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

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.

scholarly journals Different trajectories of polyploidization shape the genomic landscape of theBrettanomyces bruxellensisyeast species

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

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.

scholarly journals 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 ◽  
Vol 14 (5) ◽  
pp. e0215077 ◽  
Author(s):  
Ievgeniia A. Tiukova ◽  
Mats E. Pettersson ◽  
Marc P. Hoeppner ◽  
Remi-Andre Olsen ◽  
Max Käller ◽  
...  
Keyword(s):  
Ethanol Production ◽  
Genome Assembly ◽  
Yeast Species ◽  
Genome Structure ◽  
Brettanomyces Bruxellensis ◽  
Dynamic Genome ◽  
Production Strain

scholarly journals Evolution of the Yeast Recombination Landscape

2018 ◽  
Vol 36 (2) ◽  
pp. 412-422 ◽  
Author(s):  
Haoxuan Liu ◽  
Calum J Maclean ◽  
Jianzhi Zhang
Keyword(s):  
Recombination Rate ◽  
Yeast Species ◽  
Evolutionary Conservation ◽  
Double Strand Breaks ◽  
Strand Breaks ◽  
Crossover Interference ◽  
Recombination Hotspots ◽  
Genomic Landscape ◽  
Evolutionarily Conserved ◽  
Cold Spots

Abstract Meiotic recombination comprises crossovers and noncrossovers. Recombination, crossover in particular, shuffles mutations and impacts both the level of genetic polymorphism and the speed of adaptation. In many species, the recombination rate varies across the genome with hot and cold spots. The hotspot paradox hypothesis asserts that recombination hotspots are evolutionarily unstable due to self-destruction. However, the genomic landscape of double-strand breaks (DSBs), which initiate recombination, is evolutionarily conserved among divergent yeast species, casting doubt on the hotspot paradox hypothesis. Nonetheless, because only a subset of DSBs are associated with crossovers, the evolutionary conservation of the crossover landscape could differ from that of DSBs. Here, we investigate this possibility by generating a high-resolution recombination map of the budding yeast Saccharomyces paradoxus through whole-genome sequencing of 50 meiotic tetrads and by comparing this recombination map with that of S. cerevisiae. We observe a 40% lower recombination rate in S. paradoxus than in S. cerevisiae. Compared with the DSB landscape, the crossover landscape is even more conserved. Further analyses indicate that the elevated conservation of the crossover landscape is explained by a near-subtelomeric crossover preference in both yeasts, which we find to be attributable at least in part to crossover interference. We conclude that the yeast crossover landscape is highly conserved and that the evolutionary conservation of this landscape can differ from that of the DSB landscape.

scholarly journals Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3

2019 ◽  
Author(s):  
Michael Hagemann-Jensen ◽  
Christoph Ziegenhain ◽  
Ping Chen ◽  
Daniel Ramsköld ◽  
Gert-Jan Hendriks ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Cell Types ◽  
Mouse Strains ◽  
Rna Molecules ◽  
Counting Strategy ◽  
Long Read ◽  
Sequencing Strategy ◽  
Transcriptome Coverage ◽  
Scale Characterization

AbstractLarge-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states1. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells2,3. Here, we introduce Smart-seq3 that combines full-length transcriptome coverage with a 5’ unique molecular identifier (UMI) RNA counting strategy that enabled in silico reconstruction of thousands of RNA molecules per cell. Importantly, a large portion of counted and reconstructed RNA molecules could be directly assigned to specific isoforms and allelic origin, and we identified significant transcript isoform regulation in mouse strains and human cell types. Moreover, Smart-seq3 showed a dramatic increase in sensitivity and typically detected thousands more genes per cell than Smart-seq2. Altogether, we developed a short-read sequencing strategy for single-cell RNA counting at isoform and allele-resolution applicable to large-scale characterization of cell types and states across tissues and organisms.

scholarly journals A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

2019 ◽  
Author(s):  
Lillian K. Padgitt-Cobb ◽  
Sarah B. Kingan ◽  
Jackson Wells ◽  
Justin Elser ◽  
Brent Kronmiller ◽  
...  
Keyword(s):  
Large Scale ◽  
Humulus Lupulus ◽  
Plant Genome ◽  
Repeat Content ◽  
Haplotype Variation ◽  
Genomic Landscape ◽  
Cannabidiolic Acid ◽  
Long Read ◽  
History Of ◽  
Insight Into

AbstractHop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

scholarly journals Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective

Marine Drugs ◽  
2020 ◽  
Vol 18 (2) ◽  
pp. 103 ◽  
Author(s):  
Muhamad Afiq Akbar ◽  
Nurul Yuziana Mohd Yusof ◽  
Noor Idayu Tahir ◽  
Asmat Ahmad ◽  
Gires Usup ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Sequence Length ◽  
Gene Environment ◽  
Genomic Landscape ◽  
Potential Applications ◽  
Unicellular Organisms ◽  
Marine Dinoflagellates ◽  
Systems View ◽  
First Time ◽  
Complex Genome

Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanobacterial genera, comprising 26 genes that form a cluster ranging from 25.7 kb to 35 kb in sequence length. Due to the complexity of the genomic landscape, saxitoxin biosynthesis in dinoflagellates remains unknown. In order to reveal and understand the dynamics of the activity in such impressive unicellular organisms with a complex genome, a strategy that can carefully engage them in a systems view is necessary. Advances in omics technology (the collective tools of biological sciences) facilitated high-throughput studies of the genome, transcriptome, proteome, and metabolome of dinoflagellates. The omics approach was utilized to address saxitoxin-producing dinoflagellates in response to environmental stresses to improve understanding of dinoflagellates gene–environment interactions. Therefore, in this review, the progress in understanding dinoflagellate saxitoxin biosynthesis using an omics approach is emphasized. Further potential applications of metabolomics and genomics to unravel novel insights into saxitoxin biosynthesis in dinoflagellates are also reviewed.

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

2017 ◽  
Vol 27 (3) ◽  
pp. 147-158 ◽  
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 <i>Brettanomyces bruxellensis </i>contamination is currently a problem. This yeast causes a “horse sweat” flavor in wine, which is an undesired organoleptic attribute. To date, 6 <i>B. bruxellensis </i>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 <i>B. bruxellensis</i> LAMAP2480, obtaining a 27-Mb assembly with 5.5 kb of N50. In addition, the genome of <i>B. bruxellensis</i> 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 <i>B. bruxellensis</i> LAMAP2480 reaffirms the biotechnological potential of this strain. This research represents an interesting platform for the study of the spoilage yeast <i>B. bruxellensis</i>.

scholarly journals Modelling the growth and ethanol production of Brettanomyces bruxellensis at different glucose concentrations

2011 ◽  
Vol 53 (2) ◽  
pp. 141-149 ◽  
Author(s):  
M.G. Aguilar-Uscanga ◽  
Y. Garcia-Alvarado ◽  
J. Gomez-Rodriguez ◽  
T. Phister ◽  
M.L. Delia ◽  
...  
Keyword(s):  
Ethanol Production ◽  
Brettanomyces Bruxellensis

scholarly journals CRISPR-Mediated Knockout of Long 3′ UTR mRNA Isoforms in mESC-Derived Neurons

2021 ◽  
Vol 12 ◽  
Author(s):  
Bongmin Bae ◽  
Pedro Miura
Keyword(s):  
Genetic Manipulation ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Cellular Functions ◽  
Mrna Isoforms ◽  
Mouse Cortex ◽  
Long Read ◽  
Sequencing Strategy ◽  
Cost Efficient ◽  
A Site

Alternative cleavage and polyadenylation (APA) is pervasive, occurring for more than 70% of human and mouse genes. Distal poly(A) site selection to generate longer 3′ UTR mRNA isoforms is prevalent in the nervous system, affecting thousands of genes. Here, we establish mouse embryonic stem cell (mESC)-derived neurons (mES-neurons) as a suitable system to study long 3′ UTR isoforms. RNA-seq analysis revealed that mES-neurons show widespread 3′ UTR lengthening that closely resembles APA patterns found in mouse cortex. mESCs are highly amenable to genetic manipulation. We present a method to eliminate long 3′ UTR isoform expression using CRISPR/Cas9 editing. This approach can lead to clones with the desired deletion within several weeks. We demonstrate this strategy on the Mprip gene as a proof-of-principle. To confirm loss of long 3′ UTR expression and the absence of cryptic poly(A) site usage stemming from the CRISPR deletion, we present a simple and cost-efficient targeted long-read RNA-sequencing strategy using the Oxford Nanopore Technologies platform. Using this method, we confirmed specific loss of the Mprip long 3′ UTR isoform. CRISPR gene editing of mESCs thus serves as a highly relevant platform for studying the molecular and cellular functions of long 3′ UTR mRNA isoforms.

scholarly journals Long-Read Sequencing of the Zebrafish Genome Reorganizes Genomic Architecture

2021 ◽  
Author(s):  
Yelena Chernyavskaya ◽  
Xiaofei Zhang ◽  
Jinze Liu ◽  
Jessica S. Blackburn
Keyword(s):  
Low Complexity ◽  
Zebrafish Genome ◽  
Nanopore Sequencing ◽  
Sequencing Technology ◽  
Short Read ◽  
Short Read Sequencing ◽  
Genomic Landscape ◽  
Long Reads ◽  
Long Read ◽  
Sequencing Platforms

Nanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Although long-read sequencing has been used to resolve several vertebrate genomes, a nanopore-based zebrafish assembly has not yet been released. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers. We used nanopore sequencing to improve upon and resolve the issues plaguing the current zebrafish reference assembly (GRCz11). Our long-read assembly improved the current resolution of the reference genome by identifying 1,697 novel insertions and deletions over 1Kb in length and placing 106 previously unlocalized scaffolds. We also discovered additional sites of retrotransposon integration previously unreported in GRCz11 and observed their expression in adult zebrafish under physiologic conditions, implying they have active mobility in the zebrafish genome and contribute to the ever-changing genomic landscape.

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