therefore one of these hot spots in the plants'genome becoming repeatedly mutated if a certain phenotype is beneficial at least under some specific conditions.
The study also has unveiled two major evolutionary events that occurred millions of years ago in the kiwifruit genome.
The genome sequence will serve as a valuable resource for kiwifruit research and may facilitate the breeding program for improved fruit quality
when an extensive expansion of genes arose from an entire extra copy of the genome followed by extensive gene loss.
Fei explains The kiwifruit genome has undergone two recent whole-genome duplication events. When genes are duplicated the extra genes can mutate to perform entirely new functions that were not previously present in the organism.
They then compared kiwifruit to the genomes of other representative plant species including tomato rice grape and the mustard weed Arabidopsis.
but genome sequence data critical for its breeding and improvement had never been available. The kiwifruit genome sequence represents the first of a member in the Order ericales
thus providing a valuable resource for comparative genomics and evolutionary studies Fei says. We expect to continue generating genome sequences from other kiwifruit varieties to investigate the genetic diversity of kiwifruit
and elucidate regulatory networks of important biological processes. The sequence is accessible online at the Kiwifruit Genome Database.
Cornell University has television and ISDN radio studios available for media interviews. Story Source: The above story is provided based on materials by Cornell University.
Note: Materials may be edited for content and length. Journal Reference e
#The most widespread ant and its new relative: A revision of the genus Paratrechinalong considered to be one of the most species-rich ant genera latest research has stripped the ant genus Paratrechina down to a single species-Paratrechina longicornis.
They used 250 genetic sequences of the VP1 section of the genome from SAT 2 isolates taken from all over Sub-saharan africa
#Large-scale deep re-sequencing reveals cucumbers evolutionary enigmain a collaborative study published online today in Nature Genetics researchers from the Genome Centre of Chinese Academy of Agricultural Sciences (CAAS) BGI
In 2009 cucumber became the seventh plant to have published its genome sequence 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 3342 accessions worldwide
In addition they also identified 112 putative domestication sweeps in the cucumber genome. These findings provide additional impetus for the use of wild germplasm in future vegetable breeding.
Xin Liu Project Manager from BGI said This study not only generates valuable genomic resource including additional wild reference genome genome-wide variations for further studies
and breeding applications on cucumber but also gave us a better picture about how the cucumber genome evolved during domestication.
and genome wide analysis can be applied on different economic crops for better understanding their evolutionary process
#oethe complex Rddm machinery is composed of several proteins that guide the genome in response to growth developmental and stress signals.
Guan's collaborators had sequenced previously the genome of this family and found that the children with RP carry two copies of a mutation at the dehydrodolichol diphosphate synthase (DHDDS) gene which makes the enzyme that synthesizes organic compounds called dolichols.
Using state-of-the-art genome sequencing and bioinformatics the researchers resolved a longstanding unanswered evolutionary question. Scientists previously thought that ants
of Entomology and Nematology and visiting scientist Ernest K. Lee of the Sackler Institute for Comparative Genomics American Museum of Natural history.
The DNA from several genes of the bat parasites was sequenced at the Museum's Sackler Institute for Comparative Genomics resulting in the most comprehensive evolutionary tree of life for malaria parasites of bats to date.
The newly published study--led by professor Haja Kadarmideen--is the first in the world looking at pig to human comparative genetic mapping to reveal key genes on the human genome that are known to be involved in obesity.
With 30 million pigs produced in Denmark each year genomics scientist at University of Copenhagen Haja Kadarmideen decided to turn this to his advantage with his latest research on people's eating habits surrounding obesity and diabetes.
First kind of study in the worldas pigs are a well-known animal model for studying human obesity because of similar genomes
and eating behaviour observations on all pigs via genome wide association studies to detect eating behaviour genes--a big task equivalent to finding polar bears in a snowstorm says Kadarmideen.
This is the first study in the world looking at pig to human comparative genetic mapping to reveal key genes on the human genome (e g. on chromosomes 6 and 17) that are known to be involved in human obesity and some new genes;
Earlier sequencing of the Calas bacteria genome showed that there were no toxins or enzymes that would destroy plant cell walls
#First look at complete sorghum genome may usher in new uses for food and fuelalthough sorghum lines underwent adaptation to be grown in temperate climates decades ago a University of Illinois researcher said he
I hoping to use the sorghum findings as a launching pad for working with complex genomes of other feedstocks.
Using GBS we're now able to cover the whole genome with some gaps in individual lines he said.
Bt maize and resistance developmentgenetically engineered maize is created by introducing a gene into the plant genome that expresses a toxic protein from a bacterium i e.
and worked with former graduate student Matt Brown and others in the lab of Andrew Roger at Dalhousie University in Halifax Nova scotia Cananda on the genomics and description of this organism
Genomic analyses of single cell organisms that are specifically related to multicellular lineages often provide clues to understanding the molecular mechanisms involved in the evolution of multicellular life.
It's been hard to find regions of the genome that are associated with any kind of behavioral traits in natural populations.
Beyond its findings connecting specific behaviors with genomic regions the study also found that the same regions of the genome appear to control both the stickleback's ability to school as well as the anatomy of its lateral line a system of organs that detect movement
Zhu's team sifted through the bedbug's genome--its complete set of genes--to identify the genes responsible for this pesticide resistance.
It enabled us to perform quickly an analysis that would have taken years in the 1990s--a genome-wide analysis of the insecticide-resistance related genes in bedbugs.
#Whole genome sequencing provides researchers with a better understanding of bovine TB outbreaksthe 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
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.
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
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.
#Scientists sequence genome of high-value grape, seek secrets of wines aromademystifying the chemical processes that create a wine's aroma
and the invaluable potential application of that understanding in winemaking is the new objective of scientists in Uruguay who with European partners also recently sequenced the genome of the high-value Tannat grape from
Sequencing the grape's genome will allow vintners to protect a valuable niche in the world's $300 billion wine industry.
Discovering in more detail the health-promoting compound in the Tannat grape requires us to continue work on its genome.
#Parasitic worm genome uncovers potential drug targetsresearchers have identified five enzymes that are essential to the survival of a parasitic worm that infects livestock worldwide
The team sequenced the genome of Haemonchus contortus or the barber pole worm a well-studied parasitic worm that resides in the gut of sheep and other livestock globally.
This genome could provide a comprehensive understanding of how treatments against parasitic worms work and point to further new treatments and vaccines.
so its genome is a good model to understand how drug resistance develops in this complex group of closely related parasites
#oeour reference genome allows researchers to understand how H. contortus and other worms of this type acquire resistance to a wide range of anthelmintics#the drugs used to treat worm infections#says Dr James Cotton senior author from the Wellcome Trust Sanger Institute.#
#The team sequenced the genome of a strain of H contortus that was susceptible to all major classes of drugs against parasitic worms.
#oethe H. contortus genome provides a rich and essential platform for future research in this and other types of parasitic worms#says Professor Neil Sargison author from the University of Edinburgh Royal (Dick) School of Veterinary Studies.#
Getting to grips with genomes such as that of H. contortus is our best option to tackle the issue of drug resistance
Furthermore sorghum's special features such as a small diploid genome and phenotypic diversity make it an ideal C4 grass model.
By conducting whole-genome sequencing the team obtained the genomic data of 44 sorghum lines to represent all major races of cultivated grain sorghum (Sorghum bicolor) in addition to its progenitors and the allopatric Asian species S. propinquum.
and the first resequenced genome of S. propinquum was presented. The researchers'analyses revealed that sorghum has a strong racial structure
This is another significant breakthrough made by BGI on population genomics research after rice soybean and maize.
Not only has its genome been sequenced it is naturally transformable and able to integrate foreign DNA into its genome by swapping it with similar native strands of DNA.
and his colleagues'efforts to fully sequence the genome--think genetic blueprint--of common wheat. Wheat is the only major food plant not to have sequenced its genome.
The genome of wheat is nearly three times the size of the human genome. Researchers were able to study sequenced segments of the common wheat genome
and look for a naturally occurring resistance gene. Gill said without the sequenced segments finding the PHS gene would have been impossible.
Story Source: The above story is provided based on materials by Kansas State university. Note: Materials may be edited for content and length.
or'fancy'poultry breeders to identify at fine resolution the exact location of the mutation in the genome in blue egg laying chicken.
and diversity of species. It's quite remarkable--retroviruses are considered generally to integrate at random locations in the genome
--Males on the added-sugar diet produced 25 percent fewer offspring than control males as determined by genetic analysis of the offspring.
The researchers who conducted the genetic analysis of strains of Staphylococcus aureus known as CC97 say these strains developed resistance to methicillin after they crossed over into humans around forty years ago.
The researchers sequenced the genomes of 43 different CC97 isolates from humans cattle and other animals and plotted their genetic relationships in a phylogenetic tree.
They then searched through the subjects'genomes for areas of the DNA that differed between people who could smell a given compound
This approach--known as a genome-wide association study--is used widely to identify genetic differences. The researchers led by Sara Jaeger Jeremy Mcrae
#Full genome map of oil palm indicates way to raise yields and protect rainforest: Single gene identified
The discovery the product of a multiyear effort to provide a high-quality full genome map of the oil palm plant
The discovery was made by researchers at the MPOB in conjunction with scientists at St louis-based Orion Genomics.
and a rallying point for activists in recent years says Robert A. Martienssen Ph d. scientific cofounder of Orion Genomics who is also a professor of plant genetics at CSHL.
The Malaysian government strongly supported the genome sequencing project for the nation's most important crop.
What the full genome sequences revealthe discovery of Shell occurs in the context of a broader effort to map the genomes of both the African
and colleagues Mike Martin and Tom Gilbert from the University of Copenhagen compared the genomes
In the areas of the genome that today control virulence we found little similarity with historical strains suggesting that the pathogen has evolved in response to human actions like breeding more disease-resistant potatoes.
Knowing how the pathogen genome has changed over time will help modern-day farmers better manage the disease.
The research was carried out in collaboration with the University of East Anglia and The Genome Analysis Centre on Norwich Research Park.
A genome-wide analysis of an uropathogenic E coli revealed that expression of the gene that encodes for the bacteria's flagellar filament was decreased in the presence of cranberry PACS.
By employing next generation DNA sequencing of genomes isolated from single cells great strides are being made in the monumental task of systematically bringing to light
In an international collaboration led by the U s. Department of energy Joint Genome Institute (DOE JGI) the most recent findings from exploring microbial dark matter were published online July 14 2013 in the journal Nature.
and characterizing single genomes from complex environmental samples of millions of cells to provide a profound leap of understanding the microbial evolution on our planet.
and identify 201 distinct genomes which then could be aligned to 28 major previously uncharted branches of the tree of life.
So we have only recently become aware of their roles in various ecosystems through cultivation-independent methods such as metagenomics and single-cell genomics.
Genome sequencing of the rest of the genomes of most of these lineages is however proceeding much more slowly.
Microbial genome representation in the databases is skewed quite said Chris Rinke DOE JGI postdoctoral fellow and first author of the study.
More than three-quarters of all sequenced genomes fall into three taxonomic groups or phyla but there are over 60 phyla we know of.
The 201 genomes provided solid reference points anchors for phylogeny--the lineage history of organisms as they change over time.
Our single-cell genomes gave us a glimpse into the evolutionary relationships between uncultivated organisms--insights that extend beyond the single locus resolution of the 16s rrna tree
and the path ahead in environmental genomics is similarly daunting. There is still a staggering amount of diversity to explore Woyke said.
To try to capture 50 percent of just the currently known phylogenetic diversity we would have to sequence 20000 more genomes
http://www. jgi. doe. gov/programs/GEBA/)and closely articulates with other international efforts such as the Microbial Earth Project which aims to generate a comprehensive genome catalog of all archaeal and bacterial
The above story is provided based on materials by DOE/Joint Genome Institute. Note: Materials may be edited for content and length.
and enhance fertility in the cattle industry said Wansheng Liu associate professor of animal genomics Penn State.
fellows in animal science at Penn State and the late Ernest Retzel National Center for Genome Resources.
COMPLEMENTARY DNA is a form of DNA that is synthesized from a MESSENGER RNA templatethe bovine genome sequence was published in 2009 said Liu.
As that genome sequence was from a female the findings of the bovine Y chromosome study is a significant contribution to the completion of the bovine--male and female--genome project.
or economically smart says Busov who studies the functional genomics of plant development. Only 30 percent is used by the plants.
There are tens of thousands of genes in the poplar genome. The challenge--and it was a big one--was how to determine which genes are doing
Researchers spent nearly four years trying to identify the location of the Sr35 gene in the wheat genome which contains nearly two times more genetic information than the human genome Once the researchers narrowed the list of candidate genes they used two complementary approaches to find the Sr35 gene.
#Comparing genomes of wild and domestic tomatoyou say tomato I say comparative transcriptomics. Researchers in the U s. Europe and Japan have produced the first comparison of both the DNA sequences and
and has unexpected widespread effects across the whole genome. Maloof and colleagues studied the domestic tomato Solanum lycopersicum and wild relatives S. pennellii S. habrochaites and S. pimpinellifolium.
Comparison of the plants'genomes shows the effects of evolutionary bottlenecks Maloof noted--for example at the original domestication in South america
Genomics has tracked fast previous gene-by-gene analyses that took us years to complete she said.
The researchers used the Brown University Genomics Core Facility in their work. Story Source: The above story is provided based on materials by Brown University.
Building on Aylward's previous study of these gardens the researchers relied on genome sequencing provided by the U s. Department of energy Joint Genome Institute (JGI)
In addition to sequencing the genome of Leucoagaricus gongylophorous the fungus cultivated by leaf-cutting ants the researchers looked at the genomes of entire living garden communities.
After sequencing the L. gongylophorous genome the researchers noticed that the fungus seemed to be doing the lion's share of cellulose degradation with its specialized enzymes.
Using a technique known as Chip-Seq the researchers exposed Arabidopsis to ethylene and identified all the regions of the plant genome that bound to EIN3
They then used genome-wide mrna sequencing to identify those targeted genes whose expression actually changes due to interaction with EIN3.
#Genome hints at markers for higher-producing, better-tasting chocolatethe freshly sequenced genome of the most commonly cultivated cacao plant in the world is revealed in the open access journal Genome Biology this week.
Researchers have utilised high quality DNA sequences to demonstrate the usefulness and quality of the sequence to identify genetic markers that can lead to higher yielding cocoa plants that still produce better tasting cocoa.
and colleagues sequenced the genome of the Matina cacao variety then used genetic analyses and comparisons with other varieties to highlight a gene involved in pod colour variation.
Although the genome sequence of the Criollo cacao variety was reported two years ago it's genetically quite distinct
Since the publication of the genome sequence researchers have been working to identify genetic markers that can produce more productive cocoa plants for farmers
The genome sequence research is a part of an overall effort to use traditional breeding techniques to develop planting materials that farmers can use to be more productive.
#Norway spruce genome sequenced: Largest ever to be mappedswedish scientists have mapped the gene sequence of Norway spruce (the Christmas tree)--a species with huge economic and ecological importance
--and that is the largest genome to have ever been mapped. The genome is complex and seven times larger than that of humans.
The results have been published in the journal Nature. In addition to its scientific interest this new knowledge has immense importance to the forestry industry in many countries.
why is the spruce genome still seven times larger than ours? According to the study an explanation is caused genome obesity by extensive repetitive DNA sequences
which have accumulated for several hundred million years of evolutionary history. Other plant and animal species have efficient mechanisms to eliminate such repetitive DNA
By sequencing and analysing the largest genome in the world so far we have shown that Scilifelab has both technical and scientific capacity for research at the highest international level concludes Joakim Lundeberg.
which was developed initially for human genome and disease research. In this way Kobayashi and Shimizu identified 98 genes that are associated with the flowering of the plant-including the genes Sbft and Sbsvp
It is the first time scientists have decoded the genome of a plant pathogen and its plant host from dried herbarium samples.
The international team came to these conclusions after deciphering the entire genomes of 11 historical samples of Phytophthora infestans from potato leaves collected over more than 50 years.
Because of the remarkable DNA quality and quantity in the herbarium samples the research team could evaluate the entire genome of Phytophthora infestans and its host the potato within just a few weeks.
#Genome sequence of Tibetan antelope sheds new light on high-altitude adaptationhow can the Tibetan antelope live at elevations of 4000-5000m on the Qinghai-Tibetan Plateau?
Using next-gen sequencing technology they have decoded the genome of Tibetan antelope and studied the underlying genetic mechanism of high-altitude adaptations.
Qingle Cai Project manager from BGI said The completed genome sequence of the Tibetan antelope provides a more complete blueprint for researchers to study the genetic mechanisms of highland adaptation.
The genomics revolution has given them mountains of DNA data that they can sift through to reconstruct the evolutionary history that connects all living beings.
and analyzed more than 1000 genes--approximately 20 percent of the entire yeast genome--from each of 23 yeast species. He quickly realized that the histories of the 1000-plus genes were all slightly different from each other as well as different from the genealogy constructed from a simultaneous analysis of all the
The genomics revolution has given them mountains of DNA data that they can sift through to reconstruct the evolutionary history that connects all living beings.
and analyzed more than 1000 genes--approximately 20 percent of the entire yeast genome--from each of 23 yeast species. He quickly realized that the histories of the 1000-plus genes were all slightly different from each other as well as different from the genealogy constructed from a simultaneous analysis of all the
Dr Chatterjee's research uses an approach called TILLING (Targeting Induced Lesions In The Genome) an established non-GM method for creating
The complete genome of three H7n9 isolates from a chicken pigeon and environmental sample was sequenced
Genetic analysis of these isolates revealed high homology across all eight gene segments. The analysis of these novel H7n9 influenza virus isolates showed that that the six internal genes were derived from avian H9n2 viruses
#Carnivorous plant throws out junk DNAGENES make up about 2 percent of the human genome. The rest consists of a genetic material known as noncoding DNA
The clues lie in the genome of the carnivorous bladderwort plant Utricularia gibba. The U. gibba genome is the smallest ever to be sequenced from a complex multicellular plant.
The researchers who sequenced it say that 97 percent of the genome consists of genes--bits of DNA that code for proteins--and small pieces of DNA that control those genes.
It appears that the plant has been busy deleting noncoding junk DNA from its genetic material over many generations the scientists say.
what makes up plant genomes. What that says is that you can have a perfectly good multicellular plant with lots of different cells organs tissue types
(or cut) and paste themselves into new locations of the genome. Scientists have spent countless hours puzzling over why noncoding DNA exists--and in such copious amounts.
The new U. gibba genome shows that having a bunch of noncoding DNA is not crucial for complex life.
The U. gibba genome has about 80 million DNA base pairs--a miniscule number compared to other complex plants
which have much larger genomes of about 490 and 780 million base pairs respectively. The small size of the U. gibba genome is even more surprising given the fact that the species has undergone three complete genome doublings
since its evolutionary lineage split from that of tomato. That is at three distinct times in the course of its evolution the bladderwort's genome doubled in size with offspring receiving two full copies of the species'entire genome.
This surprisingly rich history of duplication paired with the current small size of the bladderwort genome is further evidence that the plant has been prolific at deleting nonessential DNA
but at the same time maintaining a functional set of genes similar to those of other plant species says Herrera-Estrella.
#Sacred lotus genome sequence enlightens scientiststhe sacred lotus (Nelumbo nucifera) is a symbol of spiritual purity and longevity. Its seeds can survive up to 1300 years its petals
Now researchers report in the journal Genome Biology that they have sequenced the lotus genome and the results offer insight into the heart of some of its mysteries.
and so lacks a signature triplication of the genome seen in most other members of this family said University of Illinois plant biology
Whole-genome duplications--the doubling tripling (or more) of an organism's entire genetic endowment--are important events in plant evolution Ming said.
if they're harmful they disappear from the genome. Many agricultural crops benefit from genome duplications including banana papaya strawberry sugarcane watermelon
and wheat said Robert Vanburen a graduate student in Ming's lab and collaborator on the study.
Although it lacks the 100 million-year-old triplication of its genome seen in most other eudicots sacred lotus experienced a separate whole-genome duplication about 65 million years ago the researchers found.
The study published online ahead of print last month in the journal Genome Biology. This approach is known as gene expression profiling
Determining which of the 46 P450 genes in the honey bee genome are used to metabolize constituents of their natural diet and
Her team showed that p-coumaric acid turns on not only P450 genes but representatives of every other type of detoxification gene in the genome.
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