Biology subjects

Ryder, M.

Publications and source records attributed to Ryder, M..

3 recordsLinked to original sources

bioRxiv2025

Insights from modern & historical genomes of Neorhizobium vitis, a new pathogen causing neoplastic growths on grapevine.

Grapevine crown gall is a globally significant disease typically attributed to Agrobacterium species carrying tumour-inducing (Ti) plasmids. In this study, we identify Neorhizobium vitis as a previously unrecognised crown gall-associated pathogen. Four modern isolates from symptomatic grapevines in South Australia and four historical strains collected in New South Wales in 1989 induced weak but consistent neoplastic growths on sunflower hypocotyls and carrot discs. Long-read genome sequencing revealed that all strains lack canonical Ti plasmids and the oncogenes iaaM and ipt, which are essential for classical auxin- and cytokinin-mediated tumorigenesis. Phylogenomic analyses reassigned all strains to the Neorhizobium clade, correcting the original classification of historical isolates as Agrobacterium vitis. The persistence of tumorigenic activity despite the absence of known virulence genes suggests the involvement of alternative, yet uncharacterized pathogenic mechanisms. These findings revise the non-pathogenic status of Neorhizobium, establish N. vitis as a novel tumorigenic lineage, and underscore the value of re-evaluating legacy isolates with modern genomic tools.

plant biology↗

bioRxiv2022

Identifying indels from WGS short reads of haploid genomes distinguishes variant-calling algorithms

Identification of clinically relevant strains of bacteria increasingly relies on whole genome sequencing. The downstream bioinformatics steps necessary for calling variants from short read sequences are well-established but seldom validated against haploid genomes. We devised an in silico workflow to introduce single nucleotide polymorphisms (SNP) and indels into bacterial reference genomes, and computationally generate sequencing reads based on the mutated genomes. We then applied the method to Mycobacterium tuberculosis H37Rv and used the synthetic reads as truth sets for evaluating several popular variant callers. Insertions proved especially challenging for most variant callers to correctly identify, relative to deletions and single nucleotide polymorphisms. With adequate read depth, however, variant callers that use high quality soft-clipped reads and base mismatches to perform local realignment consistently had the highest precision and recall in identifying medium-length insertions and deletions.

bioinformatics↗

bioRxiv2019

Microbial biogeography and ecology of the mouth and implications for periodontal diseases

Human-associated microbial communities differ in composition among body sites and between habitats within a site. Patterns of variation in the distribution of organisms across time and space is referred to as biogeography. The human oral cavity is a critical observatory for exploring microbial biogeography because it is spatially structured, easily accessible, and its microbiota has been linked to the promotion of both health and disease. The biogeographic features of microbial communities residing in spatially distinct but ecologically similar environments on the human body, including the subgingival crevice, have not yet been adequately explored. The purpose of this paper is twofold. First, we seek to provide the dental community with a primer on biogeographic theory, highlighting its relevance to the study of the human oral cavity. For this reason, we summarize what is known about the biogeographic variation of dental caries and periodontitis and postulate as to how this may be driven by spatial patterning in oral microbial community composition and structure. Second, we present a number of methods that investigators can use to test specific hypotheses using biogeographic theory. To anchor our discussion, we apply each method to a case study and examine the spatial variation of the human subgingival microbiota of 2 individuals. Our case study suggests that subgingival communities in the aggregate may conform to an anterior-to-posterior gradient in community composition. The gradient appears to be structured both by deterministic and non-deterministic processes, though additional work is needed to test and confirm specific hypotheses. A better understanding of biogeographic patterns and processes will advance our understanding of ways to optimize the efficacy of dental interventions targeting the oral microbiota.

ecology↗