A5012916005- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Insect-Plant Interactions and Control
- Plant Virus Research Studies
- Insect symbiosis and bacterial influences
- Bat Biology and Ecology Studies
- Advanced biosensing and bioanalysis techniques
- Evolution and Genetic Dynamics
- CRISPR and Genetic Engineering
- Plant Disease Resistance and Genetics
- RNA and protein synthesis mechanisms
- Protist diversity and phylogeny
- Forensic and Genetic Research
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Community Ecology and Physiology
- Study of Mite Species
- Molecular Biology Techniques and Applications
- Insect and Arachnid Ecology and Behavior
- Cytomegalovirus and herpesvirus research
University of Utah
2014-2022
The University of Texas at Arlington
2010
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate somatic genome. Here, we present a complete sequence assembly analyze multiple features its structure relationship genome, shedding light on mechanisms rearrangement as well evolutionary history this remarkable germline/soma differentiation. Our results strengthen notion that complex, dynamic, ongoing interplay between mobile elements host...
Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 Myr evolution radically different lifestyles. We present a 152-Mb draft assembly M. genome: Larger than that its favored prey, Tetranychus urticae, but considerably smaller those many other chelicerates, enabling extremely contiguous complete to be built-the best arachnid...
Abstract Helitron transposons capture and mobilize gene fragments in eukaryotes, but experimental evidence for their transposition is lacking the absence of an isolated active element. Here we reconstruct Helraiser , ancient element from bat genome, use this transposon as tool to unravel mechanism transposition. A hairpin close 3′-end functions a terminator. However, can be bypassed by transposase, resulting transduction flanking sequences new genomic locations. generates covalently closed...
Germline mutation rates in humans have been estimated for a variety of types, including single-nucleotide and large structural variants. Here, we directly measure the germline retrotransposition rate three active retrotransposon elements: L1, Alu , SVA. We used tools calling mobile element insertions (MEIs) (MELT, RUFUS, TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. identified 26 de novo MEIs 437 births....
Human endogenous retroviruses (HERVs) occupy a substantial fraction of the genome and impact cellular function with both beneficial deleterious consequences. The vast majority HERV sequences descend from ancient retroviral families no longer capable infection or genomic propagation. In fact, most are represented by full-length proviruses but solitary long terminal repeats (solo LTRs) that arose via non-allelic recombination events between two LTRs proviral insertion. Because LTR-LTR may...
Horizontal transfer (HT) of genes is known to be an important mechanism genetic innovation, especially in prokaryotes. The impact HT transposable elements (TEs), however, has only recently begun receive widespread attention and may significant due their mutagenic potential, inherent mobility, abundance. Helitrons, also as rolling-circle transposons, are a distinctive subclass TE with unique transposition mechanism. Here, we describe the first evidence for repeated four different families...
Rolling-circle transposons (Helitrons) are a newly discovered group of mobile DNA widespread in plant and invertebrate genomes but limited to the bat family Vespertilionidae among mammals. Little is known about long-term impact Helitron activity because where has been extensively studied predominated by young families. Here, we report comprehensive catalog vetted Helitrons from 7× Myotis lucifugus genome assembly. To estimate timing transposition, scored presence/absence across related...
The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It a worldwide pest and can potently suppress host’s natural resistance. We sequenced its genome, first of an eriophyoid, explored whether there are genomic features associated with mite’s minute size lifestyle. At only 32.5 Mb, genome yet reported for any arthropod and, reminiscent microbial eukaryotes, exceptionally streamlined. has few transposable elements, tiny intergenic regions, remarkably...
The Drosophila INterspersed Elements-1 (DINE-1/INE1) transposable elements (TEs) are the most abundant component of melanogaster genome and have been associated with functional gene duplications. DINE-1 TEs do not encode any proteins (non-autonomous) thus moved by autonomous partners. identity partners has a mystery. They allied to Helitrons (rolling-circle transposons), MITEs (DNA non-LTR retrotransposons different authors.We report multiple lines bioinformatic evidence that illustrate...
Ongoing retrotransposition of Alu, LINE-1, and SINE-VNTR-Alu elements generates diversity variation among human populations. Previous analyses investigating the population genetics mobile element insertions (MEIs) have been limited by ascertainment bias or relatively small numbers populations low sequencing coverage. Here, we use 296 individuals representing 142 global from Simons Genome Diversity Project (SGDP) to discover characterize MEI deeply sequenced whole-genome data. We report 5,742...
Alu retrotransposons account for more than 10% of the human genome, and insertions these elements create structural variants segregating in populations. Such polymorphic Alus are powerful markers to understand population structure, they represent that can greatly impact genome function, including gene expression. Accurate genotyping other mobile has been challenging. Indeed, we found genotypes previously called 1000 Genomes Project sometimes erroneous, which poses significant problems...
Abstract Germline mutation rates in humans have been estimated for a variety of types, including single nucleotide and large structural variants. Here we directly measure the germline retrotransposition rate three active retrotransposon elements: L1, Alu, SVA. We utilized tools calling Mobile Element Insertions (MEIs) (MELT, RUFUS, TranSurVeyor) on blood-derived whole genome sequence (WGS) data from 603 CEPH individuals, comprising 33 three-generation pedigrees. identified 27 de novo MEIs...
ABSTRACT Human endogenous retroviruses (HERVs) occupy a substantial fraction of the genome and impact cellular function with both beneficial deleterious consequences. The vast majority HERV sequences descend from ancient retroviral families no longer capable infection or genomic propagation. In fact, most are represented by full-length proviruses but solitary long terminal repeats (solo LTRs) that arose via non-allelic recombination events between two LTRs proviral insertion. Because LTR-LTR...
ABSTRACT Alu retrotransposons account for more than 10% of the human genome, and insertions these elements create structural variants segregating in populations. Such polymorphic are powerful markers to understand population structure, they represent that can greatly impact genome function, including gene expression. Accurate genotyping other mobile has been challenging. Indeed, we found genotypes previously called 1000 Genomes Project sometimes erroneous, which poses significant problems...