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 |
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| 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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