First peanut genome sequenced

The International Peanut Genome Initiative — a group of multinational crop geneticists who have been working in tandem for the last several years — has successfully sequenced the peanut’s genome.Scott Jackson, director of the University of Georgia Center for Applied Genetic Technologies in the College of Agricultural and Environmental Sciences, serves as chair of the International Peanut Genome Initiative, or IPGI.The new peanut genome sequence will be available to researchers and plant breeders across the globe to aid in the breeding of more productive and more resilient peanut varieties.Peanut, known scientifically as Arachis hypogaea and also called groundnut, is important both commercially and nutritionally. While the oil- and protein-rich legume is seen as a cash crop in the developed world, it remains a valuable sustenance crop in developing nations.”The peanut crop is important in the United States, but it’s very important for developing nations as well,” Jackson said. “In many areas, it is a primary calorie source for families and a cash crop for farmers.”Globally, farmers tend about 24 million hectares of peanuts each year and produce about 40 million metric tons.”Improving peanut varieties to be more drought-, insect- and disease-resistant can help farmers in developed nations produce more peanuts with fewer pesticides and other chemicals and help farmers in developing nations feed their families and build more secure livelihoods,” said plant geneticist Rajeev Varshney of the International Crops Research Institute for Semi-Arid Tropics in India, who serves on the IPGI.The effort to sequence the peanut genome has been underway for several years. While peanuts were successfully bred for intensive cultivation for thousands of years, relatively little was known about the legume’s genetic structure because of its complexity, according to Peggy Ozias-Akins, a plant geneticist on the UGA Tifton campus who also works with the IPGI and is director of the UGA Institute of Plant Breeding, Genetics and Genomics.”Until now, we’ve bred peanuts relatively blindly, as compared to other crops,” said IPGI plant geneticist David Bertioli of the Universidade de Braslia. “We’ve had less information to work with than we do with many crops, which have been more thoroughly researched and understood.”The peanut in fields today is the result of a natural cross between two wild species, Arachis duranensis and Arachis ipaensis, which occurred in north Argentina between 4,000 and 6,000 years ago. Because its ancestors were two different species, today’s peanut is a polyploid, meaning the species can carry two separate genomes, designated A and B subgenomes.To map the peanut’s structure, researchers sequenced the genomes of the two ancestral parents because together they represent the cultivated peanut. The sequences provide researchers access to 96 percent of all peanut genes in their genomic context, providing the molecular map needed to more quickly breed drought- and disease-resistant, lower-input and higher-yielding varieties of peanuts.The two ancestor wild species had been collected in nature, conserved in germplasm banks and then used by the IPGI to better understand the peanut genome. The genomes of the two ancestor species provide excellent models for the genome of the cultivated peanut. A. duranenis serves as a model for the A subgenome of the cultivated peanut while A. …

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Contagious yawning a mystery: May not be linked to empathy after all

While previous studies have suggested a connection between contagious yawning and empathy, new research from the Duke Center for Human Genome Variation finds that contagious yawning may decrease with age and is not strongly related to variables like empathy, tiredness and energy levels.The study, published March 14 in the journal PLOS ONE, is the most comprehensive look at factors influencing contagious yawning to date.The researchers said a better understanding of the biology involved in contagious yawning could ultimately shed light on illnesses such as schizophrenia or autism.”The lack of association in our study between contagious yawning and empathy suggests that contagious yawning is not simply a product of one’s capacity for empathy,” said study author Elizabeth Cirulli, Ph.D., assistant professor of medicine at the Center for Human Genome Variation at Duke University School of Medicine.Contagious yawning is a well-documented phenomenon that occurs only in humans and chimpanzees in response to hearing, seeing or thinking about yawning. It differs from spontaneous yawning, which occurs when someone is bored or tired. Spontaneous yawning is first observed in the womb, while contagious yawning does not begin until early childhood.Why certain individuals are more susceptible to contagious yawning remains poorly understood. Previous research, including neuroimaging studies, has shown a relationship between contagious yawning and empathy, or the ability to recognize or understand another’s emotions. Other studies have shown correlations between contagious yawning and intelligence or time of day.Interestingly, people with autism or schizophrenia, both of which involve impaired social skills, demonstrate less contagious yawning despite still yawning spontaneously. A deeper understanding of contagious yawning could lead to insights on these diseases and the general biological functioning of humans.The current study aimed to better define how certain factors affect someone’s susceptibility to contagious yawning. The researchers recruited 328 healthy volunteers, who completed cognitive testing, a demographic survey, and a comprehensive questionnaire that included measures of empathy, energy levels and sleepiness.The participants then watched a three-minute video of people yawning, and recorded the number of times they yawned while watching the video.The researchers found that certain individuals were less susceptible to contagious yawns than others, with participants yawning between zero and 15 times during the video. Of the 328 people studied, 222 contagiously yawned at least once. When verified across multiple testing sessions, the number of yawns was consistent, demonstrating that contagious yawning is a very stable trait.In contrast to previous studies, the researchers did not find a strong connection between contagious yawning and empathy, intelligence or time of day. The only independent factor that significantly influenced contagious yawning was age: as age increased, participants were less likely to yawn. …

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‘Severe reduction’ in killer whale numbers during last Ice Age

Whole genome sequencing has revealed a global fall in the numbers of killer whales during the last Ice Age, at a time when ocean productivity may have been widely reduced, according to researchers at Durham University. The scientists studied the DNA sequences of killer whale communities across the world.They found a severe decline in whale numbers leading to a bottleneck and consequent loss of genetic diversity approximately 40,000 years ago when large parts of Earth were covered in ice.The only exception to this was found in a killer whale population off the coast of South Africa that retained high variations in genetic diversity.As greater genetic diversity indicates larger population size, the researchers believe the South African community of killer whales escaped the bottleneck faced by other communities.They said an important factor could have been the Bengeula upwelling system — which delivers nutrient rich cold water to the oceans off South Africa — remaining stable despite the last glacial period.This nutrient rich water would have been able to sustain the supplies of fish and dolphins that killer whales in this part of the world feed on.The researchers added that other major upwelling systems around the world — the California current off North America; Humboldt off South America; and the Canary current off the coast of North Africa — were either disrupted or collapsed altogether during the last glacial or Pleistocene periods (40,000 to 2.5 million years ago).This could potentially have reduced the food supply to killer whales in these areas, leading to the fall in their numbers.Further research looking at the genetic diversity of the ocean’s other top predators, such as sharks, might potentially suggest a negative impact on their numbers too, the researchers suggested.Such a finding could support concerns about the potential impact changes in climate could have on ocean ecosystems in future, the researchers added.The reseach, funded by the Natural Environment Research Council in the UK, is published in the journal Molecular Biology and Evolution.During earlier glacial periods, killer whale populations were likely to have been stable in size, the researchers said.While it was likely that other factors affecting killer whale populations were “overlapping and complex,” the researchers ruled out hunting as an effect on the bottleneck in populations, as hunting by early man could not have happened on a sufficient enough scale to promote the global decline in killer whale numbers during that period.Corresponding author Professor Rus Hoelzel, in the School of Biological and Biomedical Sciences, said: “Killer whales have a broad world-wide distribution, rivalling that of humans. At the same time, they have very low levels of genetic diversity.”Our data suggest that a severe reduction in population size during the coldest period of the last ice age could help explain this low diversity, and that it could have been an event affecting populations around the world.”However, a global event is hard to explain, because regional modern-day killer whale populations seem quite isolated from each other. What could have affected multiple populations from around the world all at the same time?”The uniquely high levels of diversity we found for the population off South Africa suggest a possible explanation. These whales live in an environment that has been highly productive and stable for at least the last million years, while some data suggest that ocean productivity may have been reduced during the last glacial period elsewhere in the world.”If this is the case, then further research may suggest an impact on other ocean top predators during this time. It would also support concerns about the potential for climate disruptions to impact ocean ecosystems in future.”Story Source:The above story is based on materials provided by Durham University. Note: Materials may be edited for content and length.

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Large-scale deep re-sequencing reveals cucumber’s evolutionary enigma

Oct. 20, 2013 — In a collaborative study published online today in Nature Genetics, researchers from the Genome Centre of Chinese Academy of Agricultural Sciences (CAAS), BGI, and other institutes present a cucumber genomic variation map that includes about 3.6 million variants revealed by deep resequencing of 115 cucumbers worldwide. This work provides new insights for understanding the genetic basis of domestication and diversity of this important crop, and provides guidance for breeders to harness genetic variation for crop improvement.Cucumber is a major vegetable crop consumed worldwide as well as a model system for sex determination and plant vascular biology. In 2009, cucumber became the seventh plant to have its genome sequence published, following the well-studied model plant Arabidopsis thaliana, the poplar tree, grapevine, papaya, and the crops rice and sorghum. More efforts have been put into cucumber genomics research since then.As a part of these efforts, researchers from CAAS and BGI re-sequenced 115 cucumber lines sampled from 3,342 accessions worldwide, and also conducted de novo sequencing on a wild cucumber. In total, they detected more than 3.3 million SNPs, over 0.33 million small insertion and deletions (indels), and 594 presence-absence variations (PAVs), and then constructed a comprehensive variation map of cucumber.Furthermore, researchers did a suite of model-based analyses of population structure and phylogenetic reconstruction. The results indicated that the three cultivated groups (Eurasian, East Asian, and Xishuangbanna) each are monophyletic and genetically quite homogeneous, but the Indian group shows clear evidence of substructure and genetic heterogeneity. Their further analysis also provide evidence on the ancestral status of the Indian group, which holds great potential for introducing new alleles into the cultivated gene pool.To understand the population bottlenecks during domestication, researchers made a comparison analysis between vegetable and grain food crops. The comparison result indicated that the three vegetable crops (cucumber, watermelon, and tomato) probably underwent narrower bottleneck events during domestication than the grain food crops (rice, maize, and soybean). In addition, they also identified 112 putative domestication sweeps in the cucumber genome. …

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Whole genome sequencing provides researchers with a better understanding of bovine TB outbreaks

Sep. 3, 2013 — The use of whole bacterial genome sequencing will allow scientists to inexpensively track how bovine tuberculosis (TB) is transmitted from farm to farm, according to research presented this week at the Society of General Microbiology Autumn Conference.Bovine TB is primarily a disease of cattle, caused by the bacterium Mycobacterium bovis. The disease is hugely expensive, costing the Government over £91 million in England in 2010/11.Researchers from the University of Glasgow, working in collaboration with the Agri-Food and Biosciences Institute and the Department of Agriculture and Rural Development, Northern Ireland, sequenced the genomes of 147 M. bovis samples, collected over a decade of outbreaks in Northern Ireland. By combining the genomic sequences of the bacteria with information about when and where the sample was isolated, in addition to data on the movement of cattle from farm to farm, the researchers were able to build a detailed forensic map of bovine TB spread.The results showed that, even on a scale of few kilometres, M. bovis samples from neighbouring farms were more closely genetically related than geographically distant farms that had had cattle moved between them. This finding confirms that, while long distance spread via cattle movements plays a role, local transmission mechanisms appear to drive the spread of the disease, although the researchers are unable to determine what these are at the present time.Hannah Trewby, who is presenting this work says, “The inclusion of whole genome information in our data will give us unprecedented insight into how bovine TB spreads, and will help us to develop better control methods for the disease.”The role of infected wild badgers in spreading bovine TB remains controversial. This work will help to clarify the role that badgers may have in spreading the disease and continue to build a sound scientific evidence base on which control measures can be built.Professor Rowland Kao, the Principle Investigator of the project, explains, “Our results suggests that the establishment and local persistence of the pathogen in cattle has a distinct spatial signature — we believe that explaining this signature is the key to quantifying the role that badgers play in the persistence of bovine TB in Britain and Ireland. While we do not yet have sufficient data to be definitive, it is clear that whole genome sequencing of the bacterium will play an important part in solving this puzzle. Given the extensive collection of samples already collected from cattle and badgers, we are optimistic that this approach will help accumulating the right scientific evidence over the coming years to tackle this important problem.”

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First full genome sequencing for autism: Promise for future diagnosis, prevention and treatment

July 11, 2013 — A collaborative formed by Autism Speaks, the world’s leading autism science and advocacy organization, has found full genome sequencing examining the entire DNA code of individuals with autism spectrum disorder (ASD) and their family members to provide the definitive look at the wide ranging genetic variations associated with ASD. The study published online today in American Journal of Human Genetics, reports on full genome sequencing on 32 unrelated Canadian individuals with autism and their families, participants in the Autism Speaks Autism Genetic Resource Exchange (AGRE). The results include both inherited as well as spontaneous or de novo, genetic alterations found in one half of the affected families sequenced.This dramatic finding of genetic risk variants associated with clinical manifestation of ASD or accompanying symptoms in 50 percent of the participants tested is promising, as current diagnostic technology has only been able to determine a genetic basis in about 20 percent of individuals with ASD tested. The large proportion of families identified with genetic alterations of concern is in part due to the comprehensive and uniform ability to examine regions of the genome possible with whole genome sequencing missed in other lower resolution genome scanning approaches.”From diagnosis to treatment to prevention, whole genome sequencing efforts like these hold the potential to fundamentally transform the future of medical care for people with autism,” stated Autism Speaks Chief Science Officer and study co-author Robert Ring, Ph.D.The study identified genetic variations associated with risk for ASD including de novo, X-linked and other inherited DNA lesions in four genes not previously recognized for ASD; nine genes previously determined to be associated with ASD risk; and eight candidate ASD risk genes. Some families had a combination of genes involved. In addition, risk alterations were found in genes associated with fragile X or related syndromes (CAPRIN1 and AFF2), social-cognitive deficits (VIP), epilepsy (SCN2A and KCNQ2) as well as NRXN1 and CHD7, which causes ASD-associated CHARGE syndrome.”Whole genome sequencing offers the ultimate tool to advance the understanding of the genetic architecture of autism,” added lead author Dr. Stephen Scherer, senior scientist and director of the Centre for Applied Genomics at The Hospital for Sick Children (SickKids) and director of the McLaughlin Centre at the University of Toronto. “In the future, results from whole genome sequencing could highlight potential molecular targets for pharmacological intervention, and pave the way for individualized therapy in autism. It will also allow for earlier diagnosis of some forms of autism, particularly among siblings of children with autism where recurrence is approximately 18 per cent.”This $1 million collaboration of Autism Speaks, SickKids, BGI and Duke University piloted Autism Speaks’ initiative to generate the world’s largest library of sequenced genomes of individuals with ASD announced in late 2011. “As we continue to test more individuals and their family members from the AGRE cohort, we expect to discover and study additional genetic variants associated with autism. …

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A 700,000-year-old horse gets its genome sequenced

June 26, 2013 — It is nothing short of a world record in DNA research that scientists at the Centre for GeoGenetics at the Natural History Museum of Denmark (University of Copenhagen) have hit. They have sequenced the so far oldest genome from a prehistoric creature. They have done so by sequencing and analyzing short pieces of DNA molecules preserved in bone-remnants from a horse that had been kept frozen for the last 700,000 years in the permafrost of Yukon, Canada. By tracking the genomic changes that transformed prehistoric wild horses into domestic breeds, the researchers have revealed the genetic make-up of modern horses with unprecedented details.The spectacular results are now published in the international scientific journal Nature.DNA molecules can survive in fossils well after an organism dies. Not as whole chromosomes, but as short pieces that could be assembled back together, like a puzzle. Sometimes enough molecules survive so that the full genome sequence of extinct species could be resurrected and over the last years, the full genome sequence of a few ancient humans and archaic hominins has been characterized. But so far, none dated back to before 70,000 years.Now Dr. Ludovic Orlando and Professor Eske Willerslev from the Centre for GeoGenetics have beaten this DNA-record by about 10 times. Thereby the two researchers — in collaboration with Danish and international colleagues — have been able to track major genomic changes over the last 700.000 years of evolution of the horse lineage.First, by comparing the genome in the 700,000 year old horse with the genome of a 43,000 year old horse, six present day horses and the donkey the researchers could estimate how fast mutations accumulate through time and calibrate a genome-wide mutation rate. This revealed that the last common ancestor of all modern equids was living about 4.0-4.5 million years ago. …

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Self-fertilizing plants contribute to their own demise

June 10, 2013 — Many plants are self-fertilizing, meaning they act as both mother and father to their own seeds. This strategy — known as selfing — guarantees reproduction but, over time, leads to reduced diversity and the accumulation of harmful mutations. A new study published in the scientific journal Nature Genetics shows that these negative consequences are apparent across a selfing plant’s genome, and can arise more rapidly than previously thought.In the study, an international consortium led by Stephen Wright in the Department of Ecology and Evolutionary Biology at the University of Toronto sequenced the genome of the plant species Capsella rubella, commonly known as Red Shepherd’s Purse. They found clear evidence that harmful mutations were accumulating over the species’ relatively short existence.”The results underscore the long-term advantages of outcrossing, which is the practice of mating between individuals, that gives us the wide array of beautiful flowers,” said Wright. “Selfing is a good short-term strategy but over long timescales may lead to extinction.”Red Shepherd’s Purse is a very young species that has been self-fertilizing for less than 200,000 years. It is therefore especially well-suited for studying the early effects of self-fertilization. By contrasting Red Shepherd’s Purse with the outcrossing species that gave rise to it, the researchers showed that self-fertilization has already left traces across the genome of Red Shepherd’s Purse.”Harmful mutations are always happening,” said Wright. “In crops, they could reduce yield just as harmful mutations in humans can cause disease. The mutations we were looking at are changes in the DNA that change the protein sequence and structure.”The findings represent a major breakthrough in the study of self-fertilization.”It is expected that harmful mutations should accumulate in selfing species, but it has been difficult to support this claim in the absence of large-scale genomic data,” says lead author Tanja Slotte, a past member of Wright’s research team and now a researcher at Uppsala University. “The results help to explain why ancient self-fertilizing lineages are rare, and support the long-standing hypothesis that the process is an evolutionary dead-end and leads to extinction.”The researchers said that with many crops known to be self-fertilizing, the study highlights the importance of preserving crop genetic variation to avoid losses in yield due to mutations accumulating.

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