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

AbstractPolyploidization events are observed across the tree of life and occurred in many fungi, plant and animal species. Polyploidy is thought to be an important source of speciation and tumorigenesis. However, the origins of polyploid populations are not always clear and little is known about the precise nature and structure of their complex genome. Using a long-read sequencing strategy, we sequenced a large number of isolates from theBrettanomyces bruxellensisyeast species, which is found in anthropized environments (e.g.beer, contaminant of wine, kombucha and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid genomes, we phased them by using different strategies and we found that each subpopulation had a unique polyploidization history with distinct trajectories. The polyploid genomes contain either genetically closely related (with a genetic divergence < 1%) or diverged copies (> 3%), indicating auto- as well as allopolyploidization events. These latest events have occurred independently with a specific and unique donor in each of the polyploid subpopulations, and exclude the knownBrettanomycessister species as possible donors. Finally, loss of heterozygosity events have shaped the structure of these polyploid genomes and underline their dynamic. Overall, our study highlights the multiplicity of the trajectories leading to polyploid genomes within a same species.

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Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species

Genome Research ◽

10.1101/gr.275380.121 ◽

2021 ◽

Author(s):

Chris Eberlein ◽

Omar Abou Saada ◽

Anne Friedrich ◽

Warren Albertin ◽

Joseph Schacherer

Keyword(s):

Ethanol Production ◽

Loss Of Heterozygosity ◽

Genetic Divergence ◽

Animal Species ◽

Yeast Species ◽

Brettanomyces Bruxellensis ◽

Genomic Landscape ◽

Long Read ◽

Sequencing Strategy ◽

Complex Genome

Polyploidization events are observed across the tree of life and occur in many fungi, plant, and animal species. During evolution, polyploidy is thought to be an important source of speciation and tumorigenesis. However, the origin of polyploid populations is not always clear, and little is known about the precise nature and structure of their complex genome. Using a long-read sequencing strategy, we sequenced 71 strains from the Brettanomyces bruxellensis yeast species, which is found in anthropized environments (e.g., beer, contaminant of wine, kombucha, and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid genomes, we phased them by using different strategies and found that each subpopulation had a unique polyploidization history with distinct trajectories. The polyploid genomes contain either genetically closely related (with a genetic divergence <1%) or diverged copies (>3%), indicating auto- as well as allopolyploidization events. These latest events have occurred independently with a specific and unique donor in each of the polyploid subpopulations and exclude the known Brettanomyces sister species as possible donors. Finally, loss of heterozygosity events has shaped the structure of these polyploid genomes and underline their dynamics. Overall, our study highlights the multiplicity of the trajectories leading to polyploid genomes within the same species.

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Transcriptome of the Alternative Ethanol Production Strain Dekkera bruxellensis CBS 11270 in Sugar Limited, Low Oxygen Cultivation

PLoS ONE ◽

10.1371/journal.pone.0058455 ◽

2013 ◽

Vol 8 (3) ◽

pp. e58455 ◽

Cited By ~ 27

Author(s):

Ievgeniia A. Tiukova ◽

Mats E. Petterson ◽

Christian Tellgren-Roth ◽

Ignas Bunikis ◽

Thomas Eberhard ◽

...

Keyword(s):

Ethanol Production ◽

Low Oxygen ◽

Dekkera Bruxellensis ◽

Production Strain

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A Deep Dive into Genome Assemblies of Non-vertebrate Animals

10.20944/preprints202111.0170.v1 ◽

2021 ◽

Author(s):

Nadège Guiglielmoni ◽

Ramón Rivera-Vicéns ◽

Romain Koszul ◽

Jean-François Flot

Keyword(s):

Genome Assembly ◽

Current Knowledge ◽

Genome Structure ◽

Deep Dive ◽

Sequencing Technologies ◽

Current State ◽

Animal Diversity ◽

And Function ◽

Genome Assemblies ◽

Genome Projects

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

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De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

10.1101/730762 ◽

2019 ◽

Cited By ~ 2

Author(s):

Kenta Shirasawa ◽

Akifumi Azuma ◽

Fumiya Taniguchi ◽

Toshiya Yamamoto ◽

Akihiko Sato ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

De Novo ◽

Sequence Data ◽

Genome Structure ◽

Table Grape ◽

Sequencing Analysis ◽

Entire Genome ◽

Table Grapes ◽

Eukaryotic Genes

AbstractThis study presents the first genome sequence of an interspecific grape hybrid, ‘Shine Muscat’ (Vitis labruscana × V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a “haploid” genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of ‘Shine Muscat’ was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of ‘Shine Muscat’ and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the ‘Shine Muscat’ genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as ‘Shine Muscat’.

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A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae

Genome Biology and Evolution ◽

10.1093/gbe/evz269 ◽

2019 ◽

Vol 12 (1) ◽

pp. 3635-3646 ◽

Cited By ~ 3

Author(s):

Arnab Ghosh ◽

Matthew G Johnson ◽

Austin B Osmanski ◽

Swarnali Louha ◽

Natalia J Bayona-Vásquez ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Genome Structure ◽

Protein Domain ◽

Alligator Mississippiensis ◽

Structure Evolution ◽

Functional Protein ◽

High Quality ◽

Saltwater Crocodile ◽

Crocodylus Porosus

Abstract Crocodilians are an economically, culturally, and biologically important group. To improve researchers’ ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple noncoding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, 10 in C. porosus and 6 in Alligator mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological, and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.

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Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480

Journal of Molecular Microbiology and Biotechnology ◽

10.1159/000471924 ◽

2017 ◽

Vol 27 (3) ◽

pp. 147-158 ◽

Cited By ~ 3

Author(s):

Liliana Godoy ◽

Evelyn Silva-Moreno ◽

Wladimir Mardones ◽

Darwin Guzman ◽

Francisco A. Cubillos ◽

...

Keyword(s):

Ethanol Production ◽

Survival Strategies ◽

Whole Genome ◽

Biotechnological Applications ◽

Genome Sequences ◽

Wine Production ◽

Brettanomyces Bruxellensis ◽

Biotechnological Potential ◽

Spoilage Yeast ◽

Genome Comparisons

Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to Brettanomyces bruxellensis contamination is currently a problem. This yeast causes a “horse sweat” flavor in wine, which is an undesired organoleptic attribute. To date, 6 B. bruxellensis annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited. In this article, we reassembled and reannotated the genome of B. bruxellensis LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of B. bruxellensis LAMAP2480 was analyzed in the context of spoilage yeast and potential as a biotechnological tool. In addition, we carried out an exploratory transcriptomic analysis of this strain grown in synthetic wine. Several genes related to stress tolerance, micronutrient acquisition, ethanol production, and lignocellulose assimilation were found. In conclusion, the analysis of the genome of B. bruxellensis LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast B. bruxellensis.

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