Category Archives: Genome

An international study coordinated by researchers from IRD, the CEA (Genoscope), CIRAD, the CNRS, and the University of Buffalo (United States), and involving many laboratories, helped identify a reference genome sequence for coffee trees for the first time. This discovery is important in two ways: first, it is fundamental as it improves understanding of the organisation of the genome, its function, and its evolution; secondly, it also offers new possibilities for selection or improvement of coffee tree varieties.

These results were published in the journal Science on 5 September 2014.

In the study published in Science, the researchers were interested in Robusta coffee because of its average sized genome (710 million pairs of DNA bases) and its diploid nature (contrary to Coffea arabica, which is tetraploid). The genetic map of the coffee tree studied, produced in the 1980s by IRD in Cote d'Ivoire, also had the advantage of being a homozygous plant (two identical sets of eleven chromosomes), which is easier to analyse than natural heterozygotes.

By using several sequencing technologies, Genoscope (CEA) coordinated the mapping of the DNA sequence for the coffee tree, assembled in large fragments able to be used in various types of analysis. The IRD and CIRAD teams then anchored these sequence fragments to a high-density genetic card to reconstruct the pseudo-chromosomes. A catalogue of genes and repeated sequences was then created and validated, allowing for a comparison with other plants.

A critical stage

Thus, the researchers established a reference genome sequence for coffee trees (including for the species Coffea arabica), and more generally for the Rubiaceae, one of the largest families of flowering plants (containing nearly 12,500 species).

A comparative analysis of genomes by the international consortium also revealed that the organisation of the coffee tree genome is best preserved in the Asteridae (the family to which potatoes and tomatoes belong) and is very close to that of the ancestral species from which all true Dicotyledons (or Eudicotyledons) descended through evolution. Lastly, the study of the genome improves knowledge of the secondary metabolism of plants and its diversification. A comparative analysis with the cacao tree genome also shows that the biosynthesis of caffeine is due to enzymes unique to each species, which appeared at various moments in their evolution.

Over the longer term, the identification of the coffee tree genome sequence opens up new possibilities for varietal improvement, knowledge of the specific functions of the genes (in particular those specific to coffee trees), the possibility of transferring results to other species, and refining diagnostic tools for the function of the plant.

It will facilitate the completion of applied projects, such as the selection or creation of coffee tree varieties with improved technological and/or qualitative characteristics; more resistant to environmental constraints and to bioagressors, such as for example orange leaf rust. In fact, this disease still has a considerable impact on coffee cultivation and the economy of small producer countries in Central America such as Guatemala, Honduras, and Costa Rica. Lastly, it should help guide producers toward ecologically intensive agriculture.

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Coffee tree genome sequenced

New DNA sequencing technologies have greatly advanced genomic and metagenomic studies in plant biology. Scientists can readily obtain extensive genetic information for any plant species of interest, at a relatively low cost, rapidly accelerating the pace of genome sequencing.

However, since plant tissues harbor three separate genomes (nuclear, chloroplast, and mitochondrial), it can often be challenging to isolate the particular genome of interest from extracted DNA samples. Sequencing DNA containing all three genomes therefore results in a considerable amount of wasted data, for example, if only the chloroplast genome is desired for the study.

Methods exist to isolate particular genomic regions, but each of these has drawbacks. For example, some protocols require extensive lab work, while others (e.g., long-range PCR and hybrid enrichment) require prior knowledge of the genomic regions of interest.

A new method by researchers from New England Biolabs and New Mexico State University provides plant biologists with a quick and simple approach for separating plant nuclear DNA from organellar DNA for genomic and metagenomic studies. The approach, published in the November issue of Applications in Plant Sciences, targets the methyl-CpG-binding domain, following a similar method applied for genomic studies of humans.

The method relies on differences in CpG methylation between nuclear and organellar (i.e., chloroplast and mitochondrial) genomes in plants. Compared to the nuclear genome, the chloroplast and mitochondrial genomes essentially lack CpG methylation (i.e., the addition of methyl groups to sites in the genome where cytosine and guanine occur side by side).

Given these different methylation patterns, the researchers used specialized magnetic beads that hybridize with methyl-CpG-rich DNA regions in an attempt to separate nuclear DNA from organellar DNA in total genomic DNA samples. They then sequenced the methyl-enriched portion and the methyl-depleted portion separately. They found that the methyl-enriched sample contained a considerable increase in concentration of nuclear DNA, while the methyl-depleted sample contained an increased concentration of organellar DNA.

Dr. Donovan Bailey, senior author of the study and professor at New Mexico State University, said this approach has several advantages over previously established methods for enriching either nuclear or organellar DNA for genome sequencing.

"Our primary perceived benefit includes the development of a means of partitioning DNA by genomic origin when one has no prior knowledge of the genomes being studied, other than the domain of origin -- nuclear, organellar, or prokaryote. Furthermore, not requiring extensive starting material and the speed are benefits relative to some methods."

According to Bailey, this approach can also be used to target genomes of endophytes (i.e., fungi that live in plants) and prokaryotic parasites in plant DNA samples. Endophyte genomes undergo CpG methylation, while prokaryotic genomes do not, making it easy to sequence either of these along with the particular plant genome(s) of interest. This will provide researchers with greater insight on the diversity of other eukaryotes and prokaryotes living inside plant tissues.

Although this study focused on flowering plants, Bailey said the approach will likely work well across other major plant groups (e.g., ferns, gymnosperms).

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Plants: Breaking down DNA by genome

Destiny and DNA:: Our Pliable Genome
Our genes strictly dictate our personalities, appearance and diseases. Or do they? Research has revealed that genes can turn on and off; they can be expressed for years and then silenced. Sometimes.

By: World Science Festival

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Destiny and DNA:: Our Pliable Genome - Video

Uncovering Genome Mysteries - World Community Grid
Uncovering Genome Mysteries expects to examine close to 200 million genes from a wide variety of life forms, such as seaweeds from Australian coastlines and ...

By: SETIKAH

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Uncovering Genome Mysteries - World Community Grid - Video

Webinar: Genome Editing Transfecting ZFNs, TALENs or CRISPR/Cas Using Nucleofector Technology
View the archived webinar and learn how to successfully perform genome editing using ZFNs, TALENs or CRISPR in combination with Lonza #39;s Nucleofector Technology.

By: Lonza

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Webinar: Genome Editing Transfecting ZFNs, TALENs or CRISPR/Cas Using Nucleofector Technology - Video

As potential next-generation therapeutics and research tools, few life sciences technologies hold more promise than genome-editing proteins -- molecules that can be programmed to alter specific genes in order to treat or even cure genetic diseases.

There's at least one catch though -- getting genome-editing proteins into cells, where they need to be to access the genome, is a major challenge, especially in live animals or human patients.

Conventionally, researchers have delivered the DNA encoding these genome-editing proteins into cells and then relied on the cells to produce the corresponding genome-editing proteins. But many DNA delivery strategies cannot be used in animals or human patients. Other DNA delivery strategies such as infecting with viruses that inject DNA into cells can raise complicating long-term safety issues, especially when the editing the human genome is involved.

What may be more promising, the new study finds, is the direct delivery of genome-editing proteins into cells, rather than delivery of the corresponding genes that encode these proteins. And a class of molecules that can open the door for genome-editing proteins, as it turns out, is probably already on the shelves of many biologists.

Led by Professor of Chemistry and Chemical Biology David Liu and his group members Drs. John Zuris and David Thompson, a team of Harvard researchers have developed a system that uses commercially-available molecules called cationic lipids -- essentially long, greasy molecules that carry a positive charge at one end -- to efficiently introduce genome-editing proteins into cells, and have even demonstrated that the technology can be used to modify genes in living animals. The study is described in an October 30 paper in Nature Biotechnology.

"Current drugs that treat genetic diseases cannot address the root cause of the disease," Liu explained. "Unlike infectious diseases, for example, which we treat by killing the disease-causing agent, in the case of diseases that come from mutations in our own genes, one has to go into the cells and do surgery on our genomes to fix the root cause. Thanks to recent discoveries by scientists around the world, we now have genome-editing proteins that can do the surgery. But the challenge is that these proteins, like virtually all proteins, do not enter cells spontaneously.

"In this study we describe a method to very potently deliver genome-editing proteins into cells," Liu added. "And we observed efficient genome modification using this method not just in cultured cells, but also in living animals."

Though he warned that no system, including this one, will be a one-size-fits-all delivery solution, Liu believes that delivering genome-editing proteins into cells could offer hope to patients suffering from a host of conditions, including certain diseases of the eye, ear, liver, muscles, and blood.

One condition that's already in researchers' crosshairs is deafness.

Working with Zheng-Yi Chen, an Associate Professor of Otology and Laryngology at Harvard Medical School and researcher at Massachusetts Eye and Ear Infirmary, Liu and colleagues used the newly-developed system to modify genes in specialized "hair cells" in the inner ear of mice. Hair cell damage, either from environmental or genetic factors, is a common cause of hearing loss.

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Efficient genetic editing developed

PUBLIC RELEASE DATE:

31-Oct-2014

Contact: Beth Parada apps@botany.org American Journal of Botany @Botanical_

New DNA sequencing technologies have greatly advanced genomic and metagenomic studies in plant biology. Scientists can readily obtain extensive genetic information for any plant species of interest, at a relatively low cost, rapidly accelerating the pace of genome sequencing.

However, since plant tissues harbor three separate genomes (nuclear, chloroplast, and mitochondrial), it can often be challenging to isolate the particular genome of interest from extracted DNA samples. Sequencing DNA containing all three genomes therefore results in a considerable amount of wasted data, for example, if only the chloroplast genome is desired for the study.

Methods exist to isolate particular genomic regions, but each of these has drawbacks. For example, some protocols require extensive lab work, while others (e.g., long-range PCR and hybrid enrichment) require prior knowledge of the genomic regions of interest.

A new method by researchers from New England Biolabs and New Mexico State University provides plant biologists with a quick and simple approach for separating plant nuclear DNA from organellar DNA for genomic and metagenomic studies. The approach, published in the November issue of Applications in Plant Sciences, targets the methyl-CpG-binding domain, following a similar method applied for genomic studies of humans.

The method relies on differences in CpG methylation between nuclear and organellar (i.e., chloroplast and mitochondrial) genomes in plants. Compared to the nuclear genome, the chloroplast and mitochondrial genomes essentially lack CpG methylation (i.e., the addition of methyl groups to sites in the genome where cytosine and guanine occur side by side).

Given these different methylation patterns, the researchers used specialized magnetic beads that hybridize with methyl-CpG-rich DNA regions in an attempt to separate nuclear DNA from organellar DNA in total genomic DNA samples. They then sequenced the methyl-enriched portion and the methyl-depleted portion separately. They found that the methyl-enriched sample contained a considerable increase in concentration of nuclear DNA, while the methyl-depleted sample contained an increased concentration of organellar DNA.

Dr. Donovan Bailey, senior author of the study and professor at New Mexico State University, said this approach has several advantages over previously established methods for enriching either nuclear or organellar DNA for genome sequencing.

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Breaking down DNA by genome

PUBLIC RELEASE DATE:

31-Oct-2014

Contact: Peter Reuell preuell@fas.harvard.edu 617-496-8070 Harvard University @HarvardResearch

As potential next-generation therapeutics and research tools, few life sciences technologies hold more promise than genome-editing proteins molecules that can be programmed to alter specific genes in order to treat or even cure genetic diseases.

There's at least one catch though getting genome-editing proteins into cells, where they need to be to access the genome, is a major challenge, especially in live animals or human patients.

Conventionally, researchers have delivered the DNA encoding these genome-editing proteins into cells and then relied on the cells to produce the corresponding genome-editing proteins. But many DNA delivery strategies cannot be used in animals or human patients. Other DNA delivery strategies such as infecting with viruses that inject DNA into cells can raise complicating long-term safety issues, especially when the editing the human genome is involved.

What may be more promising, the new study finds, is the direct delivery of genome-editing proteins into cells, rather than delivery of the corresponding genes that encode these proteins. And a class of molecules that can open the door for genome-editing proteins, as it turns out, is probably already on the shelves of many biologists.

Led by Professor of Chemistry and Chemical Biology David Liu and his group members Drs. John Zuris and David Thompson, a team of Harvard researchers have developed a system that uses commercially-available molecules called cationic lipids essentially long, greasy molecules that carry a positive charge at one end to efficiently introduce genome-editing proteins into cells, and have even demonstrated that the technology can be used to modify genes in living animals. The study is described in an October 30 paper in Nature Biotechnology.

"Current drugs that treat genetic diseases cannot address the root cause of the disease," Liu explained. "Unlike infectious diseases, for example, which we treat by killing the disease-causing agent, in the case of diseases that come from mutations in our own genes, one has to go into the cells and do surgery on our genomes to fix the root cause. Thanks to recent discoveries by scientists around the world, we now have genome-editing proteins that can do the surgery. But the challenge is that these proteins, like virtually all proteins, do not enter cells spontaneously.

"In this study we describe a method to very potently deliver genome-editing proteins into cells," Liu added. "And we observed efficient genome modification using this method not just in cultured cells, but also in living animals."

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Efficient genetic editing

Sebastian Mullaert Patrick Siech - Genome (Sebastian Mullaert Remake) | Minus
Genome I [MINUSMIN31] Released: 2014-10-27 http://www.beatport.com/release/genome-i/1390849 Sebastian Mullaert Patrick Siech Announce Part One of Their Genome Trilogy Inspired in equal ...

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Sebastian Mullaert & Patrick Siech - Genome (Sebastian Mullaert Remake) | Minus - Video

Sebastian Mullaert Patrick Siech - Genome (Sebastian Mullaert Dub)
Genome I / Minus Sebastian Mullaert Patrick Siech Announce Part One of Their Genome Trilogy Inspired in equal measure by analog synthesizer technology and ...

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Sebastian Mullaert & Patrick Siech - Genome (Sebastian Mullaert Dub) - Video