Biology subjects

Botting, J.

Publications and source records attributed to Botting, J..

3 recordsLinked to original sources

bioRxiv2026

A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained production of Arabica coffee for over 150 years. Here, we present a pseudo-phased, chromosome-level genome resource for H. vastatrix, isolate Hv178a, to guide research into disease management. The Hv178a genome assembly is 665 and 638 Mbp for haplotype A and B respectively, localised to 18 chromosomes. We determined that the genomes are highly repetitive at [~]90%, with a GC content of [~]33%. We present the full annotation of 13,760 and 17,998 protein coding genes, and we predicted 452 and 496 effectors in haplotype A and B respectively. Depth-based comparisons with 11 additional H. vastatrix isolates revealed increased chromosome 17 (chr17) copy number in Hv178a. Validation with qPCR supports a chr17 trisomy in Hv178a absent from the ancestral lineage and potentially explaining the observed change in virulence.

genomics↗

bioRxiv2025

Three-dimensional quantitative characterization of Coxiella burnetii infection using focused ion beam-scanning electron microscopy

Coxiella burnetii is a highly virulent intracellular pathogen that causes acute and chronic Q fever in humans. The bacterium utilizes a Dot/Icm type IV secretion system (T4SS) to translocate over 100 effectors into host cells to facilitate biogenesis of Coxiella-containing vacuoles (CCVs), which are specialized lysosome-derived organelles that support bacterial replication. During replication in CCVs, C. burnetii undergoes a unique biphasic developmental cycle defined by two distinct cellular forms: the infectious and metabolically dormant small cell variant (SCV) that converts to a replicative large cell variant (LCV). This developmental cycle was believed to be intimately coupled with biogenesis of CCVs, but the underlying mechanisms remained unclear. Here, we combine advanced focused ion beam-scanning electron microscopy (FIB-SEM) with machine learning-based data analyses to visualize host cells infected by C. burnetii. We reveal significant pleiomorphism of both the bacteria and CCVs in three dimensions. We show that this technology can be leveraged to characterize CCV biogenesis defects displayed by C. burnetii mutants that are unable to generate the large CCV displayed by wild-type C. burnetii. Analysis of HeLa cells infected with a cig2::Tn mutant confirmed that this mutant creates vacuoles that have a defect in homotypic fusion but that the proportions of SCV to LCV in vacuoles in which this mutant resides are nearly identical to CCVs containing wild-type C. burnetii, which indicates the vacuole biogenesis defect displayed by the cig2::Tn mutant did not impact the developmental cycle intracellularly. Collectively, this study provides unprecedented three-dimensional images of the complex intracellular lifestyle of C. burnetii. This imaging technology also provides unique insights into the biphasic developmental cycle and will be a powerful approach to dissect CCV biogenesis defects displayed by mutant C. burnetii.

microbiology↗

bioRxiv2023

Response of siliceous marine organisms to the Permian-Triassic climate crisis based on new findings from central Spitsbergen, Svalbard

Siliceous marine ecosystems play a critical role on the Earths climate system through its influence on organic carbon burial and rates of marine authigenic clay formation (i.e. reverse weathering). The ecological demise of silicifying organisms associated with the Permian-Triassic mass extinction is postulated to have elevated rates of marine authigenic clay formation, resulting in a prolonged greenhouse climate during the Early Triassic. Yet, our understanding of the response of siliceous marine organisms during this critical interval is poor. Whilst radiolarians experienced the strongest diversity loss in their evolutionary history and perhaps also the greatest population decline of silica-secreting organisms during this event, only a small number of Griesbachian (post-extinction) localities that record siliceous organisms are known. Here, we report newly discovered latest Changhsingian to early Griesbachian (Clarkina meishanensis - Hindeodus parvus Zone) radiolarians and siliceous sponge spicules from Svalbard. This fauna documents the survival of a low-diversity radiolarian assemblage alongside stem-group hexactinellid sponges making this the first described account of post-extinction silica-secreting organisms from the Permian/Triassic boundary in a shallow marine shelf environment and a mid-northern palaeolatitudinal setting. Our findings indicate that latitudinal diversity gradients for silica-secreting organisms following the mass extinction were significantly altered, and that silica productivity was restricted to high latitude and deep water thermal refugia. This result has potential to further shape our understanding of changes to marine porewater and seawater dissolved silica levels and in turn rates of reverse weathering, with implications for our understanding of carbon cycle dynamics during this interval. This also suggests that the export of organic carbon to the deep ocean was not as severely impacted at non-equatorial latitudes. Key PointsO_LIWe document the first occurrence of siliceous sponge spicules and radiolarians (biogenic silica) from a mid-northern paleolatitude following the mass extinction event C_LIO_LIHoldover radiolarian species show poleward range shifts C_LIO_LIThe ecological composition and the restriction to shallow water oxygenated facies suggests a shallow mid-latitude refuge for siliceous marine organisms C_LIO_LIThis result has potential to further shape our understanding of changes to marine dissolved silica levels and in turn rates of reverse weathering, with implications for our understanding of Permian-Triassic carbon cycle dynamics. C_LI

evolutionary biology↗