- Brettanomyces ( Dekkera ) species. - Background: Yeasts of the genus Brettanomyces are of significant interest, both for their capacity to spoil, as well as their potential to positively contribute to different industrial fermentations. - However, considerable variance exists in the depth of research and knowledgebase of the five currently known species of Brettanomyces. - Results: Strains for each of the five widely accepted species of Brettanomyces (Brettanomyces anomalus, B.. - 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - Three differ- ent phylogenies were originally presented based on analyses of the 18S or 26S ribosomal RNA sequences, which showed conflicting placement of B. - are most commonly associated with spoilage in beer, wine, and soft drink due to the production of many off-flavour metabolites including acetic acid, and vinyl- and ethyl-phenols . - anomalus, are the main species encountered during wine and beer fer- mentation and has led to the majority of Brettanomyces research focusing only on these two species. - The initial assembly of the triploid B. - New genome assemblies for the Brettanomyces genus Information regarding the species and strains used in this study is listed in Table 1. - naardenensis assembly was 11.16 Mb, highly similar to the only other published assembly [37]. - The overall contiguity of the assemblies varies due to differences in heterozygosity and sequencing read lengths.. - This resulted in the lowest contiguity in the study consisting of 48 contigs for the haploid assembly with an N 50 of 640 kb. - Predicted genome completeness was high for the haploid assemblies, with between 3.8% (B. - Duplication was low for not only the homozygous strains but also for the heterozy- gous B. - Given the heterozygous nature of the B. - anomalus genome, a diploid assembly was also generated for the strain AWRI953. - The resultant diploid assembly was ap- proximately twice the size of the haploid assembly and had a slightly improved N 50 of 730 kb. - While the gen- ome size doubled, duplicated BGs only increased from 1.2% for the haploid assembly to 35.9% for the diploid assembly. - The low number of duplicated BGs was found to mainly be the result of a number of fragmented gene models being present in one of the two haplomes. - As a point of comparison, this phylogenetic methodology was also performed on the members of the Saccharomyces genus (Fig. - When compared to the distances between the mem- bers of the genus Saccharomyces, there is a much larger genetic distance separating the various Brettanomyces species. - Indeed, there is a greater genetic distance be- tween most of the Brettanomyces species than there is between any of the individual Saccharomyces species and the outgroup used for that phylogeny (Naumovozyma castellii). - Table 2 Assembly and BUSCO summary statistics for the haploid assemblies B. - The two phylogenies are transformed to the same scale (substitutions per site). - For comparison, pairwise ANIs calculated between each of the Saccharomyces species and the outgroup (N.. - bruxellensis and the B. - bruxellensis to the more distantly related species B. - anomalus genome analyzed in this study, the genome was exam- ined for the presence of large LOH tracts. - Three large contigs, comprising 2.14 Mb (15%) of the B. - genome, were predicted to be homozygous (0.0353 SNPs/kb) while the rest of the genome is heterozygous (3.21 SNPs/kb) (Figure S3). - Given the apparent adaptation of Brettanomyces to the fermentative environment, each Brettanomyces genome was investigated for the presence of specific gene family expansions (Table 5). - PIPOX exhibits broad substrate specificity, but primarily catalyzes the breakdown of sarcosine to glycine and formaldehyde, in addition to the oxidation of L-pipecolate [39]. - Alignments are coloured according to the reference assembly contigs and are layered by alignment length. - activity, associated with the utilization of alter- native sulphur sources, and an expansion of acetylor- nithine deacetylase (EC a component of the arginine biosynthetic pathway.. - Potential HGT events that may have contributed to the evolution of Brettanomyces were investigated. - for the breakdown of sucrose into fructose and glucose monomers and is required for the utilization of sucrose as a carbon source.. - To further confirm the bacterial origins of the Bretta- nomyces invertases, a protein-based phylogeny was cre- ated from the highest scoring eukaryote and prokaryote blast hits from the RefSeq non-redundant database, as well as from these three Brettanomyces invertases (Fig. - Consistent with a bacterial- derived HGT event, the Brettanomyces invertase pro- teins reside within one of the two prokaryote clades and are evolutionarily distinct from the eukaryote groups.. - To confirm the placement of the Brettanomyces invertases in the prokaryotic clade, three alternate topologies (within either of the eukaryote clades, as well as within the second prokaryote clade). - These constrained topologies were all significantly less likely compared to the unconstrained tree (Figure S4, Table S3).. - The genomic context of the invertases present in B.. - Likewise, homologues of the MPH3 and TIP1 genes that are present across all the Brettanomyces species, are only found in this specific sub-telomeric region in B. - New genome assemblies for the five Brettanomyces spe- cies are described, which generally exhibit significant im- provements over previous assemblies produced for this genus. - To the best of our knowledge, this makes the B. - When compar- ing the assemblies of the other species to the next most contiguous assembly available from other Brettanomyces sequencing studies, the B. - naardenensis and 6.5-fold improvement over GCA contigs). - The high-quality genome sequences allowed for the calculation of a Brettanomyces whole-genome phylogeny.. - The topology of the whole-genome phylogeny generally agreed with those derived from rRNA sequences in the placement of B. - While ANI values alone are generally insufficient for determining genus boundaries (at least in prokary- otes) [43], the extremely low ANIs that have been ob- served across the Brettanomyces genus merits further consideration into the taxonomy of this group and whether it may be appropriate for the Brettanomyces genus to be refined.. - bruxellensis exhib- ited expansions of families of glucosidases and galactosi- dases that are responsible for the utilization of sugars from complex polysaccharides. - These types of expan- sions are a hallmark of the domestication of beer and wine strains of S. - The ability of Brettanomyces to grow in nutrient- depleted conditions has largely been attributed to the utilization of alternative nitrogen sources such as free nitrates and amino acids [49–51]. - Proline, a substrate of PIPOX, is one of the more common amino acids in fer- mented wine and beer. - Horizontal Gene Transfer (HGT) has been reported as a mechanism of adaptative evolution in fungal species and to have contributed to the domestication of S. - Sucrose utilization likely con- ferred a significant advantage in fruit fermentations, helping to shape the evolution of the common ancestor of B. - Numerous indicators of domestication and adaptation in Brettanomyces were identified with some notable parallels to the evolution of Saccharomy- ces. - Structural differences between the genomes of the Brettanomyces species and apparent loss of heterozygos- ity in B. - For the remaining species, libraries were prepared using the SQK- LSK108 kit following the protocol GDE_9002_v108_revT_. - Illumina sequencing was performed on each strain using a combination of short-insert (TruSeq PCR-free) and mate-pair (2-5 kb insert and 6–10 kb insert) librar- ies. - The Nanopore reads were mapped to the assemblies using minimap2 [67] and ini- tial base-call polishing was performed with Nanopolish v utilizing the FAST5 signal-level sequencing data. - Further base-call polishing was performed with Illumina paired-end, and 2–4 kb and 6–10 kb mate-pair reads. - Finally, raw Nanopore reads were mapped to the base-call-polished assemblies and Purge Haplotigs v1.0.1 [38] was used to remove any duplicate or artefactual contigs.. - Paired-end reads were mapped to the haploid assembly with BWA-MEM, and high-confidence SNPs were called using VarScan v2.3.9 [72]. - Nanopore reads were mapped to the assembly using BWA-MEM.. - anomalus haplotypes were then inde- pendently reassembled from the haplotype-binned nano- pore reads using the method described for the other species.. - All other Brettanomyces assemblies were aligned to the B. - Phylogenies were created using the same method for the Saccharomyces species + N. - Genome windows (20 kb windows, 10 kb steps) were generated for the assemblies and a custom script was used to pair syntenic genome windows based on the NUCmer alignments. - The ratio of the gene-count to the average gene-count was calculated for the Brettano- myces species over all OrthoFinder orthogroups. - HGT events were predicted for the Brettanomyces spe- cies. - Protein sequences for the assemblies were used in BLAST-P searches against the RefSeqKB non-redundant Fungi and Bacteria datasets [88], the Alien Index was calculated as described in [89]. - The multiple sequence alignments and trees were retrieved for the HGT candidates’ orthogroups and several candidates were removed following manual in- spection. - orthogroup duplicity for the Brettanomyces genomes, Table S3:. - Brettanomyces species in OrthoFinder. - Rooted, unscaled coalescence-based phy- logenies were calculated from individual gene trees of all single copy orthologs for the Brettanomyces genus + Ogataea polymorpha (a), and for the Saccharomyces genus + Naumovozyma castellii (b).. - Brettanomyces invertases constrained to: the closest eukaryote invertase clade (b), the more distant eukaryote invertase clade (c), and the eukaryote invertases within the alternate prokaryote clade (d). - BUSCO: The name of the pipeline for detecting Benchmarking universal single-copy orthologs. - The AWRI, a member of the Wine Innovation Cluster in Adelaide, is supported by Australia ’ s grapegrowers and winemakers through their investment body Wine Australia with matching funds from the Australian Government. - The funding body played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.. - Parallel evolution of the make – accumulate – consume strategy in Saccharomyces and Dekkera yeasts. - The phylogenetic relationships of species of the genus Dekkera van der Walt based on the partial sequences of 18S and 26S ribosomal RNAs (Saccharomycetaceae). - Oxygen-limited cellobiose fermentation and the characterization of the cellobiase of an industrial Dekkera/Brettanomyces bruxellensis strain. - De-novo assembly and analysis of the heterozygous triploid genome of the wine spoilage yeast Dekkera bruxellensis AWRI1499. - Development of microsatellite markers for the rapid and reliable genotyping of Brettanomyces bruxellensis at strain level. - High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing. - Characterization of the recombinant Brettanomyces anomalus β -glucosidase and its potential for bioflavouring. - Complex nature of the genome in a wine spoilage yeast, Dekkera bruxellensis. - nov., the teleomorph of Brettanomyces anomalus, recovered from spoiled soft drinks. - Phylogeny of the yeast genera Hanseniaspora (anamorph Kloeckera), Dekkera (anamorph Brettanomyces), and Eeniella as inferred from partial 26S ribosomal DNA nucleotide sequences. - Assembly and analysis of the genome sequence of the yeast Brettanomyces naardenensis CBS 7540. - A proposed genus boundary for the prokaryotes based on genomic insights. - Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. - Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. - On the catabolism of amino acids in the yeast Dekkera bruxellensis and the implications for industrial fermentation processes. - In: Proceedings of the convention-institute of brewing asia pacific section, vol. - Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. - In: Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, vol
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt