Daniel B. Sloan

This study examines evolutionary rate shifts in carnivorous plants to understand convergent and lineage-specific genomic adaptations.

This study models how mitochondrial dynamics in plants enhance DNA repair efficiency by improving stoichiometry through targeted import, fusion, and metabolon exchange.

This study identifies AtMsh1 as a mismatch-directed nuclease in Arabidopsis that facilitates DNA repair in organelles, reducing mutation rates.

This study shows that MSH1 promotes DNA double-strand breaks in Arabidopsis mitochondria triggered by uracil/guanine mismatches, supporting its role in maintaining genome integrity.

The paper compares mitochondrial and chloroplast proteomes across two flowering plant species to understand how gene loss and transfer affect organellar translation machinery.

This study investigates how photosynthesis loss and horizontal gene transfer reshape organellar translation and tRNA metabolism in holoparasitic plants.

The paper uses evolutionary rate covariation to identify a novel plant proteostasis module involving non-plastid-localized proteins.

This study identifies MutS2A and MutS2B as critical for plastid ribosome quality control in Arabidopsis, resolving ribosome collisions and supporting tissue greening during de-etiolation.

This study analyzes organellar genome dynamics in Arabidopsis thaliana using high-quality long-read assemblies, revealing rapid mitochondrial rearrangements and shared structural variants with plastids.

The paper measures mutation rates in plant mitochondrial and plastid genomes of msh1 mutants and finds significantly higher rates compared to wild-type plants.

The paper assesses the sensitivity of genome-wide tests for mitonuclear genetic incompatibilities using Xiphophorus fish hybrids and finds inconsistent support for class-based covariation in mitonuclear ancestry.

The paper investigates how recombination machinery affects mutation rates in plant organellar genomes using mutant lines and sequencing techniques.

This study sequences the giant Y chromosome of Silene latifolia and reveals its structure, function, and evolutionary history.

The paper identifies fungal-derived tRNA genes in orchid mitochondria that are transcribed, modified, and aminoacylated, suggesting functional integration into the mitochondrial translation system.

This study investigates the expansion of the MutS gene family in plants, identifying origins through gene duplication, endosymbiotic gene transfer, and horizontal gene transfer, and highlights their roles in organelle genetics.

The paper characterizes tRNA aminoacylation in Arabidopsis and shows higher rates in organellar tRNAs compared to nuclear/cytosolic tRNAs.

The paper introduces ERCnet, a tool for predicting protein interaction networks using phylogenetic analysis of evolutionary rate covariation, showing improved accuracy over existing methods.

The paper analyzes mtDNA damage fragments from three species after UV exposure, finding characteristic length profiles and di-pyrimidine patterns suggesting novel repair mechanisms.

The paper uses Duplex Sequencing to measure somatic mutation rates in Arabidopsis under different temperatures, finding very low mutation frequencies in wild-type plants.

This paper presents a chromosome-level genome assembly for Silene conica using PacBio HiFi, Hi-C, and Bionano technologies, revealing a reduced chromosome number and a large mitochondrial genome.

The paper introduces a maximum likelihood approach to analyze mtDNA heteroplasmy data, showing that traditional statistics can lead to false positives in detecting selection and bottleneck effects.

The paper uses long-read sequencing to study mitochondrial and plastid genome variants in Arabidopsis msh1 mutants, revealing recombination dynamics and structural rearrangements.

The paper reports the complete sequence of a 641-kb mitochondrial DNA insertion in the Arabidopsis thaliana nuclear genome using long-read sequencing technologies.

This study identifies mitochondrial mutations in C. elegans using Duplex Sequencing, revealing oxidative damage signatures and an AT-bias in mutation patterns.

The paper provides genomic and transcriptomic resources for Silene noctiflora, including a long-read transcriptome and draft genome assembly, to support research in plant ecology and evolution.

The paper detects de novo mitochondrial mutations in Silene species, revealing variation in mutation rates and mutational spectra across closely related angiosperms.

The paper compares mutation rates between two bacterial endosymbionts in sap-feeding insects, finding that differential mutagenesis drives differences in genome conservation.

The paper develops a combined tRNA sequencing protocol to measure expression and post-transcriptional modifications in plants, finding conserved and species-specific modification patterns in Arabidopsis thaliana.

This study shows that MSH1 is critical for maintaining low mutation rates in plant mitochondrial and plastid genomes by correcting errors through homologous recombination.

The paper analyzes gene and protein domain content changes across 76 arthropod genomes to understand evolutionary patterns and their association with phenotypic adaptations.