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

Autor: Volkmar Passoth, Ievgeniia A. Tiukova, Jacques Dainat, Mats E. Pettersson, Max Käller, Remi Andre Olsen, Marc P. Hoeppner, Jonas Söderberg, Jens Nielsen, Henrik Lantz
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Gene Dosage
Yeast and Fungal Models
Genome
Contig Mapping
Genome Size
Copy-number variation
Phylogeny
Genetics
0303 health sciences
Multidisciplinary
Organic Compounds
Eukaryota
Genomics
Genome project
Mitochondria
Chemistry
Experimental Organism Systems
Physical Sciences
Saccharomyces Cerevisiae
Medicine
Chromosomes
Fungal
Ploidy
Research Article
Nuclear gene
Science
Brettanomyces
Biology
Research and Analysis Methods
Gene dosage
Evolution
Molecular
Saccharomyces
03 medical and health sciences
Model Organisms
Genetik
Genome size
Gene
030304 developmental biology
Ethanol
Whole Genome Sequencing
030306 microbiology
Organic Chemistry
Organisms
Fungi
Chemical Compounds
Gene Amplification
Biology and Life Sciences
Computational Biology
Genetic Variation
Molecular Sequence Annotation
Comparative Genomics
Genome Analysis
Genomic Libraries
Genome Annotation
Yeast
Alcohols
Animal Studies
Zdroj: PLoS ONE, Vol 14, Iss 5, p e0215077 (2019)
PLoS ONE
Popis: 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.
Databáze: OpenAIRE
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