Biology subjects

Borneman, A. R.

Publications and source records attributed to Borneman, A. R..

13 recordsLinked to original sources

bioRxiv2025

Retrotransposon-mediated duplication of SSU1 in high SO2 tolerant Brettanomyces bruxellensis winery isolates

Brettanomyces bruxellensis is an industrially relevant yeast and major spoilage organism in wine, where tolerance to sulphur dioxide (SO2), the primary preservative used for its control, varies between strains. To investigate the genetic basis of SO2 tolerance in winery populations, 26 isolates from Australian wineries were phenotypically characterised and sequenced using long-read technology. Isolates showed a wide range of SO2 tolerance that correlated with phylogenetic clade and ploidy. Haplotype phasing of SSU1, a sulphite efflux pump linked to SO2 tolerance, identified nine distinct haplotypes, including the previously described high-tolerance H1 allele. Highly tolerant strains carried duplications of H1, frequently associated with retrotransposon insertions and chromosomal rearrangements at the SSU1 locus. Comparative analyses with laboratory-evolved strains confirmed that retrotransposons facilitated the acquisition of additional SSU1 copies. These findings suggest that transposon-mediated structural variation drives adaptive increases in SO2 tolerance in B. bruxellensis populations.

microbiology↗

bioRxiv2025

Genetic and phenotypic diversity of wine-associated Hanseniaspora species

The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and enological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated from wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow- (SEL) and fast-evolving (FEL) lineages that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting specifically in the FEL lineage. Pangenome analysis within H. uvarum identified extensive copy number variation (CNV), particularly in genes related to xenobiotic tolerance, nutrient transport and metabolism. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the Hanseniaspora FEL lineage, with significant enrichment in genes within the lysine biosynthetic pathway, suggesting a key role for this amino acid in early FEL adaptation. In H. uvarum, signatures of recent positive selection were detected in genes linked to sulphur assimilation, sterol biosynthesis and glycerol production, indicating potential adaptation to the stresses imposed by grape and wine fermentation. Furthermore, phenotypic screening of 113 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO2, and cold tolerance. These findings provide novel insights into the genomic evolution and functional diversity of Hanseniaspora, expanding our understanding of yeast adaptation to wine fermentation and laying the foundation for targeted gene investigations within this important genus.

microbiology↗

bioRxiv2024

Evidence for infection of Eucalyptus camaldulensis with a Leifsonia bacterium in Australia and Syria using high throughput sequencing

A biotic hypothesis for the eucalypt disease of unknown aetiolgy, Mundulla Yellows (MY), was tested by seeking non-host nucleic acids in affected Eucalyptus camaldulensis trees using high throughput sequencing (HTS). Ten contigs were selected from a pool of nucleic acids unique to diseased trees, and oligonucleotide probes were prepared for specific dot-blot hybridisation assay of these contigs. One of the contigs was found to be associated with a few MY-affected trees collected in South Australia and Western Australia, as well as with similarly affected E. camaldulensis trees growing in Syria. The probes for this contig represented opposite polarities of the contig, and both hybridised with the same positive samples even after alkali treatment confirming that the contig that they represented was dsDNA. This contig, comprising 766 nt, showed 95% similarity to whole genome shotgun sequence of Leifsonia xyli. This preliminary microbiome analysis of MY affected trees provides the first evidence that a Leifsonia species may infect eucalypts and that it should be further studied as a potential agent of MY.

microbiology↗

bioRxiv2024

Grapevine Shiraz Disease-associated viruses lead to significant yield losses by altering transcription of genes related to defence responses and photosynthesis

Shiraz disease (SD) is a highly destructive disease of grapevines that is associated with Grapevine Virus A (GVA) infection of vineyards in Australia and South Africa. However, little is known about the transcriptional modifications in grapevine phloem tissues induced by SD. In this study, we explored the viral diversity and transcriptional changes linked to SD. Vines symptomatic for SD exhibited higher viral abundance and were also shown to be co-infected with both GVA and grapevine leafroll-associated virus (GLRaV-4) strain 9. Differential gene (DE) expression analysis revealed physiological responses of Vitis vinifera to the infection. Similar to other plant pathogen infections, SD upregulated genes associated with the systemic acquired resistance (SAR) mechanism and downregulated genes related to vine immunity. Additionally, upregulated genes suggests that callose deposition and the blocking of phloem sieve elements are likely employed by V. vinifera as a defence strategy to limit the internal spread of SD viruses. Grapevine Shiraz disease, Grapevine Virus A, Grapevine Leafroll Associated virus, Systemic Acquired Resistance, Transcriptomics

plant biology↗

bioRxiv2024

Adaptation during the transition from Ophiocordyceps entomopathogen to insect associate is accompanied by gene loss and intensified selection.

Fungal and bacterial symbiosis is an important adaptation that has occurred within many insect species, which usually results in the relaxation of selection across the symbiont genome. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to associate, infecting soft-scale insects trans-generationally without killing them. To gain an understanding of the genomic adaptations underlying this transition, long-read sequencing was utilized to assemble the genomes of both Parthenolecanium corni and its Ophiocordyceps associate from a single insect. A highly contiguous haploid assembly was obtained for Part. corni, representing the first assembly from a single Coccoidea insect, in which 97% of its 227.8 Mb genome was contained within 24 contigs. Metagenomic-based binning produced a chromosome-level genome for Part. cornis Ophiocordyceps associate. The associate genome contained 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the associate lineage. Intensified selection was most frequently observed across nuclear orthologs, while selection on mitochondrial genes was found to be relaxed. Furthermore, scans for diversifying selection identified associate specific selection within three adjacent enzymes catalyzing acetoacetates metabolism to acetyl-COA. This work provides insight into the adaptive landscape during the transition to an associate life history, along with a base for future research into the genomic mechanisms underpinning the evolution of Ophiocordyceps.

genomics↗

bioRxiv2023

Metagenomic ecosystem monitoring of soft scale and mealybug infestations in Australian vineyards

Soft scale insects and mealybugs are phloem feeding Hemipterans that are considered majors pests in agricultural and horticultural settings throughout the world. Viticulturally, scale are a major issue due to their ability to secrete honeydew, which facilitates the development of sooty mould and for their propensity as transmission vectors for several viral diseases of grapevine. To facilitate the rapid identification and quantification of vineyard-associated insects a metagenomic-based bioinformatic pipeline was developed for generalised ecosystem monitoring that automated the assembly and classification of insect mitochondrial genomes from shotgun sequencing data using the Barcode of Life Database API. Parthenolecanium corni (European fruit scale), which was thought to be absent from Australian grapevines, was identified as the dominant coccid species infesting all vines sampled, along with secondary infestation by Pseudococcus viburni (obscure mealybug) and Pseudo. longispinus (long-tailed mealybug). In addition, parisitoidism by Coccophagus scutellaris (Aphelinidae) wasps was also detected. The discovery of Parth. corni as a significant member of scale infestations in Australia has significant implications for the development of effective control strategies for this important group of pests.

ecology↗

bioRxiv2023

The genomic landscape of wild Saccharomyces cerevisiae is shaped by complex patterns of admixture, aneuploidy and recombination.

Cultural exchange of fermentation techniques has driven the spread of Saccharomyces cerevisiae across the globe, establishing wild populations in many countries. Despite this, most modern commercial fermentations are inoculated using monocultures, rather than relying on natural populations, potentially impacting wild population diversity. Here we investigate the genomic landscape of 411 wild S. cerevisiae isolated from spontaneous grape fermentations in Australia across multiple locations, years, and grape cultivars. Spontaneous fermentations contained highly recombined mosaic strains that commonly exhibited aneuploidy of chromosomes 1, 3, 6 and 9. Assigning wild genomic windows to putative ancestral origin revealed that few closely related commercial lineages have come to dominate the genetic landscape, contributing most of the genetic variation. Fine-scale phylogenetic analysis of loci not observed in strains of commercial wine origin identified widespread admixture with the Beer2 clade along with three independent admixture events from potentially endemic Oceanic lineages that last shared an ancestor with modern East Asian S. cerevisiae populations. Our results illustrate how commercial use of microbes can affect local microorganism genetic diversity and demonstrates the presence of non-domesticated, non-European derived lineages of S. cerevisiae in Australian ecological niches that are actively admixing.

genomics↗

bioRxiv2022

The phased diploid genome assembly of Vitis vinifera cv. Shiraz.

Shiraz (Syrah) is a dark-skinned cultivar of the wine grape Vitis vinifera that forms the basis of some of the worlds most iconic wines. Worldwide, Shiraz is the fourth most planted grapevine cultivar, however it represents the most planted cultivar in Australia. Given the importance of Shiraz to worldwide wine production, a long-read based reference genome assembly for this cultivar was produced and used to investigate the unique genetic diversity and ancestral origins of this iconic variety. Phylogenetic reconstruction using high-quality genome assemblies for wine grape cultivars provided further support of a kinship between Shiraz and Pinot Noir. Harnessing long-read data, transposable element insertions potentially affecting gene function were characterized in Shiraz and assessed relative to other cultivars. This revealed a heterogenous landscape of transposon insertion points across cultivars and uncovered a specific combination of allelic variants at the TPS24 terpene synthase locus, which when combined with appropriate environmental triggers, may allow Shiraz to produce high levels of rotundone, the aroma compound responsible for the distinctive peppery characteristics of this cultivar.

genomics↗

bioRxiv2022

Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements

We have designed, constructed, and debugged a synthetic 753,096 bp version of Saccharomyces cerevisiae chromosome XIV as part of the international Sc2.0 project. We showed that certain synthetic loxPsym recombination sites can interfere with mitochondrial protein localization, that the deletion of one intron (NOG2) reduced fitness, and that a reassigned stop codon can lead to a growth defect. In parallel to these rational debugging modifications, we used Adaptive Laboratory Evolution to generate a general growth defect suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss. The presence of wild-type chromosomes in the hybrid tetraploids increased post-SCRaMbLE viability and heterologous DNA integration, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.

synthetic biology↗

bioRxiv2019

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

BackgroundYeast 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. For instance, Brettanomyces bruxellensis has been heavily studied and many resources are available for this species, whereas Brettanomyces nanus is rarely studied and lacks a publicly available genome assembly altogether. The purpose of this study is to fill this knowledge gap and explore the genomic adaptations that have shaped the evolution of this genus.\n\nResultsStrains for each of the five widely accepted species of Brettanomyces (Brettanomyces anomalus, B. bruxellensis, Brettanomyces custersianus, Brettanomyces naardenensis, and B. nanus) were sequenced using a combination of long- and short-read sequencing technologies. Highly contiguous assemblies were produced for each species. Sweeping and extensive structural variation between the species genomes were observed and gene expansions in fermentation-relevant genes (particularly in B. bruxellensis and B. nanus) were identified. Numerous horizontal gene transfer (HGT) events in all Brettanomyces species, including an HGT event that is probably responsible for allowing B. bruxellensis and B. anomalus to utilize sucrose were also observed.\n\nConclusionsGenomic adaptations and some evidence of domestication that have taken place in Brettanomycesare outlined. These new genome assemblies form a valuable resource for future research in Brettanomyces.

genomics↗

bioRxiv2018

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Chardonnay is the basis of some of the worlds most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different commercial Chardonnay clones. There were 1620 markers identified that distinguish the 15 Chardonnay clones. These markers were reliably used for clonal identification of validation genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.\n\nAuthor SummaryPhenotypic variation within a grapevine cultivar arises from an accumulation of mutations from serial vegetative propagation. Old cultivars such as Chardonnay have been propagated for centuries resulting in hundreds of available clones containing unique genetic mutations and a range of various phenotypic peculiarities. The genetic mutations can be leveraged as genetic markers and are useful in identifying specific clones for authenticity testing, or as breeding markers for new clonal selections where particular mutations are known to confer a phenotypic trait. We produced a high-quality genome assembly for Chardonnay, and using re-sequencing data for 15 popular clones, were able to identify a large selection of markers that are unique to at least one clone. We identified mutations that may confer phenotypic effects, and were able to identify clones from material independently sourced from nurseries and vineyards. The marker detection framework we describe for authenticity testing would be applicable to other grapevine cultivars or even other agriculturally important woody-plant crops that are vegetatively propagated such as fruit orchards. Finally, we show that the Chardonnay genome contains extensive evidence for parental inbreeding, such that its parents, Gouais blanc and Pinot noir, may even represent first-degree relatives.

genomics↗

bioRxiv2018

Purge Haplotigs: Synteny Reduction for Third-gen Diploid Genome Assemblies

Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembling highly heterozygous genomes is still facing a major problem where the two haplotypes for a region are highly polymorphic and the synteny is not recognised during assembly. This causes issues with downstream analysis, for example variant discovery using the haploid assembly, or haplotype reconstruction using the diploid assembly. A new pipeline--Purge Haplotigs--was developed specifically for third-gen assemblies to identify and reassign the duplicate contigs. The pipeline takes a draft haplotype-fused assembly or a diploid assembly, and read alignments to produce an improved assembly. The pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing. All assemblies after processing with Purge Haplotigs were less duplicated with minimal impact on genome completeness. The software is available at https://bitbucket.org/mroachawri/purge_haplotigs under a permissive MIT licence.

bioinformatics↗

bioRxiv2017

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation

Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. To ensure a robust and reliable fermentation, most commercial wines are produced via inoculation with commercial strains of the major wine yeast, Saccharomyces cerevisiae. However, there is a growing trend towards the use of uninoculated or \"wild\" fermentations, in which the yeasts and bacteria that are naturally associated with the vineyard and winery, perform the fermentation. In doing so, the varied metabolic contributions of the numerous non-Saccharomyces species in this microbial community are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts.\n\nIn order the map the microflora of spontaneous fermentation, metagenomic techniques were used to characterize and monitor the progression of fungal species in several wild fermentations. Both amplicon-based ITS phylotyping (meta-barcoding) and shotgun metagenomics were used to assess community structure. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant over-abundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia.

microbiology↗