Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis

PLoS One. 2019 May 1;14(5):e0215077. doi: 10.1371/journal.pone.0215077. eCollection 2019.

Abstract

Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Brettanomyces / genetics
  • Brettanomyces / metabolism*
  • Chromosomes, Fungal / genetics*
  • Contig Mapping
  • Ethanol / metabolism*
  • Evolution, Molecular
  • Gene Dosage
  • Genetic Variation
  • Genome Size
  • Mitochondria / genetics*
  • Molecular Sequence Annotation
  • Phylogeny
  • Whole Genome Sequencing / methods

Substances

  • Ethanol

Grant support

This work received funding from FORMAS (Mobility starting grant #2016-00767) to IAT and from Swedish Energy Authority (#34134-1) to VP. This project was supported by the Swedish University of Agricultural Sciences (MicroDrive-program). There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.