Category Archives: Genome

Researchers in Biomedical Informatics at IMIM (Hospital del Mar Medical Research Institute) and at the Universitat Politcnica de Catalunya (UPC) have recently published a study in eLife showing that RNA called non-coding (IncRNA) plays an important role in the evolution of new proteins, some of which could have important cell functions yet to be discovered.

Ribosomes produce proteins from the instructions found in an RNA molecule. However, only 2% of the human genome is RNA containing information for the synthesis of proteins, meaning it is coding. Other parts of the genome that are transcribed could be "evolutionary noise," parts of the DNA that are copied to RNA randomly but with no concrete biological function. Now, a new sequencing technique has revealed that many of these transcripts (IncRNAs) may also translate into proteins, leading to an intense debate.

"We have confirmed that in all six species that were studied -human beings, mice, fish, flies, yeast and a plant- many of the IncRNAs were associated to ribosomes and seemed to be ready to translate RNA into proteins. This suggests that they could act as a repository for the synthesis of new proteins" explains Mar Alb, a professor at ICREA and the coordinator for the research group on Evolutionary Genomics at IMIM.

The study has found almost 2,500 IncRNAs that had not been studied, besides those identified previously, and has shown that very few IncRNAs are in more than one species. This would suggest that they have evolved recently. This hypothesis is backed by the fact that the properties of the IncRNA molecules show many similarities with the properties of "young" genes that are known to produce proteins.

"The birth of a new functional protein is a trial and error process that probably requires the production of many transcripts that will not survive the test of time, and IncRNA seems to fit this role. The study of closely related species will allow us to better understand how new coding genes are formed and identify those that can be functional. It will also be interesting to study the link between the alteration of IncRNA expression patterns and certain diseases" concludes Mar Alb.

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The above story is based on materials provided by IMIM (Hospital del Mar Medical Research Institute). Note: Materials may be edited for content and length.

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Parts of genome without a known function may play a key role in the birth of new proteins

PUBLIC RELEASE DATE:

17-Sep-2014

Contact: Maria Jesus Delgado MariaJesus.Delgado@uab.cat 34-935-814-049 Universitat Autonoma de Barcelona

A team of Spanish researchers have obtained the first partial genome sequence of an ancient pig. Extracted from a sixteenth century pig found at the site of the Montsoriu Castle in Girona, the data obtained indicates that this ancient pig is closely related to today's Iberian pig. Researchers also discard the hypothesis that Asian pigs were crossed with modern Iberian pigs.

The study, published in Heredity, sheds new light on evolutionary aspects of pig species, and particularly on that of the Iberian breed, considered to be representative of original European Mediterranean populations. The study was led by Miguel Prez-Enciso, ICREA researcher at Universitat Autnoma de Barcelona (UAB) and at the Centre for Research in Agrigenomics (CRAG). Researchers from the Institute of Evolutionary Biology (CSIC-Pompeu Fabra University) and the National Centre for Genome Analysis (CNAG) also participated in the study.

The sample dates approximately from the years 1520 to 1550 and is previous to the introduction of Asian pigs in Europe, which were later crossed with local European breeds which are the origin of today's international pig species. The sample pig is contemporary to the beginning of America's colonisation.

"Although it is a very fragmented sample, the gene sequence offers very interesting information", Miguel Prez-Enciso says. "First of all, we know it is not a white pig because it is missing a duplicated KIT gene which would make it this colour. This coincides with the majority of paintings from that period, in which the animal was always painted black or in reddish tones. We were also able to establish that it is very closely related to today's Iberian pig species, and specifically to the 'Lampio del Guadiana' strain. We could say that the Iberian pig is very similar to the pigs which existed in the sixteenth century and no great changes have been registered in this genome. Therefore, more studies will be needed before we are able to distinguish the modern species from the older ones".

The study indicates that the pig was a domestic pig, given that the sequence presents a series of markers typical of domestic pigs and which are very rare or absent in wild boars (the precursor animals to the domestic pig); moreover, this coincides with the historical registers of the castle, which clearly indicates that pig breeding was an important castle activity. Nevertheless, there is also evidence of occasional crossbreeding between wild boars and ancient pigs, as has happened between wild boars and Iberian pigs.

"This close relation between the Iberian pig, the European boar and the ancient pig confirms, as stated in previous studies, that crossbreeding between the Asian pig and modern Iberian pigs did not exist or was insignificant", Miguel Prez-Enciso points out.

The study also compared the ancient pig sample with the genome of modern pigs of different breeds, including 'Creole' pigs, which are presumably the descendents of the animals Spanish colonizers brought to America. Researchers demonstrate that this hypothesis is incorrect and that there is very little remaining of those first Spanish animals in today's creole pigs, which were crossbred mainly with international pig breeds.

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Iberian pig genome remains unchanged after 5 centuries

Oxytricha trifallax lives in ponds all over the world. Under an electron microscope it looks like a football adorned with tassels. The tiny fringes are the cilia it uses to move around and gobble up algae. What makes Oxytricha unusual, however, is the crazy things it does with its DNA.

Unlike humans and most other organisms on Earth, Oxytricha doesnt have sex to increase its numbers. It has sex to reinvent itself.

When its food is plentiful, Oxytricha reproduces by making imperfect clones of itself, much like a new plant can grow from a cutting. If theyre well fed, they wont mate, said Laura Landweber, a molecular biologist at Princeton University and lead author of a recent study on Oxytricha genetics. But when Oxytricha gets hungry or stressed, it goes looking for sex.

When two cells come together (as in the image above), the ultimate result is: two cells. Theyve perfected the art of sex without reproduction, Landweber said. The exterior of the two cells remains, but each cell swaps half of its genome with the other. Theyre entering into this pact where each one is going to be 50 percent transformed, Landweber said. They emerge with a rejuvenated genome.

In size, Oxytrichas genome is roughly comparable to ours. It has about 18,500 genes, compared to 20,000 or so for humans. But thats one of the few things we have in common with this pond-dwelling protist.

Unlike the cells of plants and animals (fungi too, for that matter), an Oxytricha cell has at least two nuclei. You can see them under the microscope if you stain for DNA, Landweber said. One nucleus contains a working copy of the genomeall the DNA it uses to make the RNA and proteins essential for everyday life. Last year, Landwebers team discovered that the DNA in Oxytrichas working nucleus is partitioned into approximately 16,000 nanochromosomes, most containing just a single gene. Its a staggering numbermost common plants and animals have somewhere between a dozen and a hundred chromosomes (we humans have 23 pairs).

In a recent paper in the journal Cell, Landweber and colleagues describe an even stranger arrangement in Oxytrichas second nucleus, which contains the genes it will pass on to the next generation. In this nucleus, Oxytricha has about a hundred chromosomes, made up of a total of about 225,000 pieces of DNA. Tens of thousands of these pieces are encrypted: The letters of the genetic code are flipped or scrambled relative to the corresponding copy in the working nucleus.

When two cells mate, each partner transfers a set of these chromosomes to the other. Then, each cell breaks the chromosomes down into their constituent 225,000 pieces and uses those pieces to assemble a new working genome, decrypting the encrypted piecesalong the way.

It really is like its running an algorithm, and its a cellular computer, Landweber said.

In the process of rebuilding its genome, which takes about 2 days, each cell discards more than 90 percent of its DNA to end up with a newly remodeled set of 16,000 nanochromosomes in its working nucleus. The final result for both cells is a new genome that incorporates pieces from its original stash of DNA as well as new pieces of DNA from its partner.

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This Bizarre Organism Builds Itself a New Genome Every Time It Has Sex

September 15, 2014 Sophie Langley

Genome research means zero-caffeine coffee bean could soon grow in Queensland

It will soon be possible to grow premium-quality caffeine-free coffee, tea and cocoa, thanks to research from the University of Queensland.

The University of Queensland researchers said the developments will offer the 12 per cent of coffee drinkers who choose decaf access to a pure, less-processed product with all the full-bodied flavour of the real thing.

Professor Robert Henry, at UQs Queensland Alliance for Agriculture and Food Innovation (QAAFI), said this was one outcome of an international research effort analysing the coffee genome.

It should soon be possible to select and grow coffee with a pre-determined level of caffeine ranging from zero-caf to jumpstart, Professor Henry said. Helping Queensland producers to grow export-quality coffee destined for high-value niche markets is our ultimate goal, he said.

Professor Henry said genome sequencing of the coffee plant Coffea canephora confirmed that caffeine had developed independently in various plants. Professor Henry contributed much of the DNA sequence data used in assembling the coffee genome.

Coffee, cacao (the source of cocoa and chocolate) and tea appear to share an ability to produce caffeine in their leaves, shoots or stems, Professor Henry said.

Although such plants are not closely related, they all synthesise caffeine, Professor Henry said. It seems that during their evolution, each plant independently developed the ability to make caffeine, he said.

Professor Henry said the researchers thought caffeine offered plants several advantages, including insecticidal properties and an inhibitory function that prevents seed germination in competing species.

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Genome research means zero-caffeine coffee bean could soon grow in Queensland

Bob Wright Talks Genome Project, ABLE Act on Varney Co.
Autism Speaks co-Founder Bob Wright appeared on Fox Business #39; Varney Co. to discuss embattled NFL star Ray Rice, Autism Speaks #39; collaboration with Google a...

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Bob Wright Talks Genome Project, ABLE Act on Varney & Co. - Video

Sequencing and analysis of gibbon genome sheds light on its complex evolution
Sequencing and analysis of gibbon genome sheds light on its complex evolution.

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Sequencing and analysis of gibbon genome sheds light on its complex evolution - Video

11.09.2014 - (idw) Deutsches Primatenzentrum GmbH - Leibniz-Institut fr Primatenforschung

Mobile DNA element allows conclusions on the evolution of apes An international team of researchers that includes Christian Roos, Markus Brameier and Lutz Walter from the German Primate Center (DPZ) in Gttingen, have decoded the genome of gibbons from Southeast Asia. With this, the entire genetic information of five different species of this primate family has been sequenced for the first time. Comparisons with the genome data of humans and our closest relatives, the great apes, show that while we all genetically have the same ancestors, the genetic information of the gibbons has changed more rapidly and stronger in the course of the evolutionary process. The researchers could identify a new DNA element that only occurs in gibbons. This DNA element increases the mutation rate, and is thus of crucial importance for the evolutionary development. Thanks to the DNA element, the gibbon is also known as the one with the long, strong arms who elegantly moves through the forests of Southeast Asia. The study published in the current issue of Nature, allows important insights in the molecular fundamentals of the evolutionary process (Carbone et al. 2014)

The gibbons, known as small apes are genetically farther from humans than the great apes chimpanzees, bonobos, gorillas and orang-utans. In the genealogy of the evolutionary developments of primates, the gibbons do occupy a key position. In the course of the evolutionary process, they were the first to split from the hereditary line of the great apes and humans.

The complete sequencing of the gibbon genome was pending until now, says Christian Roos, a scientist from the Primate Genetics Laboratory at the DPZ. In order to fully understand the human evolution and to draw conclusions on our evolutionary roots, we need to conduct phylogenetic research of our more distant relatives.

Genetic disorder and jumping gene sections

In their genome analysis, the researchers discovered that the genetic information of the gibbons differs in their entirety from that of humans and of apes. The genetic information itself is similar to ours, explains Christian Roos. However, large segments of DNA and in such, many genes are arranged differently on the individual chromosomes. This "chromosomal disorder" is a key feature of the gibbon genome and has probably occurred after their secession from the ancestral line of the apes and humans.

Through further research on the gibbon DNA, scientists were finally able to identify a possible cause for these changes in the genome: A jumping DNA element called LAVA transposon can be copied and integrated elsewhere in the genome. So far, transposons or jumping genes have been detected in many different organisms. However, the LAVA transposon is unique to the gibbon genome. The special feature of this DNA element is its positioning in precisely those genes that play a role in the chromosome distribution during cell division and thus influences them. Analyses of the phylogenetic development of the gibbon line also indicate a connection to the existence of the LAVA transposons. Their first appearance can be traced back with a high probability to the time of the splitting of the gibbons from the line of apes and humans.

Through comparative DNA analyses, the researchers could also identify genes subjected to a positive selection. In the course of evolution, genes that favored the adaptation of the gibbons to their way of life, continued to develop. These include genes responsible for anatomical specifications such as longer arms or stronger muscles. Gibbon genes, which have undergone a positive selection are, for example TBX5, which is required for the development of the front extremities and COL1A1, responsible for the development of the protein collagen. The latter is one of the main components of connective tissues in bones, teeth and tendons.

"These genes are positively selected only in the gibbon genome", says Christian Roos. In future projects, sequencing will be performed on other gibbon species. We hope to be able to further characterize these genes and to identify other gibbon-specific genes.

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Gibbon genome sequenced

RTP 180: "Social Genome: Putting Big Data to Work to Advance Society"
Hye-Chung Kum is a data scientist cross trained in computer science and social science. She founded and currently leads the Population Informatics Research G...

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RTP 180: "Social Genome: Putting Big Data to Work to Advance Society" - Video

Genome Hazard Movie Trailer [Eng Sub] ()
Genome Hazard Movie Trailer [Eng Sub] () Click Here to Subscribe: http://bit.ly/10TNEL1 Click here to sign up for an alert: http://bit.ly/1lQ6jUY DramaFever Saturday Movie Night...

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Washington Gibbons - the small, long-armed tree swingers that inhabit the dense tropical forests of Southeast Asia - have become the last of the planet's apes to have their genetic secrets revealed.

"We now have whole genome sequences for all the great apes and, with this work, also the small apes - gibbons," said Jeffrey Rogers, a primate genetics researcher at the Human Genome Sequencing Center at Baylor College of Medicine in Houston.

"This provides new information and insight into the history of the human genome, in evolutionary terms," added Rogers, who participated in the study published in the journal Nature.

Scientists on Wednesday unveiled the genome of gibbons, a close cousin of humans genetically but still the most distantly related to people among the apes.

The study found the genetic underpinning for the fantastic ability of gibbons to swing from tree to tree at speeds of up to 35 mph. It also detected an extraordinary number of structural changes in their DNA. Such changes can be troublesome in other species, including causing cancer in people, but do not seem to have been problematic during the evolution of gibbons.

Among the great apes, the chimpanzee genome was published in 2005, followed by the orangutan in 2011 and the gorilla and the bonobo in 2012.

The gibbon genome fills the gap between Old World Monkeys like macaques and baboons and the great apes, said the study leader, primate genomics expert Lucia Carbone of the Oregon Health & Science University and the Oregon National Primate Research Center.

Carbone said other studies have estimated the gibbon genome as 96 percent similar to people, compared with 98 percent for chimpanzees, our closest ape cousin.

Gibbons are critically endangered. One species, the Hainan gibbon, has only 20 individuals left. Carbone expressed hope the genome will help forge conservation strategies, for instance to assess genetic diversity in wild populations and identify ones that are most at risk.

These omnivores forage for food in the high forest canopy, eating fruit, leaves, bird eggs, insects and birds. Gibbons are monogamous, forming long-term pairs. Individuals from their 19 species range from roughly 11 pounds to 26 pounds.

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Scientists unveil gibbon genome, reveal secrets of our endangered ape relatives