A5046883178- Genomics and Phylogenetic Studies
- Fungal and yeast genetics research
- Fermentation and Sensory Analysis
- Plant Pathogens and Fungal Diseases
- Antifungal resistance and susceptibility
- Microbial Natural Products and Biosynthesis
- Yeasts and Rust Fungi Studies
- Mycotoxins in Agriculture and Food
- Mycorrhizal Fungi and Plant Interactions
- Genetic diversity and population structure
- Fungal Biology and Applications
- Microbial Metabolic Engineering and Bioproduction
- Plant and animal studies
- RNA and protein synthesis mechanisms
- Birth, Development, and Health
- Genetic factors in colorectal cancer
- Preterm Birth and Chorioamnionitis
- Bioinformatics and Genomic Networks
- Pregnancy and preeclampsia studies
- Plant Disease Resistance and Genetics
- Neonatal Respiratory Health Research
- Evolution and Paleontology Studies
- Insect symbiosis and bacterial influences
- Evolution and Genetic Dynamics
- Fungal Infections and Studies
Vanderbilt University
2016-2025
Heidelberg Institute for Theoretical Studies
2022-2024
Baylor University
2023
Université Laval
2023
Vanderbilt University Medical Center
2013-2022
Nashville Oncology Associates
2020
University of California, Riverside
2020
ORCID
2017
Center for Human Genetics
2012-2014
University of Minnesota
2013
Wood is a major pool of organic carbon that highly resistant to decay, owing largely the presence lignin. The only organisms capable substantial lignin decay are white rot fungi in Agaricomycetes, which also contains non-lignin-degrading brown and ectomycorrhizal species. Comparative analyses 31 fungal genomes (12 generated for this study) suggest lignin-degrading peroxidases expanded lineage leading ancestor reconstructed as species, then contracted parallel lineages mycorrhizal Molecular...
Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying evolution metazoan multicellularity, we sequenced and analysed genome unicellular choanoflagellate Monosiga brevicollis. The contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion signalling protein domains otherwise restricted to Here show physical linkages among often differ between M. brevicollis metazoans, suggesting abundant domain...
Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of explore new avenues vector control, we sequenced genomes 16 anopheline from diverse locations spanning ~100 million years evolution. Comparative analyses show faster rates gene gain loss, elevated shuffling on X chromosome, more intron losses, relative to Drosophila. Some determinants capacity,...
Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods extracting information from such remain limited. Although various biological processes may cause different genes to genealogical histories (and hence tree topologies), we also expect that the number of distinct topologies among a set is relatively small compared with possible topologies. Therefore evidence about topology one gene should influence our...
One of the hallmarks Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety debilitating diseases or immune deficiencies. Here we report complete sequence and comparative analysis genomes two representative P. strains isolated from cystic fibrosis (CF) patients whose genetic disorder predisposes them infections by this pathogen. The comparison CF those other presents picture mosaic genome, consisting conserved core...
Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying removing these prior However, a recent study reported that doing so worsen inference, underscoring the need alternative alignment strategies. Here, we introduce ClipKIT, an software that, rather than putatively...
The relative contribution of taxon number and gene to accuracy in phylogenetic inference is a major issue phylogenetics central importance the choice experimental strategies for successful reconstruction broad sketch tree life. Maximization taxa sampled strategy favored by most phylogeneticists, although its necessity remains subject debate. Vast increases are now possible due advances genomics, but large numbers genes will be available only modest taxa, raising question whether such...
The phylogenetic relationships among most metazoan phyla remain uncertain. We obtained large numbers of gene sequences from metazoans, including key understudied taxa. Despite the amount data and breadth taxa analyzed, remained unresolved. In contrast, same genes robustly resolved within a major clade Fungi approximately age as Metazoa. differences in resolution two kingdoms suggest that early history metazoans was radiation compressed time, finding is agreement with paleontological...
High-quality, well-annotated genome sequences and standardized laboratory strains fuel experimental evolutionary research. We present improved of three species Saccharomyces sensu stricto yeasts: S. bayanus var. uvarum (CBS 7001), kudriavzevii (IFO 1802T ZP 591), mikatae 1815T), describe their comparison to the genomes cerevisiae paradoxus. The new sequences, derived by assembling millions short DNA sequence reads together with previously published Sanger shotgun reads, have vastly greater...
Significance The highly diverse Ascomycete yeasts have enormous biotechnological potential. Collectively, these convert a broad range of substrates into useful compounds, such as ethanol, lipids, and vitamins, can grow in extremes temperature, salinity, pH. We compared 29 yeast genomes with the goal correlating genetics to traits. In one rare species, we discovered genetic code that translates CUG codons alanine rather than canonical leucine. Genome comparison enabled correlation genes...
Phylogenies inferred from different data matrices often conflict with each other necessitating the development of measures that quantify this incongruence. Here, we introduce novel use information theory to degree or incongruence among all nontrivial bipartitions present in a set trees. The first measure, internode certainty (IC), calculates for given by considering frequency bipartition defined (internal branch) trees jointly most prevalent conflicting same tree set. second IC All (ICA),...
Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that comprising SM pathways exhibit environmentally dependent coregulation, we hypothesized within a pathway would form tight associations (modules) with each other in coexpression networks, facilitating identification. To evaluate this hypothesis, used 10 global data sets, meta-analysis of hundreds...
Abstract Understanding the phylogenetic relationships among yeasts of subphylum Saccharomycotina is a prerequisite for understanding evolution their metabolisms and ecological lifestyles. In last two decades, use rDNA multilocus data sets has greatly advanced our yeast phylogeny, but many deep remain unsupported. contrast, phylogenomic analyses have involved relatively few taxa lineages that were often selected with limited considerations covering breadth biodiversity. Here we used genome...
Ants are a highly successful family of insects that thrive in variety habitats across the world. Perhaps their best-known features complex social organization and strict division labor, separating reproduction from day-to-day maintenance care colony, as well discrimination against foreign individuals. Since these characteristics ants thought to be mediated by semiochemicals, thorough analysis signals, receptors detect them, is critical revealing mechanisms lead stereotypic behaviors. To...
Filamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that SMs are found in contiguous gene clusters fungal genomes, an atypical arrangement other eukaryotes. Comparative studies filamentous species have shown SM often either highly divergent or uniquely present one handful species, hampering efforts to determine the genetic basis evolutionary drivers cluster divergence. Here, we examined variation...