PacBio sequencing can be found under the accession number SRR9845579.