Biomedical subjects
Publications and source records attributed to Kerrie Barry.
One hundred diatom species have been selected for genome and transcriptome sequencing. The 100 Diatom Genomes Project aims to provide a scalable framework for understanding diatom biodiversity, ecology and evolution, and for investigating their use in biotechnology.
BACKGROUND: Characterizing population structure and admixture events between ancestral groups plays a key role in understanding the evolutionary history of species and crops. Most tools for inferring admixture have been developed for diploids and are not suitable for polyploids, in particular those with high and mixed ploidy such as Saccharum. RESULTS: Here we present AdmixPoly, an R-package designed to infer admixture in polyploid species both at the genome-wide scale and locally along chromosomes. We compare AdmixPoly with state-of-the-art methods using simulations, demonstrating its precision and computational efficiency. Notably, local admixture inference in complex scenarios, such as high ploidy levels, large numbers of ancestral groups and alleles per marker is enabled through efficient approximations of emission and transition probabilities within a hidden Markov model framework. We apply this approach to characterize the contributions of wild Saccharum species to the complex polyploid genome of modern sugarcane cultivars. A panel of wild and cultivated Saccharum accessions is genotyped for 80K genomic regions, each revealing approximately 50 read-scale haplotypes. CONCLUSIONS: The results reveal that most of the approximately 12 copies of each basic chromosome in modern cultivars are derived from the domesticated species Saccharum officinarum, with one to four copies typically contributed by distinct subgroups of the wild species Saccharum spontaneum. In addition, contributions from an unknown wild Saccharum group originating from the Pacific were identified in most cultivars. The conserved pattern of these introgressions suggests that they can be traced back to the early stages of sugarcane breeding approximately a century ago.
Fungi are important and hyperdiverse organisms, yet chronically understudied. Most fungal clades have no reference genomes, impeding our understanding of their ecosystem functions and use as solutions in health and biotechnology. Also, opportunities for training in fungal biology and genomics are lacking, creating a bottleneck that hinders the recruitment and cultivation of a talented future mycological workforce. To address these issues, we developed Myco-Ed, an educational program offering training and scientific contributions through genome sequencing and analysis. Myco-Ed empowers students to pursue careers in fungal biology while improving fungal resources. Myco-Ed has been piloted at 12 institutions (15 classrooms) ranging from online e-Campuses to R1 universities, resulting in hundreds of fungal observations and many new high-quality reference genomes.
Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ectomycorrhiza (ECM) first requires the association of compatible partners. However, host and fungal genetic determinants governing mycorrhizal compatibility are unknown. To identify such factors in poplar and its fungal associates, we mined existing and de novo tree and fungal transcriptional datasets. We identified co-expressed genes enabling ECM symbiosis at early and mature stages of the interaction. These sets of genes can be divided into general fungal-sensing and ECM-specific components. We highlight the importance of fungal modulation of plant JA-related defenses and the regulation of secretory pathways for ECM compatibility, including upregulation of key fungal small secreted proteins, the downregulation of plant secreted peroxidases, and the downregulation of plant cell wall remodeling proteins concomitantly with the upregulation of fungal glycosyl hydrolases acting on pectin. Not only gene regulation, but also its temporal scale and dynamics seem to play a crucial role for mycorrhizal compatibility. The expression profile of the host Common Symbiosis Pathway and nutrient transporters was also studied, revealing constitutive levels of expression and moderate upregulation in compatible ECM interactions. Overall, these results underscore the importance of novel biological functions during the establishment of ECM symbiosis, help us gain insights into the molecular events determining mycorrhiza compatibility, and serve as a data-rich transcriptomic resource to open new research questions in the field.
Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.