Category Archives: Genome

Illumina, the global leader in next-generation sequencing technology, has announced that their latest gene sequencing machine could finally make the $100 genome a reality.

The new machine is more efficient and cost effective, and will allow for sequencing on an unprecedented scale by making it possible to sequence more samples at greater depth and take on projects that would otherwise be too expensive.

This not only allows for deeper understanding and better treatments for complex disease but will also make it possible for more people than ever to benefit from precision medicine.

The previous system enabled the $1,000 genome and was first announced in 2010.

'The 20 Academic Books That Shaped Modern Britain'

Misha Kapushesky, founder of Cambridge-based Genestack, speaking to Cambridge Business magazine, said of the increasingly available dataset: As a proportion of genomics and sequencing the production costs are going down its getting cheaper and data management is going up. The progression of this technology goes in leaps and bounds. The last leap was six or seven years ago which was NGS next-generation sequencing. That allowed David Cameron to announce the 100,000 Genome Project. This project meant 100,000 UK patients with cancer and rare diseases had their entire genome decoded, leading to targeted therapies which could make chemotherapy a thing of the past.

The Human Genome Project, which started in 1990, meant that the first full human genome cost $1 billion to be sequenced and today, as Misha points out, all across the world people are generating genetic data at tremendous scale.

Then, earlier this year, Illumina announced the $100 genome, so its becoming commoditised, but finding the right data and the right tools to work with this data is where the challenge is.

NovaSeq is the most powerful sequencer Illumina has ever launched and will open new horizons for the discovery of rare genetic variants.

Illumina is building its new European headquarters at Granta Park.

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A genome for $100 could be a reality - Cambridge News

OpGen Presents Rapid Acuitas Genetic Test Data at Advances in Genome Biology and Technology Meeting P&T Community The data were presented at the Advances in Genome Biology and Technology (AGBT) meeting, which is taking place from February 13-16, 2017 in Hollywood Beach, FL. These preliminary results support OpGen's ongoing genomic and bioinformatics efforts ... and more »

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OpGen Presents Rapid Acuitas Genetic Test Data at Advances in Genome Biology and Technology Meeting - P&T Community

February 13, 2017 A Salk team developed a tool that maps functional areas of the genome to better understand disease. Credit: Salk Institute

Most of us would be lost without Google maps or similar route-guidance technologies. And when those mapping tools include additional data about traffic or weather, we can navigate even more effectively. For scientists who navigate the mammalian genome to better understand genetic causes of disease, combining various types of data sets makes finding their way easier, too.

A team at the Salk Institute has developed a computational algorithm that integrates two different data types to make locating key regions within the genome more precise and accurate than other tools. The method, detailed during the week of February 13, 2017, in Proceedings of the National Academy of Sciences, could help researchers conduct vastly more targeted searches for disease-causing genetic variants in the human genome, such as ones that promote cancer or cause metabolic disorders.

"Most of the variation between individuals is in noncoding regions of the genome," says senior author Joseph Ecker, a Howard Hughes Medical Institute investigator and director of Salk's Genomic Analysis Laboratory. "These regions don't code for proteins, but they still contain genetic variants that cause disease. We just haven't had very effective tools to locate these areas in a variety of tissues and cell typesuntil now."

Only about two percent of our DNA is made up of genes, which code for proteins that keep us healthy and functional. For many years, the other 98 percent was thought to be extraneous "junk." But, as science has developed ever more sophisticated tools to probe the genome, it has become clear that much of that so-called junk has vital regulatory roles. For example, sections of DNA called "enhancers" dictate where and when the gene information is read out.

Increasingly, mutations or disruption in enhancers have been tied to major causes of human disease, but enhancers have been hard to locate within the genome. Clues about them can be found in certain types of experimental data, such as in the binding of proteins that regulate gene activity, chemical modifications of proteins (called histones) that DNA wraps around, or in the presence of chemical compounds called methyl groups in DNA that turn genes on or off (an epigenetic factor called DNA methylation). Typically, computational methods for finding enhancers have relied on histone modification data. But Ecker's new system, called REPTILE (for "regulatory-element prediction based on tissue-specific local epigenomic signatures"), combines histone modification and methylation data to predict which regions of the genome contain enhancers. In the team's experiments, REPTILE proved more accurate at finding enhancers than algorithms that rely on histone modification alone.

"The novelty of this method is that it uses DNA methylation to really narrow down the candidate regulatory sequences suggested by histone modification data," says Yupeng He, a Salk graduate student and first author of the paper. "We were then able to test REPTILE'S predictions in the lab and validate them with experimental data, which gave us a high degree of confidence in the algorithm's ability to find enhancers."

The REPTILE algorithm operates in two general steps: training and prediction. For training, the Salk team taught REPTILE to recognize mammalian enhancers by feeding into the algorithm both the locations of known enhancers as well as genomic areas other than enhancers in the DNA. In the prediction step, the algorithm ran on nine mouse and five human cell lines and tissues whose enhancer regions were unknown and pinpointed the locations of potential enhancers. Finally, the team utilized data from laboratory experiments to test whether the predictions made by REPTILE in the prediction step corresponded to real regulatory regions. Because enhancers increase the activity of target genes, researchers can test the activity of DNA sequences by connecting them to a reporter gene and watching to see whether the supposed target gene ramps up. Using molecular tools, the team engineered mouse embryos so that enhancer activation would trigger the expression of linked reporters, which can be monitored by staining. So, if REPTILE predicted that a specific enhancer was linked to mouse forebrain development, the team was able to look for a staining pattern in the embryo's forebrain region. If they saw it, REPTILE's prediction was considered valid. The Salk team also tested REPTILE's predictions against four other commonly used enhancer-finding algorithms. Overall, REPTILE outperformed each one, finding enhancer regions with greater accuracy (getting closer to them along the DNA strand) and fewer errors (misidentifications). In particular, REPTILE was more successful than the other systems at the invaluable task of finding enhancers in different tissue types than those it was trained on.

"The number of genetic variants in the genome is enormous," says Ecker. "So in terms of finding ones that cause disease, you really want to shine a spotlight on the regions you think are most important and identifying enhancers is a critical step in the process."

Explore further: 'Mysterious' non-protein-coding RNAs play important roles in gene expression

More information: Improved regulatory element prediction based on tissue-specific local epigenomic signatures, PNAS, http://www.pnas.org/cgi/doi/10.1073/pnas.1618353114

In cells, DNA is transcribed into RNAs that provide the molecular recipe for cells to make proteins. Most of the genome is transcribed into RNA, but only a small proportion of RNAs are actually from the protein-coding regions ...

Scientists at the Gladstone Institutes have invented a new way to read and interpret the human genome. The computational method, called TargetFinder, can predict where non-coding DNAthe DNA that does not code for proteinsinteracts ...

The complex process regulating gene expression is often compared to following a recipe. Miss a genetic ingredient, or add it in the wrong order, and you could have a disaster on your hands.

Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered "junk" because they do not code for specific ...

Purdue University and Indiana University School of Medicine scientists were able to force an epigenetic reaction that turns on and off a gene known to determine the fate of the neural stem cells, a finding that could lead ...

Most of us would be lost without Google maps or similar route-guidance technologies. And when those mapping tools include additional data about traffic or weather, we can navigate even more effectively. For scientists who ...

Monash University and Danish researchers have discovered a gene in worms that could help break the cycle of overeating and under-exercising that can lead to obesity.

A new study shows how errors in a specific gene can cause growth defects associated with a rare type of dwarfism.

Specific genetic errors that trigger congenital heart disease (CHD) in humans can be reproduced reliably in Drosophila melanogaster - the common fruit fly - an initial step toward personalized therapies for patients in the ...

A newly discovered mutation in the INPP5K gene, which leads to short stature, muscle weakness, intellectual disability, and cataracts, suggests a new type of congenital muscular dystrophy. The research was published in the ...

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Team develops tool that maps functional areas of the genome to ... - Medical Xpress

smithsonian.com February 13, 2017 3:09PM

Quinoa is commonly considered the ultimate "superfood." Packed with protein, vitamins and minerals, thisSouth American grain was once revered by the Inca, but its fanbase has grown worldwide. Now, asReuters reports, new research into the genome of the grain shows that it has potential to be even more superand, perhaps, cheaper to produce.

An international team of researchers mapped the genome of quinoa, determining that the grain has 1.3 billion nucleotides (the building blocks of DNA) spread over 18 chromosomes. The hope is that access to the genome will help researchers figure out how to breed more productive strains of quinoa that could be cultivated in food insecure areas of the globe with harsh growing conditions. The research appears this week in the journal Nature.

Having the genome would enable the wider community both to study how this plant does all the amazing things it does, and also use that knowledge of the genome to make much faster and greater improvements in the crop, improvements that really haven't been so easy to do over the past couple of decades, Mark Tester, leader of the project and professor at King Abdullah University of Science and Technology in Saudi Arabia tells Mengqi Sun at The Christian Science Monitor.

Quinoa was an important food crop in the Andes when the Spanish arrived in South America in the 1500s, according toa press release. Because it had religious significance for the Inca, the Spanish forbade the cultivation of quinoa and forced the Inca to grow wheat instead, Reuters reports. As European grains became more prevalent, quinoa, which was not as easy to grow or process, the superfood couldn't keep pace on a global stage.

One reason quinoa has only recently become popular outside the Andesis that the grains are covered by saponins, a bitter tasting substance. That means quinoa needs processing before eating, which raises its cost. On the other hand, it also has the ability to grow at high altitude, in poor soils and even saline conditions, making it an important crop in many parts of the world.

AsRyan F. Mandelbaum at Gizmodo reports,outside of its home range, quinoa is currently seen a high-end specialty food. And prices reflect that, tripling between 2006 and 2013 when the grain's popularity grew overseas. Tester, however, thinks the grain has the potential to be as common and cheap as rice if breeders can produce the right varieties.

[The goal is to] move this crop from its current status as a crop of importance in South America, and a crop of novelty in the West, to become a true commodity in the world, he tells Cici Zhang at Popular Science. Id like to see quinoa changed into a crop that can be grown much more widely and become much cheaper. I want the price to come down by a factor of fiveI want it out of the health food section.

The hope is that other researchers will use the genome data to find other adaptations that will help scientists breed strains of quinoa for various soils and climates around the world. For example, we discovered mutations which ensure that certain quinoa varieties cannot produce bitter tasting saponins, Robert van Loo, quinoa breeder at Wageningen University in the Netherlands says in the press release. These 'sweet' varieties do not need to be polished to remove the bitter substances, saving some 15 to 20 per cent. With the new knowledge of quinoa DNA, we can quickly and easily select plants that do not produce bitter substances in the breeding process."

Similar projects with other grains have resulted in new varieties of crops in the last decade. The rice genome, for instance, was first publicly released in 2006. Last week, Chinese scientists announced that they were cultivating new varieties of insect and disease resistant rice based on studies of the rice genome.

But Douglas Cook, the director of the Feed the Future Innovation Lab for Climate Resilient Chickpea at the University of California, Davis, cautions that there is no silver bullet when it comes to solving food insecurity, and that developing new strains of quinoa wont be a food revolution all on its own.

Personally, I think it could mean an important part of the solution, but it's not going to be a game changer, he tells Sun. The places where bigger changes are going to occur are in crops that have already had significant investments and that are already mainstayin the human diet.

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Genome Mapping Could Lead to Cheaper and More Abundant Quinoa - Smithsonian

Is there treasure in the DNA's so-called "junk" pile? Well, as the first half of a popular saying goes, money talks. The National Institutes of Health (NIH) just funded five centers to explore what the "dark matter genome" (the non-protein-coding part) is doing. Two of the centers will be at the University of California, San Francisco, which describes the new project:

Grammar -- there's an ID-friendly analogy for you. Language students and their teachers don't look for grammar and punctuation in gibberish. The statement implies purpose: functional information that has a beginning and end. Rules that organize information for communication. Genes without grammar are like words without sentences.

Launched in 2003 after the Human Genome Project found that only 2 percent of DNA codes for proteins, ENCODE was tasked "to find all the functional regions of the human genome, whether they form genes or not." Initial results were spectacular, showing that at least 80 percent of DNA is transcribed. This made the #1 spot in our top ten evolution-related stories for 2012 an "easy pick," as Casey Luskin wrote at the time, since it "buries" the "junk DNA" dogma -- the idea that evolution left our genome littered with useless leftovers of mutation and natural selection.

Darwinians don't give up easily, though, as we have often noted. Transcription is not proof of function, they argue. But why use costly resources to transcribe junk for no purpose? In the intervening years, more and more functions have come to light.

The new grants from NHGRI [National Human Genome Research Institute] will allow the five new centers to work to define the functions and gene targets of these regulatory sequences.

We anticipate future spectacular discoveries will continue to come from ENCODE. And now researchers have new lights to shine: including faster DNA barcoding and the CRISPR-Cas9 gene-editing tool.

In addition to the two centers at UCSF, others will be set up at labs including Cornell, Stanford, and Lawrence Berkeley. The National Center for Human Genome Research explains the goals, in which it will invest an initial outlay of $31.5 million for 2017:

Other Junk-Busting Research

Meanwhile, labs all over are finding treasure in the formerly dismissed junk. It has become something of a scientific sport these days to get the function ball downfield ahead of other labs.

Enhancer RNAs. Last month, Penn Medicine News threw this touchdown, "'Mysterious' Non-protein-coding RNAs Play Important Roles in Gene Expression." Realizing that transcribing junk didn't make sense, researchers at the University of Pennsylvania suspected that there must be more going on. They asked, Why do body cells turn out so different when they all have the same genome? Seeking function, they learned about the role of enhancer RNAs that regulate which genes get expressed in different types of cells.

DNA repeats. It looks so boring, repetitive DNA. It must be unimportant, right? Not so, found two researchers from Rockefeller University. Writing in PNAS, they discovered that three proteins carefully protect those repeats around centromeres -- the locations on chromosomes where the spindle attaches during cell division. "Our study reveals the existence of a centromere-specific mechanism to organize the repetitive structure and prevent human centromeres from suffering illegitimate rearrangements." Some could lead to cancer and aging. Doesn't the converse, legitimate arrangements, imply complex specified information?

Disordered proteins. Most proteins fold into compact shapes. What are disordered proteins doing, flailing like air dancers in the wind? Canadian researchers publishing in PNAS found one that has a signaling function. It's not alone; intrinsically disordered regions (IDRs) are "widespread" and have "diverse functions," they say. Since they are maintained by "stabilizing selection," they must be doing something important. Oddly, the function remains the same even when the underlying amino acid sequence changes. In one instance in yeast, they found evidence for "selection maintaining this quantitative molecular trait despite underlying genotypic divergence." This could be a major paradigm change, since 40 percent of proteins are predicted to contain "disordered" regions. The one they studied appears to have a signaling function. Now, the hunt is on to find other functions in "disorder" (synonymous with junk).

Accordion genomes. Protein-making is not the only function of DNA. Some of it, we know, provides structural support or anchor points. Researchers at the University of Utah are exploring another mystery: why genomes grow and shrink. By studying the genomes of birds and mammals (including flying mammals, the bats), they speculate that shedding DNA can streamline a bird or bat for flight, but allow other creatures to grow their supply. The stretching and squeezing of genomes they liken to an accordion mechanism. It would seem that extra scaffolding could be jettisoned without harm. Whatever is going on, it doesn't match the old dogmas of neo-Darwinism. "Evolution is often thought of as a gradual remodeling of the genome, the genetic blueprints for building an organism," this article begins. "In some instances it might be more appropriate to call it an overhaul." Since overhauling a genome non-gradually would likely be catastrophic, we suspect scientists will find this process is under careful regulation. "I didn't expect this at all," the lead author remarked. "The dynamic nature of these genomes had remained hidden because of the remarkable balance between gain and loss." Watch this space.

The research strategy of looking for function continues to prove fruitful. It's an attitude that says, If it's there, it's probably doing something important. True, just because some things are designed doesn't imply that everything is designed. But science was hindered for decades by the junk-DNA myth and the vestigial-organs myth, which we now know are being discarded. Science is playing catch-up after years of lazy thinking that reasoned, If it's not doing something I understand right now, it must be junk. It's time now to assume function, until the case is shown to be otherwise. As Paul Nelson says, "If something works, it's not happening by accident."

Photo credit: Metro St. Louis [CC BY 2.0], via Wikimedia Commons.

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With Fresh Funding, ENCODE Team Continues Demolition of "Junk DNA" Myth - Discovery Institute

An international team of researchers has successfully mapped the entire quinoa genome, which will help breed varieties that could thrive on Australia's marginal cropping land.

The study was led by Australian scientist Mark Tester, of Saudi Arabia's King Abdullah University of Science and Technology (KAUST).

The team of 33 researchers, from institutions around the world, produced a complete picture of the ancient plant's genome, publishing their work in the journal Nature.

Australian researchers played a key role in the project, drawing heavily on their knowledge of salt-tolerant plants and genes.

The University of Melbourne's Metabolomics Institute was tasked with finding whereabouts in the seed the bitter-tasting saponin compounds were located.

Quinoa is native to South America where it was once a staple crop, but it fell out of favour when Spanish colonists arrived.

University of Melbourne's Professor Ute Roessner said the team was attracted to the plant because of its nutritional qualities and its ability to grow for millennia in some of the world's harshest environmental conditions.

"Quinoa is a highly nutritious grain, full of essential amino acids [and is] a nice balance of lipids and proteins, low GI and gluten-free," she said.

"Is is highly salt-tolerant and it grows in very low quality soils, which makes it interesting from an Australian perspective."

With the genome sequenced, researchers can now start selective breeding programs with one of the first goals likely to be removing the saponin compounds from the seed.

"These are the least nutritional parts of the quinoa plant," Dr Roessner said.

"There's already been some success in producing 'sweet quinoa' and within the paper we've identified the saponin genes.

"Knowing the genome will also help us breed varieties that can stand up the range of pests and diseases the plants face when growing in Australia."

Quinoa growing at the Ord River Irrigation Area trial site (file photo).

(ABC Rural: Tom Edwards)

Quinoa growing at the Ord River Irrigation Area trial site (file photo).

Australia's largest grower and processor of quinoa, Ashley Wiese of Narrogin in Western Australia's Great Southern region said growing quinoa in Australia had been extremely challenging.

"It's extremely drought tolerant, and salt tolerant, but its's a very weak seedling that doesn't compete well," Mr Wiese said.

Most of the weed and pest controls available to cereal grain farmers will not work on quinoa, so more resistant varieties would boost yields."

Processors must also wash away the saponin from the seed, and varieties free of the bitter tasting compound would save time, energy and money.

"Quinoa shouldn't be a rich person's food, it's just a better quality replacement for rice," Mr Wiese said.

"Part of the reason it is so expensive is that it's a risky crop to grow, and the saponin coating is expensive to remove but it's a two-edged sword, because that coating protects the plants from pests."

Science communicator Chris Smith told RN Breakfast any research that helped increase production of the quinoa would help efforts to protect food security, because of its ability to grow on marginal land.

"It grows pretty much anywhere, particularly on those poor soils where people are hungry, so they can produce nutritious food without putting huge amounts of energy and labour into growing it," he said.

Quinoa can grow in the harshest of environments.

(ABC Rural: Eliza Wood)

Quinoa can grow in the harshest of environments.

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Researchers decode quinoa genome, allowing them to learn why it thrives in harsh environments - ABC Online

Scientists have produced the first high-quality genomic sequence for the South American supergrain quinoa, a feat that may lead to improvements in the grains properties and the expansion of its cultivation worldwide (Nature 2016, DOI: 10.1038/nature21370).

First domesticated in the Andes about 7,000 years ago, quinoa (Chenopodium quinoa) has recently come into vogue as a nutritional powerhouse, with its high quantities of protein, fiber, vitamins, and minerals. The United Nations even proclaimed 2013 as the International Year of Quinoa.

But despite its potential as a significant food source for an expanding world population, the lack of knowledge about its genetic makeup has hindered its widespread cultivation.

A large international team led by Mark Tester, professor of plant science at King Abdullah University of Science and Technology (KAUST), mapped out the plants complex, 1.5-gigabase genome using a number of sequencing strategies, including single-molecule real-time sequencing, as well as optical and chromosome-contact mapping.

Having the quinoa genome on hand might reduce traditional plant breeding times by half, notes Karina B. Ruiz, a plant physiologist at the University of Bologna, who studies the biology of quinoa in stressful environments.

The work may also address one of quinoas most vexing properties. The grains are coated with saponins, a class of triterpene glycosides that are bitter-tasting and foamy. To make the grain palatable, producers must rinse it thoroughly, which means quinoa cultivation can stress increasingly scarce water supplies.

Testers team identified a gene that they believe is responsible for regulating quinoas production of saponins. This new information may allow scientists to engineer strains with reduced saponin levels.

Andrew H. Paterson at the University of Georgia and Alan L. Kolata at the University of Chicago note in a perspective accompanying the research that the sequencing technology employed by Testers group may find use beyond quinoa. Sequencing the genomes of other neglected food crops could lay the foundations for further contributions to global food security, they write.

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Quinoa genome sequenced - Chemical & Engineering News (subscription)

Its already a protein-packed ancient grain beloved by foodies. Now scientists say theyve mapped the genome of quinoa, potentially unlocking a way to mass produce at prices that could help feed the worlds hungry.

By tinkering with the genetic makeup of the plant, a team of researchers based out of King Abdullah University in Saudi Arabia say its possible to grow a strain of quinoa thats easier to process. In doing so, scientists hope the cost of the grain could one day be comparable to wheat.

Most quinoa on the market is grown in South Americatypically Peru, Bolivia, and Ecuador. For decades it was a quiet crop, the food of peasants around the Andean mountains. But that changed sometime around 2006, when its categorization as a superfood by some in the nutrition sphere sparked a craze in Europe and the US. In 2007, the US imported about 7 million pounds (3.2 million kg) of the grainwhich had skyrocketed to 70 million pounds by 2013, according to the Agricultural Marketing Resource Center.

In that same period, the price of quinoa tripled. The prices fell slightly (paywall) in 2015, the result of a better supply-demand balance, but it still remains a nutritious food mostly cordoned of to the middle classes.

Eventually, researchers hope to discover ways to grow the grain with a stockier plant that wont fall over as easily as it does currently and find ways to grow it in different climates. The grain naturally contains a toxic compound called saponins, a bitter component of quinoa seeds thats used by the plant to ward off predators.

But by finding a way to grow the plant without its saponins, scientists say the seeds will taste sweeter and companies can spend less money and time removing the compound.

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Scientists have mapped the genome for quinoa, potentially making the superfood super cheap - Quartz

From Genome to Body Plan: A Mystery Discovery Institute Decoding genomes has been one of the most important advances of the last sixty years, but it's really just a start of a far larger mystery: the mystery of development. You can appreciate the magnitude of the problem in Illustra's animation of a chick ...

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From Genome to Body Plan: A Mystery - Discovery Institute

Bangladeshi scientists' work disclosing the genome sequence of jute has earned them international recognition. Confirming that the genome sequence of jute has been recognised by the US, agriculture minister Matia Chowdhury said, "Three genome codes of jute now belong to Bangladesh".

HERE'S ALL YOU NEED TO KNOW

Matia told the parliament that US agency National Center for Biotechnology Information (NCBI) has given the numbers for the codes of three genome sequences.

The minister made the statement in a thanksgiving motion on the president's address to Parliament.

She also informed that the outcome of the Bangladeshi scientists' research was published in the Nature Plants journal on January 30.

Bangladesh prime minister Sheikh Hasina has always encouraged jute research which led to the groundbreaking success.

Late professor Dr Maqsudul Alam and his team discovered the genome sequence of 'Tosha' jute in June 2010. The premier announced the news in the Parliament on June 16, 2010.

In August 2013, Sheikh Hasina, in the presence of Dr Maqsudul, announced that the team has sequenced the DNA of the traditional variety of jute known as 'Tosha'.

Their conquest continued as the team sequenced the DNA make-up of a fungus (Macrophomina Phaseolina) which reduces yield time of more than 500 species of crops including jute, tobacco, cotton, maize, soybean and sunflower in the following years.

A genome is an organism's complete set of DNA, including all its genes which is responsible for the characteristics of an organism. Each genome contains all the information needed to build and maintain that organism.

The decoding allowed Bangladesh to own all the genetic documents of this natural fibre.

According to experts, this sequencing will help improve the length and quality of the fiber. It will also help develop high yielding variety of the crop, including colour, strength, saline soil-and pest-resistant jute varieties.

ALSO READ| Bengal: Jute mill reopens after facing demonetisation crisis

Dhaka: 68 jute-laden trucks stranded at Benapole border as India imposes anti-dumping duty

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Bangladesh gets international recognition for disclosing genome sequence of jute - India Today