Draft Genome Sequence of Metschnikowia australis Strain UFMG-CM-Y6158, an Extremophile Marine Yeast Endemic to Antarctica

ABSTRACT

Here we report the draft genome sequence of Metschnikowia australis strain UFMG-CM-Y6158, a yeast endemic to Antarctica. We isolated the strain from the marine seaweed Acrosiphonia arcta (Chlorophyta). The genome is 14.3 Mb long and contains 4,442 predicted protein-coding genes.

GENOME ANNOUNCEMENT

The genus Metschnikowia comprises a clade consisting of approximately 81 species. The sexual life cycles of the members of this clade involve the formation of elongated asci containing two, often needle-shaped, spores (1). M. australis is a species endemic to Antarctica, and has been isolated from seawater, marine invertebrates, sponges, and macroalgae (2–6). Owing to the extremely cold environment of Antarctica, M. australis may have unique metabolic traits enabling it to survive under such stressful conditions; exploring these can help identify potential antifreeze compounds for biotechnological use.

We isolated M. australis strain UFMG-CM-Y6158 from a marine macroalgae, Acrosiphonia arcta (Chlorophyta), collected in Admiralty Bay of King George Island in Keller Peninsula, Antarctica (5). We cultivated the strain on marine agar (Himedia, India) at 10°C for 15 days, and the genomic DNA was isolated by phenol:chloroform (1:1) extraction. We assessed DNA quality by gel electrophoresis and determined its purity and quantity using both the NanoDrop 1000 UV-Vis spectrophotometer and the Qubit version 2.0 fluorometer with the Qubit dsDNA HS assay kit (Thermo Fisher Scientific). We used the Nextera XT DNA kit (Illumina) to construct paired-end libraries and assessed their quality using Bioanalyzer HS Assay (Agilent Technologies). Generated fragments with a mean length of 1,167 bp were sequenced using the Illumina MiSeq sequencer, whereas those with a mean length of 550 bp were sequenced using the Illumina HiSeq 2500 sequencer. The former generated 1,585,122 reads (2 × 301) with 35× coverage, while the latter generated 103,312,458 reads (2 × 101) with 745× coverage. We assembled the genome using SPAdes version 3.9.1 (7). The assembled draft genome consisted of 14,356,710 bp over 160 contigs (>505 bp) with a G+C content of 47.2%. The longest contig was 1,116,518 bp long, and the N₅₀ contig length was 542,232 bp. CEGMA (8) analysis showed that the assembly was 95.9% complete, whereas analysis with BUSCO version 2 (9) using the Saccharomycetales lineage data set indicated 90.2% completeness based on the presence of conserved orthologous genes among species of the genus. We identified 4,442 protein-coding genes using MAKER2 (10). A sequence similarity search using the BLASTx tool in BLAST version 2.2.31+ (11) returned 4,348 protein matches (97.8%), with e-value ≤1e⁻⁶, against NCBI’s nonredundant database. We identified 249 tRNAs using tRNAscan-SE (12).

Using the OrthoVenn web platform (13), we compared M. australis protein-coding genes with those of two previously sequenced Metschnikowia genomes—M. fructicola and M. bicuspidata. The analysis showed that M. australis has a much shorter predicted proteome than that of M. fructicola (5,851 protein-coding genes) and M. bicuspidata (6,028 protein-coding genes). Additionally, we found six exclusive clusters of paralogous genes, of which four did not match any protein in the NCBI and UniProt-Swissprot databases. These results highlight the importance of investigating yeast endemic to Antarctica, such as M. australis, not only to identify novel genes associated with adaptation to extreme environments, but also for potential application in biotechnology.

Accession number(s).

Data related to this whole-genome shotgun project have been deposited at DDBJ/ENA/GenBank under the accession number MVNQ00000000. The version described in this paper is the first version, MVNQ01000000.