A5031048725- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Plant-Microbe Interactions and Immunity
- Plant Diversity and Evolution
- Evolution and Genetic Dynamics
- Photosynthetic Processes and Mechanisms
- Plant Disease Resistance and Genetics
- Genetic diversity and population structure
- Plant Pathogens and Resistance
- Marine Ecology and Invasive Species
- Plant and Fungal Species Descriptions
- Chromosomal and Genetic Variations
- Bacteriophages and microbial interactions
- Plant and animal studies
- Fungal and yeast genetics research
- Plant Pathogens and Fungal Diseases
- Evolution and Paleontology Studies
- Plant Parasitism and Resistance
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Chromatin Dynamics
- Plant Stress Responses and Tolerance
- Computational Drug Discovery Methods
- Zoonotic diseases and public health
- Gene Regulatory Network Analysis
Stony Brook University
2015-2025
University of Chicago
2005-2020
New York University Press
2020
University of Georgia
2014
Harvard University
2014
University of Michigan
2001-2005
Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding origin early evolution plants. We analyzed three different complementary data sets: a multigene supermatrix, genomic structural character matrix, chloroplast genome sequence using maximum likelihood, parsimony, compatibility methods. Analyses all sets strongly supported liverworts as sister...
Abstract Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span diversity of eukaryotic tree life. However, genetic tractability has been limited to a few species, which do not represent or environmentally relevant taxa. Here, we report on development tools range protists primarily from marine environments. We present evidence for foreign DNA delivery and expression 13 species never before transformed advancement eight other as...
Determining an absolute timescale for avian evolutionary history has proven contentious. The two sources of information available, paleontological data and inference from extant molecular genetic sequences (colloquially, 'rocks' 'clocks'), have appeared irreconcilable; the fossil record supports a Cenozoic origin most modern lineages, whereas estimates suggest that these same lineages originated deep within Cretaceous survived K-Pg (Cretaceous-Paleogene; formerly Cretaceous-Tertiary or K-T)...
The molecular era has fundamentally reshaped our knowledge of the evolution and diversification angiosperms. One outstanding question is phylogenetic placement Amborella trichopoda Baill., commonly thought to represent first lineage extant Here, we leverage publicly available data provide a broad coalescent-based species tree estimation 45 seed plants. By incorporating 310 nuclear genes, coalescent analyses strongly support clade containing plus water lilies (i.e., Nymphaeales) that sister...
DNA sequences of nine genes (plastid: atpB, matK, and rbcL; mitochondrial: atp1, matR, mtSSU, mtLSU; nuclear: 18S 26S rDNAs) from 100 species basal angiosperms gymnosperms were analyzed using parsimony, Bayesian, maximum likelihood methods. All these analyses support the following consensus relationships among angiosperms. First, Amborella, Nymphaeaceae, Austrobaileyales are strongly supported as a grade in angiosperm phylogeny, with either Amborella or Nymphaeales sister to all other An...
Recent studies have suggested that plant genomes undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants provided strongest evidence of HGT, which appears to be facilitated by intimate physical association between parasites and their hosts. A recent phylogenomic study demonstrated holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess world's largest flowers, about 2.1% nuclear transcripts were likely...
Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants frequently coincide with major episodes of global climatic upheaval, including the mass extinction at Cretaceous-Tertiary boundary (c. 65 Ma) during more recent periods aridification Miocene 10-5 Ma). Here, we explore WGDs diverse flowering plant clade Malpighiales. Using transcriptomes complete genomes from 42 species, applied a multipronged phylogenomic pipeline to identify, locate, determine age Malpighiales...
There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances sequencing suggest the possibility of documenting genetic changes as they populations, thus uncovering basis evolution, particularly if samples are available from both before and after Here, we had a unique opportunity directly assess natural populations following an evolutionary fluctuation climate. We analysed genome-wide differences between ancestors descendants Brassica rapa plants two...
Mammalian small heat shock proteins (sHSP) are abundant in muscles and implicated both muscle function myopathies. Recently a new sHSP, HSP22 (HSPB8, H11), was identified the human heart by its interaction with HSP27 (HSPB1). Using phylogenetic analysis we show that is true member of sHSP superfamily. sHSPs interact each other form homo- hetero-oligomeric complexes. The these complexes poorly understood. gel filtration HPLC, yeast two-hybrid method, immunoprecipitation, cross-linking,...
Abstract Background Recent studies have shown that plant genomes potentially undergone rampant horizontal gene transfer (HGT). In parasitic systems HGT appears to be facilitated by the intimate physical association between parasite and its host. in these has been invoked when a DNA sequence obtained from is placed phylogenetically very near host rather than with closest relatives. Studies of plants relied largely on fortuitous discovery phylogenies indicate HGT, no broad systematic search...
The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these lineages remain uncertain. Here, we provide the first broad coalescent-based tree estimation of genome-scale nuclear plastid data By incorporating 305 genes 47 from 14 species, identify i) gymnosperms (i.e., gnetophytes) are monophyletic, ii) gnetophytes...
Levels of gene expression show considerable variation in eukaryotes, but no fine-scale maps have been made the fitness consequences such controlled genetic backgrounds and environments. To address this, we assayed at many levels up- down-regulated a single essential gene, LCB2, involved sphingolipid synthesis budding yeast Saccharomyces cerevisiae. Reduced LCB2 rapidly decreases cellular fitness, yet increased has little effect. The wild-type level is therefore perched on edge nonlinear...
Abstract There is now abundant evidence of rapid evolution in natural populations, but the genetic mechanisms these changes remain unclear. One possible route to through expression genes that influence traits under selection. We examined contemporary evolutionary gene plant populations responding environmental fluctuations. compared genome‐wide expression, using RNA‐seq, two Brassica rapa collected over four time points between 1997 and 2014, during which precipitation southern California...
<title>Abstract</title> Mirusviruses are enigmatic double-stranded (ds) DNA viruses with a chimeric evolutionary history – they have informational genes of Nucleocytoviricota ancestry and virion module most like those herpesviruses. Mirusvirus genomes were discovered in marine metagenomic data (1) but, despite their abundance broad environmental distribution, host range is unknown. The thraustochytrid protist Aurantiochytrium limacinum was recently found to possess two mirusvirus-like...
Common fragile sites (CFSs) represent large, highly unstable regions of the human genome. CFS sequences are sensitive to perturbation replication; however, molecular basis for instability at CFSs is poorly understood. We hypothesized that a unique epigenetic pattern may underlie unusual sensitivity replication interference. To examine this hypothesis, we analyzed chromatin modification patterns within six with highest levels breakage, and their surrounding non-fragile (NCFSs). Chromatin most...
Until recently, none of the diverse elements bearing reverse transcriptase (retroids) have been known from Archaea. However, in recently published genomes acetate-utilizing archaeal methanogens, Methanosarcina acetivorans and M. mazei, several open reading frames (ORFs) are annotated as (RT). These annotations led us to characterization a retron 13 retrointrons, including three twintrons, clustered at seven loci genome, four retrointrons two mazei genome. Based on phylogeny RT ORFs, we infer...
Viruses are the most abundant biological entities in world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these recently described mirusviruses, which share some similarities with herpesviruses.
Abstract Thraustochytrids (phylum: Labyrinthulomycota) are nonphotosynthetic marine protists. Some thraustochytrids have crtIBY, a trifunctional fusion gene encoding protein capable of β-carotene biosynthesis from geranylgeranyl pyrophosphate. Here we show that crtIBY is essential in, and encodes the sole pathway for, carotenoid in thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381. We explore evolutionary origins CrtIBY discover closest related domains present small but diverse group...