Articles tagged with Genome Sequencing
Genomics holds key to understanding ecological and evolutionary processes as Next-Generation Sequencing (NGS) technique is underutilised in invasion biology. NGS can transform our understanding of why non-native species adapt and thrive in new environments.
A team at the DOE JGI has developed ProDeGe, a computational protocol for quick and automated removal of contaminant sequences from draft genomes. The tool classifies sequences as 'clean' or 'contaminant' and runs at a rate of 0.30 CPU core hours per megabase of sequence.
Researchers found that modern toothed whales have inherited defunct copies of the Mx1 and Mx2 genes, profoundly altering their immune systems. The study aims to preserve these cetaceans as they face extensive die-offs.
A study on social amoebae reveals that genes for cooperation and cheating have reached a stalemate, with increased genetic diversity near the social genes suggesting a prolonged stalemate. The findings suggest that cheating can be successful only when it is rare, and fail when it becomes so numerous it pushes out cooperators.
A new study at Cornell University identifies a gene duplication causing cucumbers to produce only female flowers, leading to increased yields in greenhouse production. The research builds on previous work and shows that the genetic variation affects over 1,600 genes in the cucumber genome.
Researchers observed genome-editing proteins using a combination of sliding and hopping to navigate the vast genome. The discovery provides insight into how these proteins can be engineered for improved efficiency and reduced off-target binding, potentially leading to more effective gene therapies.
A new online tool called TB-Profiler can predict genetic resistance to tuberculosis drugs in a matter of minutes, improving the likelihood of cure for patients with drug-resistant TB. The tool uses genome sequence data to analyze and interpret resistance to 11 drugs used for treatment.
Researchers at the University of Michigan have identified the genetic blueprint of a bacteria that produces ET-743, a compound extracted from a marine invertebrate. This discovery expands understanding of the microbe and could lead to lab-grown production of the cancer-fighting drug.
A team of researchers used DNA from frozen and dried specimens to analyze a dataset of 39 genomes, defining seven new suborders and the 'trunk' of the Agaricales tree. The study provides a framework for testing hypotheses of mushroom evolution and highlights the importance of fungaria as scientific resources.
Researchers find single protein, nuclear Fibroblast Growth Factor Receptor 1 (nFGFR1), orchestrates gene expression in embryo development. This discovery has potential to enhance understanding and treatment of cancers and congenital diseases.
Two bumblebee species' genomes have been sequenced, providing insights into their behavior and responses to environmental threats. The research highlights the importance of understanding bumblebee biology to address declining populations and ensure their conservation.
The study analyzed ancient mammoth genomes to understand population dynamics and genetic diversity. The results showed low genetic variation and inbreeding, indicating a small population size. The research provides insight into the woolly mammoth's evolutionary history and potential reasons for their extinction.
Researchers at the University of New Hampshire have discovered a new method to detect Vibrio parahaemolyticus, a bacterium that has contaminated oyster beds and sickened consumers in the Northeast. The detection platform uses genome sequencing and analysis to identify specific genes found only in the invasive strain.
Researchers found a common genetic link between child prodigies and autism, specifically on chromosome 1. The study identified shared genetic markers in five prodigies and their family members with autism, suggesting a potential genetic component to exceptional abilities.
A detailed genetic road map of Upland cotton has been created to improve crop yields, reduce water usage, and minimize pesticide applications. The new sequence will enable researchers to better understand the interactions between genes that determine fiber production and oil content in seeds.
Researchers analyzed whole genomes of seven mountain gorillas, revealing genetic adaptations to small populations and a surprisingly low number of harmful genetic variations. This new understanding provides valuable insight into how apes adapt genetically to living in small populations.
Researchers aim to create the first complete genome sequence for dogwoods, enabling plant breeders to develop new varieties with improved traits. Citizen scientists will collect data on flowering patterns, flower color, and susceptibility to diseases.
Research suggests that inbreeding has genetically benefited mountain gorillas by eliminating deleterious variations, contributing to their survival. This discovery challenges the assumption that low genetic diversity makes these animals more susceptible to environmental changes and diseases.
Researchers used longer-read sequencing technology to reconstruct microbial communities, revealing over 400 previously unknown species and improving understanding of environmental processes.
Researchers developed a strategy to identify and genotype SNPs in complex cotton genomes using genotyping-by-sequencing. The approach employs Stacks software to enrich for orthologous DNA fragments, allowing for detection of polymorphisms between individuals.
Scientists at Kansas State University have developed a haplotype map of wheat that provides a detailed description of genetic differences in worldwide wheat lines. This study enables the precise mapping of genes and increases the selection of best lines for breeding, leading to faster release times for new varieties.
Researchers at Virginia Tech have developed a more efficient method to edit the mosquito genome using CRISPR-Cas9, enabling faster studies of disease-causing genes. This breakthrough may aid in developing novel strategies to control mosquito-borne diseases and reduce their impact on human health.
A recent study found that MRSA can persist in households for years, spreading from person to person and evolving genetically. The bacteria can be transmitted through household members, especially those with skin infections, and can even acquire extraneous DNA over time.
A research group including a UF expert has located and narrowed down genes that play a role in Type 1 diabetes. The findings will help predict who might develop the disease and how to prevent it, leading to more effective treatments.
The genome of Ancylostoma ceylanicum, a nematode that infects up to 400 million people worldwide, has been sequenced. The study identified genes active during infection and potential drug targets. The findings could lead to new treatments for parasitic hookworms.
Scientists capture first detailed images of ultra-small bacteria, average volume of 0.009 cubic microns, with unique internal structure and metabolism. The discovery sheds light on the role of microbes in climate, food and water supply, and ecosystems.
An international team analyzed 49 fungal genomes, revealing that key genome adaptation enabling symbiosis evolved independently in numerous lines of fungi. The study provides crucial information on how symbiosis between fungi and trees evolved, enabling scientists to improve prediction of reaction to environmental modifications.
A team of researchers analyzed 49 fungal genomes, revealing that mycorrhizal fungi evolved independently in many fungal lineages. The study also found that up to 40% of symbiosis-induced genes were restricted to a single mycorrhizal species.
Researchers have discovered that Alu RNAs form complexes with specific proteins, regulating ribosome activity and contributing to cell immunity. This process helps cells adapt to stress and defend against viruses, such as HIV and hepatitis C.
A University of Michigan-led study has found that penguins have lost the genes for the umami and bitter tastes, as well as a sweeter taste, which is puzzling given their diet of fish. The loss of these tastes likely occurred due to ancient climate-cooling events in Antarctica.
The Eastern tiger swallowtail's genome has been sequenced, revealing mutations in proteins responsible for its unique circadian rhythm and stinky substance used to scare off predators. This breakthrough opens the door for more insect genome sequencing projects at an affordable price.
A large-scale study confirms BGI's NIFTY test accuracy for trisomy 21, 18, and 13 in nearly 147,000 pregnancies, showing high sensitivity and specificity. The study also found that high-quality NIPT service can be achieved with strict protocols and standards.
Scientists have identified a fast-growing cyanobacterial strain, Synechococcus elongatus UTEX 2973, which grows at over 50% per hour. The strain's genome is remarkably similar to another widely studied cyanobacterium, and its genetic determinants of rapid growth may hold the key to unlocking new biotech applications.
Researchers identified a set of gene loci responsible for thermostatic regulation in Chinese pigs, highlighting the importance of introgression in adaptation. The study found that adaptations to cold and hot environments were triggered by interspecies introgression, providing insights into evolutionary history and adaptation mechanisms.
A recent study of 340 whole genomes from 85 families with two children affected by autism found that most siblings share different autism-linked genes. The research, led by Stephen Scherer, provides new insights into the complex genetic underpinnings of autism and suggests that each child with autism is unique.
Researchers have developed a detailed positional cloning protocol to locate genes within the large and complex maize genome. This technique allows for the identification of genetic markers linked to specific traits, enabling precise localization of candidate regions until the gene is identified.
A new pipeline combines multiple gene-finding tools to identify genetic markers for phylogenetic study from limited genomic data. The approach, MAKER2, was used to develop loci useful for phylogenetic study in the flowering plant genus Penstemon.
A nationwide project has revealed 12 new genetic causes of developmental disorders, including intellectual disabilities and congenital heart defects. The Deciphering Developmental Disorders (DDD) project sequenced DNA from over 1,000 children to identify the genes responsible for their conditions.
A novel orthomyxovirus, Wellfleet Bay virus (WFBV), has been linked to cyclic mass mortality events in eider ducks on Cape Cod. The study found that WFBV is likely tick-borne and contributes to the deaths, but other factors such as parasitic worms and stress may also play a role.
A recent study using whole genome sequencing of ancient and modern horses has identified 125 candidate genes involved in physical and behavioral traits. The research also highlights the 'cost of domestication', including increased levels of inbreeding and deleterious mutations in domesticated horses.
Scientists sequenced the genomes of 48 bird species to reveal a new family tree for birds and understand their rapid evolution after the mass extinction. The study resolves fundamental questions about bird diversity and adaptations.
The study provides insights into how penguins have adapted to the cold Antarctic environment through complex biological systems. The researchers identified genes related to beta-keratins, lipid metabolism, and forelimb evolution that are unique to penguins.
An international team has sequenced and compared full genomes of 48 bird species to resolve the timing and relationships of modern birds. The study suggests that only a few bird lineages survived the mass extinction event, giving rise to the 10,000 Neoaves species that comprise 95% of all bird species.
Researchers reconstructed a partial genome of the common ancestor of crocodiles, birds, and dinosaurs, showing an exceptionally slow rate of genome evolution in crocodilians. The team found that population sizes declined sharply during the last ice age, with alligator populations experiencing a continuous decline.
A team of scientists completed the largest whole genome study of a single class of animals to date, sequencing and comparing full genomes of 48 bird species. The study resolves early branches in the tree of life of modern birds, providing new insights into their evolutionary history and adaptation to different lifestyles.
A global collaboration has sequenced and compared full genomes of 48 bird species, revealing the origins of feathers, flight, song, and sex chromosomes. The study resolves key debates on bird family trees and evolutionary timelines.
A team of scientists has developed a detailed map of the bird genome, shedding light on their evolution and diversification. The study reveals that birds have lost hundreds of genes compared to humans, leading to unique traits such as lighter skeletons and respiratory systems.
A four-year project studied the genome sequence of 48 bird species, shedding light on how they evolved and adapted. The research revealed new candidate gene associations with vocal learning, skeletal development, and plumage for mating display.
A large international group of scientists has published the results of a first-ever look at the genome of dozens of common birds, revealing how modern birds evolved after the mass extinction that wiped out dinosaurs. The research also provides insight into how songbirds learn to sing and brain connection with human speech.
Researchers at Scripps Translational Science Institute are using DNA to investigate sudden deaths in San Diego County, aiming to identify genetic mechanisms and develop preventative screening programs. The study hopes to provide closure for families and potentially save lives.
Researchers at Texas Biomed are using new genomic tools to analyze individual malaria parasites, allowing for more effective treatment and vaccine design.
A new study published in Genome Research tracked the spread of MRSA in a hospital with high transmission rates using genome sequencing. The team identified multiple distinct clades of MRSA and confirmed numerous transmission events between patients, highlighting the importance of infection control measures such as hand-washing.
Researchers used genome sequencing to track MRSA spread in a Thai hospital with high transmission rates, revealing multiple distinct clades and transmission events between patients and staff. The study highlights the need for improved hand hygiene practices and measures of within-host bacterial diversity.
A study published in Genetics in Medicine found that most new parents are interested in genomic sequencing for their newborns. The study surveyed 514 parents within 48 hours of birth and found that 82.7% were somewhat, very, or extremely interested in the testing.
Researchers have discovered that electric eels use a Taser-like system to locate and incapacitate their prey. The eel emits high-frequency pulses that cause muscle contractions, temporarily paralyzing the prey within three to four milliseconds.
A new study published in Science Translational Medicine confirms the benefits of genomic medicine in diagnosing children with neurologic disorders. Genomic testing has ended diagnostic odysseys for families, leading to changes in clinical impressions and management, while also reducing wait times by over six years.
The genome of Strigamia maritima, a blind Scottish centipede, has been sequenced, providing insights into the genetic basis of centipede biology and the diversification of arthropods. The study reveals that these animals have lost genes encoding light receptors and circadian rhythm, suggesting alternative detection mechanisms.
Researchers used whole genome sequencing to track and control an Acinetobacter baumannii outbreak at Queen Elizabeth Hospital Birmingham, identifying transmission hotspots and implementing new decontamination protocols. The study demonstrates the effectiveness of real-time genome sequencing in controlling hospital outbreaks.
Researchers discovered contaminating bacterial and viral sequences in animal and plant genomes, highlighting the importance of careful screening. The study found unexpected DNA mixtures, including cow and sheep DNA in a supposedly finished genome, emphasizing the need for rigorous data analysis.
The house fly genome project has uncovered genes responsible for male traits that evolve exceptionally fast and are gained and lost from the genome at a high rate. These findings hold promise for developing pest control strategies that do not rely on chemical pesticides, by targeting sex determination systems.