Biology subjects

Ward, C. M.

Publications and source records attributed to Ward, C. M..

11 recordsLinked to original sources

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

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↗

bioRxiv2024

Temporal and spatial dynamics within the fungal microbiome of grape fermentation

Wine fermentation is a highly complex and competitive environment, imposing harsh selective pressures on fungal community ecology and diversity. The composition of fungal communities inhabiting the surface of grapes will directly impact fermentation progression, wine quality, and contribute to the distinctiveness between wines from different geographical regions. Despite this, the extent of microbial community diversity between geographies, termed microbial terroir, remains highly debated. We amassed a large survey of grape spontaneous ferments over six years, encompassing 3105 fungal microbiomes across 14 geographically separated grape-growing regions, and nine grape cultivars. Investigation into the biodiversity of these ferments identified that few high abundance genera form the core of the initial grape microbiome. In line with previous studies, various consistent taxa were linked to specific geographical locations and grape varieties. However, these taxa accounted for a small portion of the overall diversity in the dataset. Through unsupervised clustering, we identified three distinct community types in the grape fungal microbiome, each exhibiting variations in the abundance of key genera. Analysing ferments across temporal and spatial scales revealed significant differences in species richness and compositional heterogeneity between wineries and grape growing regions. However, microbial communities were transient between years in the same winery, regularly transitioning between the three broad community types. We then investigated microbial community composition throughout the fermentative process and observed that initial microbial community composition is predictive of the diversity during the early stages of fermentation, with Hanseniaspora uvarum detected as the main non-Saccharomyces species within this large cohort of samples. Our results help to formulate a clear understanding of the spatial and temporal characteristics of the grape juice fungal microbiome and suggest that these communities are mainly defined by the grape niche and in a minor way shaped by local environmental conditions.

microbiology↗

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↗

bioRxiv2021

Chromosome-level assembly of the common vetch reference genome (Vicia sativa)

BackgroundVicia sativa L. (Common Vetch, n = 6) is an annual, herbaceous, climbing legume that is distributed in tropical, sub-tropical and temperate climates. Originating in the Fertile Crescent of the Middle East, V. sativa is now widespread and grows in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we here present a chromosome-level reference genome sequence for V. sativa. ResultsWe applied a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis to construct a chromosome-level genome of V. sativa. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.9 gigabases (Gb) with a median contig length of 684 kb. Benchmarking Universal Single-Copy Orthologs (BUSCO) of the assembly demonstrated a very high completeness of 98 % of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 58,415 protein-coding genes. ConclusionsThe high-quality chromosome-level genome assembly of V. sativa will provide novel insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.

genomics↗

bioRxiv2020

Genomic evolutionary analysis in R with geaR.

The analysis and interpretation of datasets generated through sequencing large numbers of individual genomes is becoming commonplace in population and evolutionary genetic studies. Here we introduce geaR, a modular R package for evolutionary analysis of genome-wide genotype data. The package leverages the Genomic Data Structure (GDS) format, which enables memory and time efficient querying of genotype datasets compared to standard VCF genotype files. geaR utilizes GRange object classes to partition an analysis based on features from GFF annotation files, select codons based on position or degeneracy, and construct both positional and coordinate genomic windows. Tests of genetic diversity (eg. dXY,{pi} , FST) and admixture [Formula] along with tree building and sequence output, can be carried out on partitions using a single function regardless of sample ploidy or number of observed alleles. The package and associated documentation are available on GitHub at https://github.com/CMWbio/geaR.

genomics↗

bioRxiv2020

White pupae genes in the Tephritids Ceratitis capitata, Bactrocera dorsalis and Zeugodacus cucurbitae: a story of parallel mutations

Mass releases of sterilized male insects, in the frame of sterile insect technique programs, have helped suppress insect pest populations since the 1950s. In the major horticultural pests Bactrocera dorsalis, Ceratitis capitata, and Zeugodacus cucurbitae, a key phenotype white pupae (wp) has been used for decades to selectively remove females before releases, yet the gene responsible remained unknown. Here we use classical and modern genetic approaches to identify and functionally characterize causal wp− mutations in these distantly related fruit fly species. We find that the wp phenotype is produced by parallel mutations in a single, conserved gene. CRISPR/Cas9-mediated knockout of the wp gene leads to the rapid generation of novel white pupae strains in C. capitata and B. tryoni. The conserved phenotype and independent nature of the wp− mutations suggest that this technique can provide a generic approach to produce sexing strains in other major medical and agricultural insect pests.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2018

ngsReports: An R Package for managing FastQC reports and other NGS related log files.

MotivationHigh throughput next generation sequencing (NGS) has become exceedingly cheap facilitating studies to be undertaken containing large sample numbers. Quality control (QC) is an essential stage during analytic pipelines and can be found in the outputs of popular bioinformatics tools such as FastQC and Picard. Although these tools provide considerable power when carrying out QC, large sample numbers can make identification of systemic bias a challenge.\n\nResultsWe present ngsReports, an R package designed for the management and visualization of NGS reports from within an R environment. The available methods allow direct import into R of FastQC output as well as that from aligners such as HISAT2, STAR and Bowtie2. Visualization can be carried out across many samples using heatmaps rendered using ggplot2 and plotly. Moreover, these can be displayed in an interactive shiny app or a HTML report. We also provide methods to assess observed GC content in an organism dependent manner for both transcriptomic and genomic datasets. Importantly, hierarchical clustering can be carried out on heatmaps with large sample sizes to quickly identify outliers and batch effects.\n\nAvailability and ImplementationngsReports is available at https://github.com/UofABioinformaticsHub/ngsReports.

bioinformatics↗

bioRxiv2017

A global Brassica pest and a sympatric cryptic ally, Plutella australiana (Lepidoptera: Plutellidae), show strong divergence despite the capacity to hybridize

The diamondback moth, Plutella xylostella, has been intensively studied due to its ability to evolve insecticide resistance and status as the worlds most destructive pest of brassicaceous crops. The surprise discovery of a cryptic ally, Plutella australiana Landry & Hebert, with apparent endemism to Australia, immediately raised questions regarding the extent of ecological and genetic diversity between these two species, whether gene flow could occur, and ultimately if specific management was required. Here, we show that despite sympatric distributions and the capacity to hybridize in controlled laboratory experiments, striking differences in genetic and phenotypic traits exist that are consistent with contrasting colonization histories and reproductive isolation after secondary contact. Almost 1500 Plutella individuals were collected from wild and cultivated brassicaceous plants at 75 locations throughout Australia. Plutella australiana was commonly found on all Brassica host types sampled except commercial vegetables, which are routinely sprayed with insecticide. Bioassays using four commonly-used insecticides found that P. australiana was 19-306 fold more susceptible than P. xylostella. Genome-wide SNPs derived from RADseq revealed substantially higher levels of genetic diversity across P. australiana compared with P. xylostella nuclear genomes, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5 % of P. xylostella. Although P. australiana is a potential pest of brassica crops, it is of secondary importance to P. xylostella.

genetics↗