Articles tagged with Genome Sequencing
A recent study published in Nature Genetics has shed light on the genetic diversity of European flint maize, revealing distinct differences between lines. The research highlights the importance of sequencing the entire pangenome of a species to fully understand its genetics.
Scientists charted SARS-CoV-2 transmission in Brazil, revealing that non-pharmaceutical interventions were insufficient to control the spread. The study found over 100 internationally-sourced virus introductions from Europe and estimates that more than 75% of Brazilian strains fell under three clades introduced during a specific period.
Researchers sequenced over 1,000 viral genomes to identify 35 clusters of genetically identical viruses involving 159 patients. The study also showed a decline in patient admissions with COVID-19 and a rapid decrease in asymptomatic healthcare workers testing positive.
Researchers have identified 32 genes associated with cannibalistic eating behavior in mandarin fish, which feed exclusively on living juvenile fish of their own species. This behavior leads to high mortality rates and economic losses in aquaculture.
Researchers mapped non-coding genome in maize during early developmental window to understand inflorescence differentiation. The study provides a roadmap for adjusting gene expression precisely to improve grain yield and ear traits.
Researchers at OIST Graduate University have identified previously unknown sections of DNA that are silenced by epigenetic regulation in plant cells. The study reveals a crucial role of these sites in suppressing the activity of disruptive 'jumping genes' called transposons, which can threaten genome integrity.
Researchers sequenced ancient DNA from a 9,500-year-old dog, revealing that modern sledge dogs share a common origin with the ancient breed. The study also found genetic adaptations similar to those of polar bears and Arctic people.
Researchers sequenced and compared the genomes of 100 different tomato varieties, identifying over 230,000 structural variants that underpin the vast diversity among tomatoes. These genomic variations affect flavor, yield, and other traits, providing breeders with new power to improve tomato properties.
A Neandertal fossil found in Chagyrskaya Cave suggests that the species may have lived in small groups of less than 60 individuals. The study's findings also suggest a unique role for the striatum region of the brain in Neandertals, potentially influencing cognition and behavior.
Scientists have identified long-concealed genetic mutations in tomatoes using a new technique called long-read sequencing. The analysis reveals that these mutations can alter key characteristics such as flavor and weight. By studying the impact of these mutations, researchers hope to create new tomato varieties with improved traits.
Researchers at Johns Hopkins University have discovered over 230,000 DNA differences across 100 tomato varieties, allowing for rapid identification and evaluation of genetic mutations. This breakthrough enables breeders to create new crops with desirable traits, such as increased size and flavor.
The bitter gourd's genome shows unusual domestication patterns, revealing its divergence from wild strains 6000 years ago. The study provides insights into the evolution of this summer vegetable, which has been prized for its health benefits and medicinal properties.
A new platform enables researchers to track changes in the SARS-CoV-2 virus' genetic structure, providing insights for vaccine design and combating the pandemic. The tool, developed by UHN AI scientist Dr. Bo Wang, analyzes nasal swab samples and compares them to global data, generating results in under 15 minutes.
Data scientists create new statistical models and visualization software to understand COVID-19 pandemic. They integrate diverse factors like airline traffic patterns, socioeconomic data, and weather conditions into a single platform.
The study mapped bacterial resistance to last-line antibiotics in the Philippines, enabling better tracking of resistant bacteria and controlling outbreaks. The genomic capacity has enhanced national infection control efforts and improved understanding of antimicrobial resistance at local, national, and international scales.
Researchers created a way to track the spread of Agrobacterium, a bacterium causing crown-gall disease affecting over 100 plant species, worth $16 billion annually. The method can also be applied to human and animal diseases and foodborne outbreaks.
A new study of 84 patients reveals that the first COVID-19 cases in New York City were mainly introduced through untracked transmission from Europe and the US, with limited evidence suggesting a potential Asian origin. The findings also highlight the importance of early and broad testing to identify community transmission clusters.
A collaboration between Otago University and ESR has received a grant to sequence all of New Zealand's positive COVID-19 cases. The team will create a web browser application to track the virus's evolution, epidemiology, and transmission chains in NZ.
MetaviralSPAdes is a new assembler for virus genomes, enabling biologists to reconstruct complete viral genomes from metagenome sequencing results. This tool tackles the challenge of identifying and stitching together viral sequences from thousands of bacterial genomes.
Researchers from St Petersburg University have deciphered the Intoshia variabili gene, revealing a genome size of 15.3 million base pairs and 5,120 genes, including orphan genes unique to orthonectids. The study provides genetic evidence that orthonectids belong to Annelida, a type of animal with no real intraorganism parasites.
Researchers create true diploid genomes from a single individual using an innovative genome assembly strategy, applicable to cattle breeds and potentially other species including humans. The technique, called trio binning, disentangles maternal and paternal genomes, revealing important genetic differences between breeds.
Researchers at ASU have found a unique SARS-CoV-2 mutation with 81 deleted letters, similar to one from the 2003 SARS outbreak. The discovery was made using next-generation sequencing technology and has attracted global interest from scientists, including the World Health Organization.
A team of HKUST researchers has analyzed the genome sequence of the scaly-foot snail, a deep-sea creature with armor-like scales. The study reveals that the snail's unique morphology is largely determined by genes already present in other mollusks, such as squid and pearl oysters.
The study found that wild and domesticated cotton genomes are remarkably similar, with less diversity between species than within humans or cells. This limits the ability to introduce beneficial traits like disease resistance through gene mining.
The study reveals that despite its widespread distribution, the cotton genome is remarkably stable, with only minor differences between species. This knowledge can inform breeding practices and improve crop yields.
Researchers at UC Davis cleared a major obstacle to using CRISPR-Cas9 gene drive technology to control mosquito-borne diseases. A study found that 90% of protein-coding genes in mosquito populations have suitable target sequences for the gene drive, making it effective against disease-causing viruses and parasites.
Researchers have identified extremely rare variants that affect the boundaries of a 3D genome structure called topologically associated domains (TADs) in people with schizophrenia. These variants may contribute to dysregulation of gene expression, leading to the development of the disease.
A research team led by Jonathan Losos will sequence the genomes of 200 species of Anolis lizards and introduce genetic changes using CRISPR to test their effects on adaptation. The study aims to identify genes responsible for evolutionary adaptation in Central American lizards.
A study found that 54.8% of COVID-19 cases imported to Brazil by March 5 came from Italy, while 24.9% traveled from Italy to São Paulo. The virus spread quickly in Brazil, with the first cases reported in São Paulo City, and sustained community transmission now prevails.
Scientists have mapped the genome of the German shepherd, providing a reference for future studies of diseases that afflict this breed. The completed genome will enable early detection and development of breeding programs to reduce genetic diseases like hip dysplasia.
Scientists from University of Würzburg successfully sequenced sturgeon genome, showing genetic material has changed little over 250 million years. The study sheds light on the ancestry of vertebrates and provides important insights for protecting species.
Researchers highlight the challenges of identifying new pathogens, citing a review that explores cutting-edge genetics methods. The study discusses the promise of next-generation sequencing but notes its high cost and complexity. Despite these limitations, experts predict the technology's growing potential in healthcare.
Researchers at the University of São Paulo, Adolfo Lutz Institute, and Oxford University have published the complete genome sequence of SARS-CoV-2 in Brazil. The study reveals differences between the genomes of viruses isolated from two Brazilian patients, suggesting internal transmission is occurring in European countries.
Research in China suggests a strong association between avian influenza and the country's live poultry trade network. Movement of virus lineages was often associated with major evolutionary divergences and was much more likely to occur within regional trade communities.
Researchers are developing new algorithms to quickly compare genetic data from viruses, bacteria, and other organisms to identify pathogenic genes. This project, Pangaia, aims to make computer-assisted pangenomics faster and more user-friendly for biomedicine applications.
A recent study found that the monkeyface prickleback, a unique fish species, has an efficient digestive system capable of breaking down plant material. This discovery holds promise for developing new, sustainable sources of protein for human consumption and could be an important alternative to traditional livestock farming.
Scientists from China's top research institutes discovered the novel coronavirus responsible for the Wuhan pneumonia epidemic through next-generation sequencing and bronchoalveolar lavage fluid samples. The virus is 99.8-99.9% similar among all patients' samples, closely related to bat SARS-like CoVs.
The Christen Lab has successfully produced a fully artificial genome, the Caulobacter ethensis-2.0, with over 580 functional genes. This breakthrough demonstrates the promise of synthetic biology in producing designer genomes for industrial and health applications.
A recent study analyzing over 200 mumps virus genomes provides insights into the US outbreaks, revealing a dominant strain responsible for many cases. The research also demonstrates the value of high-quality genomic data in public health surveillance and suggests future efforts should incorporate whole genome sequencing.
Researchers at New York University have sequenced the genome of two basmati rice varieties, including one with improved drought tolerance and resistance to bacterial disease. The study provides insights into the evolutionary history of basmati rice and its unique genetic traits.
A recent study by Dr. Mark Chapman optimizes protocols for identifying simple sequence repeats (SSRs) in genomic and transcriptomic data, increasing efficiency in microsatellite discovery. The research found that small assemblies of two million read pairs can generate sufficient markers for basic population genetic studies.
Plant scientists combined second- and third-generation genomic technologies to create a more accurate and efficient method for resolving plant pathogen genomes. This breakthrough reduces the time required to sequence genome data from one-and-a-half years to just nine days, while lowering costs from $2 million to $1,000.
A recent study led by JGI uncovered a broad diversity of large and giant viruses belonging to the NCLDV supergroup. The genomes of these viruses are significantly larger than previously known, with some being up to 100 times the size of typical viruses.
The new tool, 'Kmasker plants', enables researchers to identify repetitive sequences in plant genomes and assign them to positions. This allows for the rapid analysis of complex genomes and can help identify sequence candidate regions with agronomic importance.
Researchers successfully sequenced and annotated the giant squid's genome, providing a unique opportunity to explore its evolutionary history. The genomic draft reveals insights into the giant squid's size, growth rate, and age.
African swine fever virus can replicate in various pig cells and has a relatively conservative genome. Whole-genome sequencing is crucial for understanding the transmission route of ASFV. Nanopore sequencing technology proved more efficient than traditional next-generation sequencing methods in obtaining viral genomes.
Researchers integrated genomic and transcriptomic sequencing to classify AML and MDS into distinct biologic subgroups. This new understanding may lead to personalized treatment approaches, improving patient outcomes.
A new study has discovered a way to identify disease-resistance genes in cacao trees, which could lead to the development of more sustainable farming systems and improved crop yields. The method uses genome sequencing to rapidly identify resistant genotypes and provides insights into the genetic diversity of cacao trees.
Researchers have developed a new tool that can analyze 1.4 million genetic sequences simultaneously, allowing them to study species relationships on a larger scale than before. This technology has the potential to reconstruct how life has evolved over hundreds of millions of years and unlock secrets about the code of life.
A team from the Earlham Institute is exploring the chemical diversity of UK plants to identify new medicines, including those found in foxgloves and willow trees. The project aims to understand how plants produce complex chemicals and unlock new pathways for biomanufacturing.
Researchers have developed a new technique to study flagellate organisms, tiny eukaryotic creatures that provide clues about the emergence of complex life on Earth. By analyzing mitochondrial DNA and exploiting unique protein structures, scientists can fill in the gaps of the eukaryotic puzzle and better understand the history of life.
A study on valley oak found that populations grow faster at cooler temperatures, suggesting the need for new conservation methods to mitigate warming temperature effects. Selecting seed sources based on genotype may alleviate declining growth rates.
Researchers tracked genomic changes in hybrid orangethroat and rainbow darters, finding regions with genetic divergence contributing to reproductive incompatibility. These differences likely disrupt cell division and alter gene expression, driving the evolution of distinct traits.
The Devil Worm's genome reveals an unusually large number of heat-shock proteins and extra copies of cellular survival genes, suggesting its evolutionary adaptation to lethal environmental conditions. The discovery may provide lessons for humans on how to adapt to a warming climate, with potential applications in understanding life bey...
Researchers at Karolinska Institutet developed a new analytical tool to diagnose intellectual disability through whole-genome sequencing, discovering point mutations, structural chromosome aberrations, and expansions. This method was found to be more effective than traditional gene dose array tests in identifying genetic causes.
An international team of researchers has created a comprehensive watermelon genome resource to help plant breeders increase the domestic fruit's quality and ability to thrive during an era of climate change. The resource includes genetic insights into wild watermelon species and their potential for disease resistance, paving the way fo...
Researchers analyzed genome assemblies of 20 butterfly species and found a high amount of gene flow among them, even between distantly related species. This challenges the idea that species are fixed entities and suggests hybridization as a key process in biological diversity.
A new study reveals that chromosomal abnormalities in couples with recurrent miscarriage can be detected using low-pass genome sequencing, increasing the number of couples identified at risk. This technique may help couples conceive through in vitro fertilization and personalize their treatment.
New studies reveal a broader range of genetic code deviations than previously thought, particularly among green algae. The research suggests that these changes may have driven the evolution of unique mitochondrial genome organizations.
Researchers developed a novel genomic analysis method for classifying Yersinia strains, revealing unexpected biodiversity and new species. The tool enables accurate identification of pathogenicity, guiding patient monitoring and public health initiatives.