Category Archives: Genome

Research published today in BMC Biology finds that whole genome duplication, a process in which an organisms entire genome duplicates, occurred in the lineage leading to spiders but not their distant arachnid relatives, ticks and mites. Here to discuss this research and whole genome duplication in the ancestors of vertebrates and other chelicerates is author of the study, Alistair P. McGregor.

Alistair P. McGregor 31 Jul 2017

Luka Miles

It is thought that gene duplication plays an important role in generating new genetic material for the evolutionary diversification of species. Gene duplication can be caused by several mechanisms and in the extreme case two copies of all of the genes in a genome can be generated by whole genome duplication (WGD).

In a recent study published in BMC Biology, my colleagues and I analyzed the genome of the common house spider Parasteatoda tepidariorum and we have found evidence for a WGD in the lineage leading to spiders.

This event was likely shared with scorpions and probably other arachnopulmonates like whip-scorpions and whip spiders, but not with more distantly related arachnids such as ticks and mites. This suggests that the approximately 45,000 extant species of arachnopulmonates evolved from a polyploid ancestor over 400 million years ago.

Our study also suggests that this WGD in arachnids was likely independent of WGD in another group of chelicerates, the horseshoe crabs. Our findings thus offer an exciting opportunity to discover more about the outcomes of WGD in terms of gene content and regulation, and how such events may contribute to animal diversification.

In the ancestor of vertebrates there were two rounds of WGD and these events may have led to the diversification of these animals through the retention and utilization of duplicated genes. For example, while most animals contain a single cluster of Hox genes, vertebrates, like ourselves, have four Hox clusters and these additional genes play many important roles in development. However, genes can be retained or lost for many reasons after WGD events, including random mutation, recombination and dosage effects.

A better understanding of the patterns of gene retention and loss after WGD and identification of commonalities, as well as potentially the genes that may underlie evolutionary innovation, requires the study of independent events. This comparison, however, suffers from the fact that only a few examples of WGD have been described in animals to date.

Our identification of a WGD in arachnids, consequently, provides a much-needed new data point for understanding the general and lineage specific impact of WGD events.

Our identification of a WGD in arachnids, consequently, provides a much-needed new data point for understanding the general and lineage specific impact of WGD events. The duplicated genes that have been retained in both spiders and scorpions represent many that encode proteins with important roles in development, including two copies of most Hox genes arranged in two (nearly) complete clusters.

Furthermore the paralogs of each of the spider Hox genes differ in their timing and spatial expression during embryogenesis suggesting that some of the new copies perform novel functions with respect to the single copy ancestral gene. Therefore our study reveals an intriguing parallel between the outcomes of WGD in arachnids and vertebrates.

Interestingly, our study and previous work also reveals a high rate of retention of duplicated microRNAs. These genes are thought to modulate the expression levels of their target genes and they have perhaps been retained in high numbers after WGD to buffer the dosage effects of targeted duplicated protein coding genes, rather than contributing to the emergence of novel traits. Indeed, a possible outcome of gene duplication is developmental systems drift, whereby different genes and interactions can be used to achieve the same phenotypic outcome, but this remains to be investigated systematically.

Cave Whip Spiders Damon variegates

Wikimedia commons

More fully understanding the consequences WGD event in arachnids requires the analysis of additional arachnid genomes to determine exactly when this event occurred and which lineages were affected. For example, it would be interesting to explore whether there is any evidence for WGD in other arachnid orders like camel spiders, harvestmen and pseudoscorpions.

In addition, comparing the genomes of whip spiders and whip scorpions with spiders and scorpions could help reveal genes that have been retained by most groups after WGD versus lineage specific retentions and losses. These data will not only provide insights into arachnid genomes before and after the WGD event, but a better understanding of how duplicated genes produced by this event have contributed to the evolution of innovations in these animals, for example, silk production in spiders and the booklungs (novel breathing organs) of arachnopulmonates.

Finally, a more detailed understanding of the patterns of gene retention and loss after WGD in arachnids will provide an excellent comparison to such events in vertebrates to better understand the broader implications and consequences of WGD for the evolution of animal genomes and their biology.

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See the article here:
Seeing double in arachnid genomes: new insights into the consequences of whole genome duplication in animals - BMC Blogs Network (blog)

Credit: Broad Institute/www.broadinstitute.org/research-highlights-cancer

Working with the genome-wide cancer "dependency map" (inset below) Broad Institute researchers identified 760 genes that cancer cells need for their growth and survival.

In one of the largest efforts to build a comprehensive catalog of genetic vulnerabilities in cancer, researchers from the Broad Institute of MIT and Harvard and Dana-Farber Cancer Institute have identified more than 760 genes upon which multiple types of cancer cells are strongly dependent for their growth and survival.

Many of these dependencies, the researchers report today in the journalCell, are specific to certain cancer types. However, about 10 percent of them are common across multiple cancers, suggesting that a relatively small number of therapies targeting these core dependencies might each hold promise for combating several tumors.

To generate these findings, the research team conducted genome-wide RNA interference (RNAi) screens on 501 cell lines representing more than 20 types of cancer, silencing more than 17,000 genes individually in each line to identify genetic dependencies unique to cancerous cells.

Cancer cells can harbor a broad variety of genetic errors, from small mutations to wholesale swaps of DNA between chromosomes. If an error shuts down a critical gene, a cancerous cell will compensate by adjusting other genes activity, frequently developing a dependence on such adaptations in order to persist.

Identifying these dependencies provides opportunities for scientists to gain deeper insight into cancer biology and determine new therapeutic targets.

Much of what has been and continues to be done to characterize cancer has been based on genetics and sequencing. Thats given us the parts list, said study co-senior author William Hahn, an institute member in the Broad Cancer Program, chief of the Division of Molecular and Cellular Oncology at Dana-Farber, and a leader in the Cancer Dependency Map initiative, a joint effort spanning the Broad Institute and Dana-Farber. Mapping dependencies ascribes function to the parts and shows you how to reverse-engineer the processes that underlie cancer.

RNAi silences genes using small pieces of RNA called small interfering RNAs (siRNAs). To run a genome-wide RNAi screen, researchers expose cells to pools of siRNAs and track the cells behavior.

The simplest thing one can do with perturbed cells is allow them to keep growing over time and see which ones thrive, explained study co-senior author David Root, an institute scientist and director of the Genetic Perturbation Platform at the Broad. If cells with a certain gene silenced disappear, for example, it means that gene is essential for proliferation.

The data revealed striking patterns in cancer cells dependencies. Many dependencies were cancer-specific, in that silencing each affected only a subset of the cell lines. However, more than 90 percent of the cell lines had a strong dependency on at least one of a set of 76 genes, suggesting that many cancers rely on a relatively few genes and pathways.

Using a set of molecular features (e.g., mutations, gene copy numbers, expression patterns) from each cell line, the team also generated biomarker-based models that helped explain the biology behind 426 of the 769 dependencies. Most of those biomarkers fell into four broad categories:

Surprisingly, more than 80 percent of the dependencies with biomarkers were associated with changes (up or down) in a genes expression. Mutations, often used as the grounds for pursuing a gene as a drug target, accounted for merely 16 percent of biomarker-associated dependencies.

Twenty percent of the dependencies the team discovered were associated with genes previously identified as potential drug targets.

We cant say weve found everything, but we can say that the genes were seeing fall into a relatively small number of bins, some of which are familiar, some less so, Hahn said. That initial taxonomy is a great starting point for building a full map.

Our results provide a starting point for therapeutic projects to decide where to focus their efforts, said study co-first author Francisca Vazquez, a Cancer Dependency Map project leader. She added that while there was still much to do to validate the list, Its becoming increasingly easier to triangulate data and generate hypotheses as more genome-scale systematic data sets, like those from the Cancer Cell Line Encyclopedia, Genotype-Tissue Expression, and the Cancer Genome Atlas projects, become available.

Bringing of all the data together will help us generate a truly comprehensive cancer dependency map.

To eliminate false-positive results caused by seed effects a phenomenon by which siRNAs inadvertently silence irrelevant genes study co-first author Aviad Tsherniak led the development of a novel computational tool dubbed DEMETER.

People sometimes take a dim view of RNAi because seed effects make the data so noisy, said Tsherniak, leader of the Broad Cancer Programs Data Science group. DEMETER models gene knockdown and seed effects within the data, and computationally subtracts the seed effects. It cleans up the data and helps you find true dependencies.

According to Hahn, the data argue that the time is ripe to pay more attention to the broader landscape of functional aspects of cancer, in addition to focusing on protein-coding gene mutations and variations.

I think were close to the end of finding genes that are mutated or focally amplified in cancer, he said. To me, thats a huge opportunity, because it means we have many heretofore untapped avenues for understanding cancer.

Jesse Boehm, associate director of the Broad Cancer Program, and Todd Golub, director of the Cancer Program and chief scientific officer of the Broad Institute, were also co-senior authors on this study.

Complete results from the study are available through a dedicated portal.

This work was conducted as part of the Slim Initiative in Genomic Medicine for the Americas (SIGMA), a joint U.S.-Mexico project funded by the Carlos Slim Foundation. SIGMA focuses on several key diseases with particular relevance to public health in Mexico and Latin America, including type 2 diabetes and cancer. Additional funding was provided by the National Cancer Institute.

By Peter Reuell, Harvard Staff Writer | July 28, 2017

See more here:
First draft of a genome-wide cancer 'dependency map' - Harvard Gazette

How much of the human genome, our genetic blueprint, actually makes us who we are? New work by an evolutionary biologist at the University of Houston suggests that only up to 25% of the human genome is functional. The other 75% are so-called junk DNA - useless sequences that dont play a role in the important chemical reactions inside us. This conclusion goes sharply against the estimate of 80% functionality proposed by the ENCODE project, an international public research consortium that has led the way in human genome exploration.

Dan Graur, professor of biology and biochemistry, calculated that about 10 to 15 percent of the genome is actually functional, with the upper limit of 25 percent.

His reasoning stems from looking at how mutations affect a populations DNA. Graurs mathematical model allowed him to calculate the mutational load - the total genetic load of a population that results from the accumulation of bad or deleterious mutations. At some point the load can become too much and the population would go extinct.

Graurs work related how reproductive success, the ability of a species to replenish itself, was decreased by the deleteriousmutations. Over time, humans would have to reproduce at an impossible high rate to keep up with the mutations, Graur concluded.

The professor explained why he finds the 80% functionality of the genome proposed by the ENCODE scientists as unrealistic:

For 80 percent of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce, writes Graur. If we use the upper bound for the deleterious mutation rate (2 108mutations per nucleotide per generation), then the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude.

This is not the first time Graur fought against the 80% claim. In a 2014 interview with Science magazine, Graur even claimed its proponents are essentially pitching the idea of intelligent design. To Graur, asserting 80% usability implies that most of the genome exists to serve a purpose. Instead, he believes that everything is shaped by evolution, a slow process that weeds out useless features through genetic mutations - the drivers of evolution. This process also accumulates a lot of junk in the human genome.

Why is it important to know that only a quarter of the human genome may have functionality? Graur believes his work can shift the focus in the field of human genomics to what is useful from a medical standpoint:

We need to know the functional fraction of the human genome in order to focus biomedical research on the parts that can be used to prevent and cure disease, said Graur.There is no need to sequence everything under the sun. We need only to sequence the sections we know are functional.

You can read the studyhere in Genome Biology and Evolution.

See the rest here:
75% of the Human Genome Is Junk DNA, Claims New Research - Big Think (blog)

Image: Kazuharu Arakawa and Hiroki Higashiyama, background edited by Ryan F. Mandelbaum

Youre probably aware that natures most badass animal is undoubtedly the tiny tardigrade, or water bear. They might be small, but unlike your weak butt, they can live a life without water, withstand temperatures from -328 to 304 degrees Fahrenheit, and even survive the depths of space. How did evolution make such a strange creature, and who are its relatives?

The answer is still: _()_/

A team of scientists in the United Kingdom and Japan sequenced one tardigrade species genome and compared it to another to unlock the animals secrets, including the genetic basis of its survival skills. But as far as a closest evolutionary relative, the datas still inconclusive.

Tardigrade durability lies in their ability to lose all of their water and curl up into tuns. Losing the water from cells should be a lethal process, but theres a host of molecules in the tardigrades cells that seem to prevent the cell death, according to past research published in PLoS One. That paper also reports that certain nematodes and arthropods seem to be able to dry up, too.

Other papers have found difficulty determining what animals the tardigrade may have evolved from and the biological basis for its superpowers, but have identified certain responsible genes, according to a new study published in PLoS Biology. Theyve also implied that lots of the water bears genome, possibly a sixth of it, came from horizontal gene transfer, genetic material acquired from other animals, including those of other species.

Water bears, known to scientists as tardigrades, are famously adorable microscopic creatures who

So, this team put together a genome for the Hypsibius dujardini tardigrade species from around 900,000 individuals and compared it to the existing genome of the Ramazzottius varieornatus species to see what they could learn.

Aside from differences in the genome sizes (H. dujardiniswas much larger), they found further information about the genes that control the proteins that protect the tardigrades cells, according to New Scientist. On top of that, the amount of horizontal gene transfer seemed much lower than previous studies have suggested, closer to one percent of their genome. That would take a major confounding factor out of their evolutionary story.

But despite all the work, the scientists still couldnt really tell whether the water bear is more closely related to the nematode, or to arthropods like insects and crustaceans.

Even the full genomes of two tardigrades, which the authors report here, were not sufficient to decide whether tardigrades were closer to the arthropods or the nematodes, biologist Thorsten Burmester from the University of Hamburg in Germany, who was not involved with the study, told The Scientist in an email.

Of course, this is a single paper and an ongoing story, so more research will naturally shed light on whats really going on.

Science has lost yet another round against the seemingly indefatigable water bear. The tardigrade refuses to be fully understood.

[PLoS Biology]

Originally posted here:
Tardigrades Are Still a Complete Evolutionary Mystery - Gizmodo

I

n a step that some of the nations leading scientists have long warned against and that has never before been accomplished, biologists in Oregon have edited the DNA of viable human embryos efficiently and apparently with few mistakes, according to a report in Technology Review.

The experiment, using the revolutionary genome-editing technique CRISPR-Cas9, was led by Shoukhrat Mitalipov of Oregon Health and Science University. It went beyond previous experiments using CRISPR to alter the DNA of human embryos, all of which were conducted in China, in that it edited the genomes of many more embryos and targeted a gene associated with a significant human disease.

This is the kind of research that is essential if we are to know if its possible to safely and precisely make corrections in embryos DNA to repair disease-causing genes, legal scholar and bioethicist R. Alta Charo of the University of Wisconsin, Madison, told STAT. While there will be time for the public to decide if they want to get rid of regulatory obstacles to these studies, I do not find them inherently unethical. Those regulatory barriers include a ban on using National Institutes of Health funding for experiments that use genome-editing technologies in human embryos.

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The firstexperiment using CRISPR to alter the DNA of human embryos, in 2015, used embryos obtained from fertility clinics that had such serious genetic defects they could never have developed. In the new work, Technology Review reported, Mitalipov and his colleagues created human embryos using sperm donated by men with the genetic mutation that they planned to try to repair with CRISPR. The embryos are described as clinical quality. A 2017 experiment, also in China, used CRISPR to edit DNA in normal, presumably viable fertilized eggs, or one-cell human embryos.

Also in contrast to the experiments in China, those led by Mitalipov reportedly produced very few off-target effects, or editing of genes that CRISPR was supposed to leave alone. And the experiment avoided what is called mosaicism, in which only some cells of an embryo have the intended DNA changes. The embryos were not allowed to develop beyond a very early stage.

Because changing the DNA of an early embryo results in changes to cells that will eventually produce sperm and eggs, if the embryo is born and grows to adulthood, any children he or she has will inherit the genetic alteration, which is called germline editing. That has led to fears that such manipulations could alter the course of human evolution.

It has also triggered warnings about designer babies, in which parents customize their IVF embryos by adding, removing, or changing genes for certain traits.

A recent report on genome-editing from the National Academies did not call for a moratorium on research into germline editing, arguing that it might one day be a way for some parents to have healthy, biological children, such as when both mother and father carry genetic mutations that cause severe diseases.

But we anticipated that there would need to be a lot of research to see if you could make these changes without any unintentional effects,said Charo, who co-chaired the Academies committee. Mitalipov, who did not respond to requests for comment, has now shown that the answer to that might be yes.

Some scholars questioned how important the new study is, however. Stanford University law professor and bioethicist Hank Greely tweeted that the key point is that no one has tried to implant any edited embryos. Research embryos that are not to be transferred for possible implantation are not a big deal, he argued.

This story has been updated with additional comments by experts and details of similar experiments.

Senior Writer, Science and Discovery

Sharon covers science and discovery.

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Read more:
Using CRISPR, scientists efficiently edit genome of viable human embryos - STAT

NRGene, the Israeli startup that has mapped the genome for bread, pasta and wild emmer wheat, said that it has now mapped the genome for the most common cotton breed and the sweet potato, giving researchers critical insights for developing healthier plants with higher yields.

NRGene said it partnered with Genosys Inc. (TGS Singapore), a distributor of genomics technologies in China, to assemble the genome makeup of Upland Cotton, the most common cotton used for clothing, in less than seven weeks. A similar effort used to take years and cost many millions of dollars, the company said.

Upland Cotton makes up 90 percent of the global cotton grown around the world and is used to produce most of the worlds clothing, the company said.

The genomic makeup of Gossypium barbadense, also known as extra-long staple cotton, which is used in luxury cotton fabric, was also mapped, the company said in a statement.

NRGenes CEO Gil Ronen (Courtesy)

Cotton is one of the worlds most important non-food agricultural crops, said NRGene CEO Gil Ronen in a statement. By delivering critical insights into its makeup, were helping researchers develop healthier plants with higher yields that require fewer resources.

Seed developers worldwide spend billions of dollars and years to develop new, more nutritious and resilient varieties of seeds. These in turn enable farmers to grow bigger quantities of more nutritious and more resilient crops. This is crucial for a world that will have to feed and dress an expected 9.7 billion people by 2050. Demand for food globally is expected to rise at least 20 percent over the next 15 years, according to a May 2017 World Bank report.

Genomes contain all the genetic makeup of organisms, be they humans, plants, animals or bacteria. By studying the genomes of the plants to determine which seeds will better suit climatic conditions and which will have high resiliency, developers can save a lot of time and money and engage in more efficient agriculture.

The assembly of the sweet potato genome was delivered to a group of scientists from Japan, China, and Korea and was part of a project to research the makeup of the sweet potato.

The sweet potato is an essential crop for the worlds communities, especially in Asia and Africa, providing high vitamin, mineral and calorie content, said Professor Qingchang Liu from China Agricultural University who was part of the consortium set up to study the starchy, sweet root. Therefore, we launched an international genome sequencing project for the sweet potato.

Sweet potatoes provide high vitamin, mineral and calorie content (Melanie Lidman/Times of Israel)

The assembly of the sweet potato (Ipomoea batatas) genome took less than two months using technology developed by US firm Illumina Inc., a developer of technology for genomic research, and NRGenes software.

The developments in genetic research over the past couple of years are startling, said Ung-Han Yoon of the Rural Development Administration of Korea. Previously, we labored for years to assemble genomes. Now NRGenes tech can deliver essential data on critical crops, such as the sweet potato, in only a matter of weeks at a fraction of the cost.

The international research team is now eyeing the creation of a sweet potato pan-genome, which will allow researchers to see unique and shared traits among all varieties of the root and then breed sweet potatoes with higher nutritional values, productivity and disease resistance.

The pan-genome will be analyzed using one of NRGenes software tools, which captures the diversity of species and allows the creation of a full genomic picture that enables a comparative analysis of multiple varieties.

With the genome and ultimately the pan-genome analysis, breeders can develop more nutritious, high yielding varieties with fewer resource requirements, said NRGenes Ronen.

NRGene, based in Ness Ziona, Israel, is a genomic big data company that develops software and algorithms to reveal the genomic makeup and diversity of crop plants, animals, and aquatic organisms which help support breeding programs. NRGenes software is being used by some of the leading seed companies worldwide, including Monsanto Company and Syngenta, as well as research teams in academia.

Set up by Ronen and Guy Kol in 2010, the company enlisted code crackers from the Israeli armys elite 8200 unit and got them to write algorithms that would do the job of deciphering genomes. The set of computational tools they developed, together with software engineers and bioinformaticians, allow NRGene to map complex genomes quickly and accurately.

Read more from the original source:
Israeli startup maps genome of cotton, sweet potato for better crops - The Times of Israel

Freshwater alga in the genus Zygnema would be one target of sequencing project.

Norbert Hlsmann/Flickr (CC BY-NC-SA 2.0)

By Dennis NormileJul. 27, 2017 , 8:00 AM

Hopes of sequencing the DNA of every living thing on earth are taking a step forward with the announcement of plans to sequence at least 10,000 genomes representing every major clade of plants and eukaryotic microbes. Chinese sequencing giant BGI and the China National Genebank (CNGB) held a workshop yesterday on the sidelines of the International Botanical Congress, being held this week in BGI's hometown of Shenzhen, to discuss what they are calling the 10KP plan. About 250 plant scientists participated in the discussions and "are raring to go," says Gane Ka-Shu Wong, a genomicist and bioinformaticist at University of Alberta in Edmonton.

The 10KP plan will be a key part of the Earth BioGenome Project (EBP), an ambitious and still evolving scheme to get at least rough sequence data on the 1.5 million eukaryotic species, starting with detailed sequences of one member of each of the 9000 eukaryotic families. The effort to sequence plants is moving ahead a bit faster than other aspects of EBP "because plant scientists are more collaborative," Wong says jokingly.

The 10KP plan is also building on a previous 1,000 plant (1KP) transcriptome project. That effort, launched in 2012 and now nearing completion, was also led by BGI, where Wong is an associate director.

"One thing we focused on (for 1KP) was sampling phylogenetic diversity, not just crops and model organisms," Wong says. That strategy will continue with 10KP. The transcriptome project has resulted in more than 50 papers, with the overall summary publication still to come. A lot of the analysis has focused on plant evolution. One surprise was that important transcription factors previously thought to have evolved as land plants colonized terrestrial habitats can actually be traced back to green algae, says Michael Melkonian, a botanist at the University of Cologne in Germany. Screening green algae also turned up new light-sensitive proteins that neuroscientists now use to study how different neurons interact and better understand neurological functioning.

Whereas the 1KP project only tackled the transcriptome, or all the messenger RNA expressed by an organism, 10KP will produce completely new sequences of the entire genome. And scientists expect an even larger bonanza of fundamental insights and economic spin-offs. The 10KP project "is 1KP on steroids," says Douglas Soltis, a plant biologist at the Florida Museum of Natural History at the University of Florida in Gainesville. He adds that one "wonderful thing" about the project is that it will provide reference genomes for "the numerous plant researchers studying non-model systems," he says. The project will also present "an unprecedented opportunity to address fundamental questions about plant evolution," says Stephen Smith, an evolutionary biologist at the University of Michigan, Ann Arbor. Study targets are expected to include the role of genome duplication, the correlation between genomic and morphological changes, and how rates of evolution changed over time.

We're ready to start sequencing yesterday.

One challenge Smith points to is the need to develop new means of analyzing and synthesizing sequencing information. "Existing tools and methods are unable to handle the extraordinary scale of the data," he says. Wong says another bottleneck will be dealing with the paperwork needed to comply with legal requirements of shipping plant material across borders, as well as complying with the Nagoya Protocol, an international pact that seeks to ensure the fair and equitable sharing of genetic resources. On the other hand, gathering specimens is easier than for other areas of genetics. "You don't have to chase down some animal, you can usually just go to a botanical garden," Wong says.

Xu Xun, who leads technical development for BGI, says the company and CNBG will cover the sequencing costs but "scientists will have to find their own funding for collecting samples and for analysis." As for timing, Wong says they hope to gather the samples in the next two years and "we hope to wrap up the sequencing and analysis in 5 years."

"We're ready to start sequencing yesterday," Wong says. And plant scientists are eager. After the meeting yesterday in Shenzhen, "several people came up people already wanting to send samples," he says.

Follow this link:
Plant scientists plan massive effort to sequence 10000 genomes - Science Magazine

July 27, 2017 by Bob Yirka report A depiction of the double helical structure of DNA. Its four coding units (A, T, C, G) are color-coded in pink, orange, purple and yellow. Credit: NHGRI

(Phys.org)A large international team of researchers has developed a Danish reference genome catalog based on the de novo assembly of 150 genomes sequenced from 50 family trios. In their paper published in the journal Nature, the group describes the multi-year effort, its purpose, and where they believe such efforts are leading.

One of the ways that scientists are learning about diseases, particularly those that are hereditary in nature, is by sequencing the genomes of large groups of peopledoing so enables searching for variants that cause or contribute to a given diseasethe ultimate goal would be to sequence every single person on Earth. In this new effort, the researchers have sequenced the genomes of 150 people in Denmark (from 50 family trios) of Danish descentnative Inuits and immigrants were screened out.

The effort, the researchers report, was carried out partly to create a Danish reference catalog and partly to learn how to conduct large-scale genome sequencing. They note that such a project required the combined efforts of multiple people and organizations working in coordinated fashion. Ultimately, the project cost approximately $10 million.

One major aspect of the project was selecting technology and determining how many people to sequence. The team wound up using samples from 50 families and did the sequencing using both combinations of paired-end and mate-pair libraries with the Illumina HiSeq2000. They note also that de novo assemblies were used because the researchers believed other approaches left out pertinent information. De novo refers to deriving a peptide sequence from a mass spectrum without the use of a sequence database. It is the preferred approach to sequencing when the aim is to identify novel peptides in organisms that have not been previously sequenced. The researchers report very few gaps in the data. They also note that three assemblies were used: Allpaths-LG14, SOAPdenovo2 and SGA. Accuracy was measured by comparing their results with the human reference genome.

The researchers hope that their effort will lead to improved medical interpretation of genetics in Denmark.

Explore further: Genome sequencing of individual Korean offers opportunity to identify parts of sequence unique to Korean population

More information: Lasse Maretty et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference, Nature (2017). DOI: 10.1038/nature23264

Abstract Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.

Journal reference: Nature

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Continued here:
Researchers conduct sequencing and de novo assembly of 150 genomes in Denmark - Phys.Org

NESS ZIONA, Israel, July 26, 2017 /PRNewswire/ --

NRGene, the worldwide leader in genomic assembly and analysis, and Genosys Inc. (TGS Singapore), a leading distributor of genomics technologies in China, have partnered to deliver two complete cotton genomes.

"We first sequenced upland cotton (Gossypium hirsutum) in 2015," said Professor Tianzhen Zhang at Zhejiang University. "Now, we wanted to leverage the advances in technology to get a more complete version of not only in Gossypium hirsutum, but also Gossypium barbadense. Therefore, we combined forces with NRGene to assemble more complete cotton genomes."

Upland cotton constitutes 90% of the global cotton grown around the world and is used to produce most of the world's clothing. Gossypium barbadense, also known as extra-long staple (ELS) cotton, is used in luxury cotton fabrics.

"We've been working very closely with Professor Zhang for this entire project, facilitating the process," said Flora Liew, Managing Director of Genosys Inc. (TGS Singapore). "We were amazed by both, the speed and high quality of the DeNovoMAGICTM results."

Upon completion of the comprehensive genomes, it will be quick and inexpensive to analyze the other thousands of varieties because the genomic infrastructure will already be in place.

NRGene's DeNovoMAGICTM 3.0 provided the genome assembly based on the raw sequence data. PanMAGICTM will be used to assemble the pan-genome. It compares all-to-all of the de-novo assemblies to get the best view of local differences such as SNPs, as well as global changes such as translocations and duplications of whole chromosomic regions and PAV/CNV/SV analysis.

"Cotton is one of the world's most important non-food agricultural crops," says NRGene CEO, Gil Ronen. "By delivering critical insights into its make-up, we're helping researchers develop healthier plants with higher yields that require fewer resources."

About NRGene NRGene is a genomic big data company developing cutting-edge software and algorithms to reveal the complexity and diversity of crop plants, animals, and aquatic organisms for supporting the most advanced and sophisticated breeding programs. NRGene tools have already been employed by some of the leading seed companies worldwide as well as the most influential research teams in academia. http://www.nrgene.com.

NRGene Contact Amy Kenigsberg K2 Global Communications rel="nofollow">amy@k2-gc.com +1-913-440-4072 (+7 ET) +972-9-794-1681 (+2 GMT)

SOURCE NRGene

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NRGene & China's Genosys Deliver Cotton Genome - Markets Insider

July 24, 2017 CRISPR-associated protein Cas9 (white) from Staphylococcus aureus based on Protein Database ID 5AXW. Credit: Thomas Splettstoesser (Wikipedia, CC BY-SA 4.0)

A research team from the Schepens Eye Research Institute of Massachusetts Eye and Ear has successfully prevented mice from developing angiogenesis of the retinathe sensory tissue at the back of the eyeusing gene-editing techniques with CRISPR-Cas9. Angiogenesis causes vision loss and blindness and is a feature of several degenerative eye conditions, including proliferative diabetic retinopathy (PDR), wet age-related macular degeneration (AMD), and retinopathy of prematurity (ROP). In a report published online today in Nature Communications, the researchers present a novel gene-editing technique to prevent retinal angiogenesis, which could lead to the development of new therapies for eye conditions marked by pathological intraocular angiogenesis.

Despite the success of vascular endothelial cell growth factor (VEGF) inhibiting agents (e.g. Lucentis, Eylea) in reducing neovascular growth and lessening vascular leakage in retinal diseases such as PDR and AMD, several therapeutic challenges remainnamely a need for sustained treatment and a modality to treat the significant number of patients who do not respond to anti-VEGF therapies.

"We know that vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2) plays an essential role in angiogenesis," said corresponding author Hetian Lei, Ph.D., Assistant Scientist at Schepens Eye Research Institute of Mass. Eye and Ear and Assistant Professor of Ophthalmology at Harvard Medical School. "The CRISPR-Cas9 system to can be utilized to edit the VEGFR2 gene, preventing intraocular pathological angiogenesis."

A feature of various eye diseases, pathological intraocular angiogenesis presents clinically when blood vessels in the retina (the structure in the back of the eye that senses and perceives light) begin to grow new, abnormal blood vessels on the surface of the retina. As the damage progresses, these vessels can leak, rupture, or cause retinal detachment leading to impaired vision.

CRISPR-Cas9 is a powerful new technology that can target and edit certain aspects of the genome, or the complete set of genetic material of an organism. In the Nature Communications report, study authors used an adeno-associated virus (AAV) to deliver genomic edits to target VEGFR2, a critical protein responsible for angiogenesis. A single injection of this therapy was able to prevent retinal angiogenesis in preclinical models.

"As this genomic editing gains traction in virtually all medical fields, we are cautiously optimistic that this powerful tool may present a novel therapy to prevent vision loss in eye disease marked by intraocular pathological angiogenesis," said Dr. Lei. "While further study is needed to determine safety and efficacy of this approach, our work shows that the CRISPR-Cas9 system is a precise and efficient tool with the potential to treat angiogenesis-associated diseases."

Explore further: Researchers identify new target for abnormal blood vessel growth in the eyes

More information: Xionggao Huang et al, Genome editing abrogates angiogenesis in vivo, Nature Communications (2017). DOI: 10.1038/s41467-017-00140-3

The discovery of a protein that encourages blood vessel growth, and especially 'bad' blood vessels the kind that characterise diseases as diverse as cancer, age-related macular degeneration and rheumatoid arthritis ...

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Genome editing with CRISPR-Cas9 prevents angiogenesis of the retina - Medical Xpress