A5088547356- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Environmental DNA in Biodiversity Studies
- Evolution and Genetic Dynamics
- RNA and protein synthesis mechanisms
- Plant Disease Resistance and Genetics
- Identification and Quantification in Food
- Microbial Community Ecology and Physiology
- Lepidoptera: Biology and Taxonomy
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Forest Insect Ecology and Management
- VLSI and FPGA Design Techniques
- Insect behavior and control techniques
- Vector-Borne Animal Diseases
- Species Distribution and Climate Change
- Insect Resistance and Genetics
- Plant and animal studies
- Advanced Battery Technologies Research
- Insect symbiosis and bacterial influences
- Genetic diversity and population structure
- Plant Virus Research Studies
- Fossil Insects in Amber
- Waste Management and Environmental Impact
- Sustainability and Ecological Systems Analysis
University of Guelph
2014-2025
Swedish University of Agricultural Sciences
2021
Google (United States)
2015
Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) provide an opportunity comprehensive annotation of TEs. Numerous methods exist each class TEs, but their relative performances not been systematically compared. Moreover, a pipeline needed produce non-redundant library TEs species lacking this resource generate whole-genome TE...
Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number ways, including chromosome structure number, repetitive DNA content, the presence introns protein-coding regions. One most differences between prokaryotic is size. Unlike their counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability genome size which not explained by gene number. Genome known to correlate with cell division rate, extension numerous...
The genomes of eukaryotes vary enormously in size, with much this diversity driven by differences the abundances transposable elements (TEs). There is also substantial structural and phylogenetic among TEs, such that they can be classified into distinct classes, superfamilies, families. Possible relationships between TE (and not just abundance) genome size have been investigated to date, though there are reasons expect either a positive or negative correlation. This study compares data from...
Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due lack sequenced voucher specimens by experts. Sometimes a large number sequences are available, but with too errors allow identification. Here, we address this problem for parasitoids Drosophila introducing curated open-access molecular reference database, DROP (Drosophila...
Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation curation, leading to varying levels of success in separation biological variation from experimental error. The 5′ region cytochrome c oxidase subunit I (COI-5P) is most common barcode gene animals, with conserved structure function that allows biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil...
Media attention and the subsequent scientific backlash engendered by claim spokespeople for Encyclopedia of DNA Elements (ENCODE) project that 80% human genome has a biochemical function highlight need clearer understanding concepts in biology. This article provides an overview two major have been developed philosophy science—the causal role concept selected effects concept—and their relevance to ENCODE. Unlike some previous critiques, ENCODE is not considered problematic here because it...
Abstract Background Advancing our knowledge of vector species genomes is a key step in battle against the spread diseases. Biting midges genus Culicoides are vectors arboviruses that significantly affect livestock worldwide. stellifer suspected with wide range distribution North America, for which cryptic diversity has been described. Results With just one specimen C. , we assembled and annotated nuclear mitochondrial genome using ultra-low input DNA PacBio protocol. The assembly 119 Mb...
The mining industry faces significant challenges in restoring mine till to support the recovery of native ecosystems. This study evaluates long‐term effects peat‐based and non‐peat soil amendments on vegetation at a boreal forest site northern Ontario, Canada. Using randomized block design with five replicates, eight amendment treatments were applied: Control, Fertilizer, Oats, Peat, Biosolids, Oats + Peat Biosolids. Four woody species—Jack Pine ( Pinus banksiana ), Prairie Willow Salix...
Flies (Diptera) are an ecologically important group that play a role in agriculture, public health and ecosystem functioning. As researchers continue to investigate this order, it is beneficial link the growing occurrence data biological traits. However, large-scale ecological trait not readily available for fly species. While some databases datasets include data, many relevant traits taxa of interest included. In study, we create dataset containing (habitat diet) species Canada Greenland...
Abstract Background The nuclear genomes of eukaryotes vary enormously in size, with much this variability attributable to differential accumulation transposable elements (TEs). To date, the precise evolutionary and ecological conditions influencing TE remain poorly understood. Most previous attempts identify these have focused on processes occurring at host organism level, whereas we explore a ecology explanation. Results As an alternative (or additional) hypothesis, propose that mechanisms...
Only a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within multigene rDNA. The only rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in freshwater microcrustacean, Daphnia pulex. Here, we present genome-wide analysis of based on recently completed whole genome sequencing project for D. pulex.Phylogenetic recovered from sequence revealed presence four...
Transposable elements (TEs) are among the most abundant components of many eukaryotic genomes. Efforts to explain TE abundance, as well diversity genomes, have led some researchers draw an analogy between genomic and ecological processes. Adopting this perspective, we conducted analysis cow (Bos taurus) genome using techniques developed by community ecologists determine whether environmental factors influence composition. Specifically, each chromosome within Bos taurus was treated a "linear...
<title>Abstract</title> <bold>Background</bold> Advancing our knowledge of vector species genomes is a key step in battle against the spread diseases. Biting midges genus <italic>Culicoides</italic> are vectors arboviruses that significantly affect livestock worldwide. <italic>Culicoides stellifer</italic> suspected with wide range distribution North America, for which cryptic diversity has been described.<bold>Results</bold> With just one specimen <italic>C. stellifer</italic>, we assembled...
Transposable elements play a major role in genome evolution. Their capacity to move and/or multiply the of their host may have profound impacts on phenotypes, and dramatic consequences structure. Hybrid polyploid clones arisen multiple times Daphnia pulex complex are thought reproduce by obligate parthenogenesis. Our study examines evolution DNA transposable element named Pokey D. complex.Portions inserted 28S rRNA genes from various hybrids (diploids polyploids) were sequenced compared...
Abstract Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation curation, leading to varying levels of success in separation biological variation from experimental error. The five-prime region cytochrome c oxidase subunit I (COI-5P) is most common barcode gene animals, with conserved structure function that allows biologically informed error identification. Here, we present coil (...
Abstract Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due lack sequenced voucher specimens by experts. Sometimes a large number sequences are available, but with too errors allow identification. Here we address this problem for parasitoids Drosophila introducing curated open-access molecular reference database, DROP (...
DNA barcoding and metabarcoding are now widely used to advance species discovery biodiversity assessments. High-throughput sequencing (HTS) has expanded the volume scope of these analyses, but elevated error rates introduce noise into sequence records that can inflate estimates biodiversity. Denoising -the separation biological signal from instrument (technical) noise-of barcode metabarcode data currently employs abundance-based methods which do not capitalize on highly conserved structure...