A5045012422- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Machine Learning in Bioinformatics
- Animal Genetics and Reproduction
- Animal Behavior and Reproduction
- Genetic and phenotypic traits in livestock
- Nuclear Structure and Function
- Biochemical Analysis and Sensing Techniques
- Congenital heart defects research
- Insect Resistance and Genetics
- Trace Elements in Health
- Research on Leishmaniasis Studies
- melanin and skin pigmentation
- Genomics and Chromatin Dynamics
- Fish Ecology and Management Studies
- Insect behavior and control techniques
- Histone Deacetylase Inhibitors Research
- MicroRNA in disease regulation
- Genetic Mapping and Diversity in Plants and Animals
- Protease and Inhibitor Mechanisms
- Silk-based biomaterials and applications
- Plant Reproductive Biology
- Evolution and Genetic Dynamics
University of Kentucky
2015-2024
Virginia Tech
2014
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed new assembly of the germline genome that integrates several complementary data sets. Analysis this highly contiguous (chromosome-scale) shows both chromosomal and whole-genome duplications have played significant roles in evolution ancestral genomes, including chromosomes carry six HOX clusters. also contains hundred genes are reproducibly...
Abstract As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution 1–3 . Here we investigate complex history, timing functional role genome-wide duplications 4–7 programmed DNA elimination 8,9 in vertebrates light chromosome-scale genome sequence for brown hagfish Eptatretus atami Combining evidence from syntenic phylogenetic analyses, establish comprehensive picture evolution, including an auto-tetraploidization (1R V )...
The axolotl ( Ambystoma mexicanum ) provides critical models for studying regeneration, evolution, and development. However, its large genome (∼32 Gb) presents a formidable barrier to genetic analyses. Recent efforts have yielded assemblies consisting of thousands unordered scaffolds that resolve gene structures, but do not yet permit large-scale analyses structure function. We adapted an established mapping approach leverage dense SNP typing information the first time assemble into 14...
Abstract Vertebrates exhibit substantial diversity in genome size and some of the largest genomes exist species that uniquely inform diverse areas basic biomedical research. For example, salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies regeneration, development evolution, yet its ~10× larger than human genome. As part hierarchical approach toward improving resources species, we generated 600 Gb shotgun sequence data developed methods sequencing individual...
The molecular genetic toolkit of the Mexican axolotl, a classic model organism, has matured to point where it is now possible identify genes for mutant phenotypes. We used positional cloning-candidate gene approach bases two historic axolotl pigment phenotypes: white and albino. White (d/d) mutants have defects in cell morphogenesis differentiation, whereas albino (a/a) lack melanin. identified transcriptional defect endothelin 3 (edn3), encoding peptide factor that promotes migration...
Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with expansion is unclear, and how acute changes regulation, as during axolotl limb regeneration, occur the context of a vast has remained riddle. Here, we describe chromosome-scale assembly giant, 32 Gb genome. Hi-C contact data revealed scaling properties interphase mitotic chromosome organization. Analysis yielded understanding evolution large, syntenic...
Programmed DNA loss is a gene silencing mechanism that employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven challenging due to high content repeats duplications corresponding lack highly accurate contiguous assemblies for regions. Here, we present an improved assembly sea lamprey (Petromyzon marinus) genome was generated...
Abstract As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution. Here, we investigate complex history, timing, functional role genome-wide duplications in vertebrates light chromosome-scale genome brown hagfish Eptatretus atami . Using robust (paralogon-based) phylogenetic methods, confirm monophyly cyclostomes, document an auto-tetraploidization (1R V ) that predated origin crown group ∼517 Mya, establish timing...
High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., islands divergence) suppress recombination to allow evolution local adaptations despite high flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis traits suggests it may be locally adapted. We addressed whether could influence adaptation lamprey. Using two new whole genome assemblies...
Abstract In the Mexican axolotl ( Ambystoma mexicanum ), sex is determined by a single Mendelian factor, yet its chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess sex-determining locus. As are theorized to differentiate rapidly, species with undifferentiated provide opportunity reconstruct early events in chromosome evolution. Whole genome sequencing 48 salamanders, targeted and situ hybridization were used identify homomorphic carries an A...
The sea lamprey (Petromyzon marinus) is one of few vertebrate species known to reproducibly eliminate large fractions its genome during normal embryonic development. This germline-specific DNA lost in the form fragments, including entire chromosomes, and available evidence suggests that elimination acts as a permanent silencing mechanism prevents somatic expression specific subset “germline” genes. However, reconstruction eliminated regions has proven be challenging due complexity karyotype....
The great diversity of color patterns observed among amphibians is largely explained by the differentiation relatively few pigment cell types during development. Mexican axolotls present a variety phenotypes that span continuum from leucistic to highly melanistic. melanoid axolotl Mendelian variant characterized large numbers melanophores, proportionally fewer xanthophores, and no iridophores. Early studies were influential in developing single-origin hypothesis development, wherein it has...
Phlebotomine sand flies employ an elaborate system of pheromone communication wherein males produce pheromones that attract other to leks (thus acting as aggregation pheromone) and females the lekking (sex pheromone). In addition, type produced varies among populations. Despite numerous studies on fly chemical communication, little is known their chemosensory genome. Chemoreceptors interact with chemicals in organism’s environment elicit essential behaviors such identification suitable mates...
Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships gene flow between populations of this enigmatic species within To help inform management, we assembled draft G. australis genome completed the first comprehensive population genomics analysis pouched Zealand using targeted sequencing (Cyt-b COI)...
The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with mitotic karyotype, linkage maps or genome assembly. We 9 LBCs using RNAseq to identify actively transcribed genes 13 BAC (bacterial artificial clone) probes containing pieces active genes. Using read coverage analysis find candidate centromere sequences, we developed a...
The suffix array and Burrows-Wheeler Transform are critical index structures in next generation sequence analysis. construction of such for mammalian-sized genomes can take thousands seconds (i.e. tens minutes). Its is complicated by computational overheads that coming from irregular or complex memory-access patterns. This paper rigorously characterizes the execution profile SA-IS algorithm order to guide its optimization. resulting optimized SA-IS, which we refer as sais-opt, outperforms...
ABSTRACT The axolotl ( Ambystoma mexicanum ) provides critical models for studying regeneration, evolution and development. However, its large genome (~32 gigabases) presents a formidable barrier to genetic analyses. Recent efforts have yielded assemblies consisting of thousands unordered scaffolds that resolve gene structures, but do not yet permit scale analyses structure function. We adapted an established mapping approach leverage dense SNP typing information the first time assemble into...
New patterns of gene expression are enacted and regulated during tissue regeneration. Histone deacetylases (HDACs) regulate by removing acetylated lysine residues from histones proteins that function directly or indirectly in transcriptional regulation. Previously we showed romidepsin, an FDA-approved HDAC inhibitor, potently blocks axolotl embryo tail regeneration altering initial responses to injury. Here, report on the concentration-dependent effect romidepsin transcription outcome,...
<title>Abstract</title> Several dozen Mendelian mutants have been discovered in axolotl (<italic>Ambystoma mexicanum</italic>) populations, including several that affect pigmentation. For recessive described the scientific literature and genes for three of these identified. Here we describe genetically dissect <italic>copper</italic>, a mutant with an albino-like phenotype known only from pet trade. We performed cross segregating <italic>copper</italic> wildtype color phenotypes used bulked...
Recent efforts to assemble and analyze the Ambystoma mexicanum genome have dramatically improved potential develop molecular tools pursue genome-wide analyses of genetic variation.To better resolve distribution origins variation with A mexicanum, we compared DNA sequence data for two laboratory one tigrinum identify 702 million high confidence polymorphisms distributed across 32 Gb genome. While wild-caught was generally more polymorphic in a sense, several multi-megabase regions were...
ABSTRACT In the Mexican axolotl ( Ambystoma mexicanum ) sex is known to be determined by a single Mendelian factor, yet chromosomes of this model salamander do not exhibit morphological differentiation that typical many vertebrate taxa possess sex-determining locus. Differentiated are thought evolve rapidly in context gene and, therefore, undifferentiated provide an exceptional opportunity reconstruct early events chromosome evolution. Whole sequencing, whole genome resequencing (48...
ABSTRACT The sea lamprey ( Petromyzon marinus ) is one of few vertebrate species that known to reproducibly eliminate large fractions its genome during normal embryonic development. In lamprey, elimination events are initiated at the 6 th cleavage and result in loss ∼20% an embryo’s genomic DNA from essentially all somatic cell lineages (these same sequences retained germline). This germline-specific lost form fragments, including entire chromosomes, available evidence suggests acts as a...
The Hadoop framework has gained significant attention from the scientific community due to its applicability large-scale data analysis in many areas. This often involves multiple stages of processing, which turn, constitutes a workflow. While some workflow are mandatory, others subject type be done. In addition, may possess dependencies between that must enforced, and it exhibit varying levels sensitivity. resources needed for such can range laptop in-house clusters (or private cloud) public...