Publications by authors named "J L Steenwyk"
Background: Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in terms of infrastructure, expertise, and security when it comes to continuous surveillance. The existing pipelines often require the user to set up and manage their own infrastructure and are not designed for continuous surveillance that demands integration of new and regularly generated sequencing data with previous analyses.
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- Multiple sequence alignments and phylogenetic trees are essential tools in biology research, providing detailed biological insights.
- PhyKIT is a software tool designed to streamline the analysis of these alignments and trees, offering various functionalities like constructing supermatrices and identifying errors in orthology inference.
- The text outlines several protocols for using PhyKIT, covering installation, data processing, and features that aid in understanding gene functions and evolutionary relationships.
f. sp. (FOLac) is a soil- and seedborne fungal pathogen that causes Fusarium wilt of lettuce, an important disease threatening global lettuce production.
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- 53 isolates of Aspergillus section Nidulantes fungi were studied, revealing that 30 clinical isolates, including four from COVID-19 patients, were misidentified as the cryptic pathogen A. latus, which resulted from a hybridization event.
- The research showed that A. latus displays significant genetic diversity and that both parental subgenomes are actively expressed in clinical isolates, responding to different environmental conditions.
- Key differences in drug resistance and growth in oxidative stress were found between A. latus hybrids and related species, along with four features that could help in accurately identifying A. latus in the future.
Article Synopsis
- Distantly related organisms, like cactophilic yeasts, can evolve similar traits and lifestyles to survive in comparable environments, with this study analyzing over 1,000 yeast species to understand their convergent evolution.
- Researchers found that cactophily (association with cacti) evolved independently about 17 times and could be predicted with 76% accuracy using genomic and phenotypic data, with thermotolerance being the most significant factor.
- The study also revealed horizontal gene transfer and duplications in genes related to plant cell wall degradation, indicating that these adaptive traits arose from different molecular pathways, and highlighted a potential link between cactophilic lifestyles and yeast becoming human pathogens.