Daniel B. Sloan

Evolutionary rates provide genomic insights into convergent and lineage-specific evolution in carnivorous plants

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

Mitochondrial dynamics can resolve stoichiometric challenges in plant mtDNA repair

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

Plant MutS Homolog 1 is a mismatch-directed nuclease required for organelle genome maintenance

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

Uracil/guanine mismatches trigger MutS HOMOLOG1-dependent mitochondrial DNA double-strand breaks in Arabidopsis

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 effects of rapid mitochondrial gene loss on organellar proteomes

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

Reshaping Organellar Translation and tRNA Metabolism: The Consequences of Photosynthesis Loss and Massive Horizontal Gene Transfer

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

Correlated evolutionary rates reveal novel components and cross-compartment connectivity in plant proteostasis systems

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

Plant MutS2 proteins function in plastid ribosome quality control

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.

The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana

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.

Flipping the switch on some of the slowest mutating genomes: Direct measurements of plant mitochondrial and plastid mutation rates in msh1 mutants

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

Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities

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.

Disruption of recombination machinery alters the mutational landscape in plant organellar genomes

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

The Silene latifolia genome and its giant Y chromosome

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

Fungal-derived tRNAs are expressed and aminoacylated in orchid mitochondria

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

Expansion of the MutS gene family in plants

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 landscape of Arabidopsis tRNA aminoacylation

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

Phylogenomic prediction of interaction networks in the presence of gene duplication

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

UV damage induces production of mitochondrial DNA fragments with specific length profiles

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

Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing

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

Chromosome-level genome assembly for the angiosperm Silene conica

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.

Avoiding misleading estimates using mtDNA heteroplasmy statistics to study bottleneck size and selection

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.

Long-read sequencing characterizes mitochondrial and plastid genome variants in Arabidopsis msh1 mutants

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

Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome

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

Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias

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

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

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.

Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates

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

Mutational pressure drives differential genome conservation in two bacterial endosymbionts of sap feeding insects

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

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

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.

MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes

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

Gene Content Evolution in the Arthropods

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