Category Archives: Genome

Public release date: 28-Apr-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

April 28, 2013, Shenzhen, China- The Joint International Turtle Genomes Consortium, led by investigators from RIKEN, BGI, and Wellcome Trust Sanger Institute, has completed the genome sequencing of soft-shell turtle (Pelodiscus sinensis) and green sea turtle (Chelonia mydas). These achievements shed new light on the origin of turtles and applied the classical evo-devo model to explain the developmental process of their unique body plan. The findings were published online in Nature Genetics.

The evolution of turtles is an enigma in science. Their distinct body design-with a sharp beak and protective hard shell has changed very little over the past 210 million years. As the smallest species of soft-shell turtles, Chinese soft-shell turtle was once commonly sold in pet shops. Green sea turtle is considered as the largest of all the hard-shelled sea turtles and is named because of the green fat beneath its shell. Its population sizes has been drastically reduced recently and it has been listed as an endangered species.

To reveal the evolutionary history of turtles and the mechanisms underlying the development of their unique anatomical features, researchers in this project sequenced and analyzed the genomes of soft-shell turtle and green sea turtle. They found the evidence that turtles are likely to be a sister group with the common ancestor of crocodilians and birds from whole genome phylogenetic analyses. The turtles were diverged from archosaurians approximately between 267.9 and 248.3 million years ago, which coincides with the time range of the Upper Permian to Triassic period that overlapped or followed shortly after the end of Permian extinction.

In the study, researchers performed the brief research on genes may be associated with the turtle-specific characteristics, and found some olfactory receptor (OR) gene families were highly expanded in both turtles. This finding suggests that turtles have developed superior olfaction ability against a wide variety of hydrophilic substances. In addition, many genes involved in taste perception, hunger-stimulating, and energy homeostasis regulating hormone ghrelin have been uniquely lost in turtles. Researchers suggested that the loss of these genes may be related to their low-metabolic rate.

The consortium also investigated the association of embryonic gene expression profiles (GXP) and their morphological evolution pattern, based on ENSEMBL soft-shell turtle gene-set. By integrating RNA-seq technology, comparative genomics method, and mathematical statistical approaches, researchers confirmed GXP divergence during embryogenesis of soft-shell turtle and chicken indeed follows the developmental hourglass model. They also revealed that the maximal conservation stage occurred at around the vertebrate phylotypic period, rather than at later stage that show the amniote-common pattern.

To clarify the morphological specifications of turtle embryogenesis in late development, especially the formation of the carapacial ridge (CR), researchers investigated into CR-specific miRNA expression, found existence of tissue-specific miRNAs and involvement of Wnt signaling. Also they revealed the Wnt expression involved in the carapacial ridge (CR) formation of the turtle shell, researchers annotated all the Wnt genes in the two turtle genomes, identifying a total of 20 Wnt genes. Intriguingly, they discovered Wnt5a is the only Wnt gene expressed in the turtle CR region, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty.

Zhuo Wang, Project Manager from BGI, said, "The genome-wide phylogenetic analysis of two turtles in our project, along with two crocodile genomic data additionally, makes clear the evolutionary history of turtles in diverging from other species and settles the disputes about the phylogenetic position of reptiles. The genomic analyses and embryonic gene expression profiles have been combined to reveal the fundamental evo-devo questions on turtle evolution and development. These works have been highly appreciated by the editor and reviewers. Besides the interesting story, the genomic data we released here will provide a platform for more scientists to initialize their genome-wide studies on turtles. "

Dr. Hongyan Zhang, Regional Director of BGI Tech Solutions Co., Ltd. for Japan, said, "The completed genome sequencing of soft-shell turtle and green sea turtle give an important hint to uncover the development and evolution mechanism of turtles. This scientific achievement is a joint effort supported by BGI's advanced sequencing technologies and excellent bioinformatics capabilities, the profound basis research background of developmental biology from RIKEN, and other partners' great contributions. We are looking forward to having more collaboration with other scientists for better exploring the secret of life together in the near future."

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Turtle genome analysis sheds light on the development and evolution of turtle-specific body plan

London, April 29 (ANI): Researchers working under the Joint International Turtle Genomes Consortium have completed the genome sequencing of soft-shell turtle (Pelodiscus sinensis) and green sea turtle (Chelonia mydas).

These achievements shed new light on the origin of turtles and applied the classical evo-devo model to explain the developmental process of their unique body plan.

The evolution of turtles is an enigma in science. Their distinct body design-with a sharp beak and protective hard shell has changed very little over the past 210 million years.

As the smallest species of soft-shell turtles, Chinese soft-shell turtle was once commonly sold in pet shops. Green sea turtle is considered as the largest of all the hard-shelled sea turtles and is named because of the green fat beneath its shell. Its population sizes have been drastically reduced recently and it has been listed as an endangered species.

To reveal the evolutionary history of turtles and the mechanisms underlying the development of their unique anatomical features, researchers in this project sequenced and analyzed the genomes of soft-shell turtle and green sea turtle.

The project, led by investigators from RIKEN, BGI, and Wellcome Trust Sanger Institute, found the evidence that turtles are likely to be a sister group with the common ancestor of crocodilians and birds from whole genome phylogenetic analyses.

The turtles were diverged from archosaurians approximately between 267.9 and 248.3 million years ago, which coincides with the time range of the Upper Permian to Triassic period that overlapped or followed shortly after the end of Permian extinction.

In the study, researchers performed the brief research on genes may be associated with the turtle-specific characteristics, and found some olfactory receptor (OR) gene families were highly expanded in both turtles.

This finding suggests that turtles have developed superior olfaction ability against a wide variety of hydrophilic substances. In addition, many genes involved in taste perception, hunger-stimulating, and energy homeostasis regulating hormone ghrelin have been uniquely lost in turtles. Researchers suggested that the loss of these genes might be related to their low-metabolic rate.

The consortium also investigated the association of embryonic gene expression profiles (GXP) and their morphological evolution pattern, based on ENSEMBL soft-shell turtle gene-set. By integrating RNA-seq technology, comparative genomics method, and mathematical statistical approaches, researchers confirmed GXP divergence during embryogenesis of soft-shell turtle and chicken indeed follows the developmental hourglass model. They also revealed that the maximal conservation stage occurred at around the vertebrate phylotypic period, rather than at later stage that show the amniote-common pattern.

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Genome analysis sheds light on origin of turtles

Neanderthal Genome Results

By: outthetube

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Neanderthal Genome Results - Video

Director of the National Human Genome Research Institute, Eric Green, with a double helix model at the National Institutes of Health in Bethesda | credits: New York Times Service

Eight years of work, thousands of researchers around the world, $1bn spent and finally it was done. On April 14, 2003, a decade ago this week, scientists announced that they had completed the Human Genome Project, compiling a list of the three billion letters of genetic code that make up what they considered to be a sort of everypersons DNA.

To commemorate the anniversary, Eric D. Green, the director of the National Human Genome Research Institute at the National Institutes of Health, spoke about what has been accomplished, what it means and what is coming next. Our conversation has been condensed and edited.

Take us back to that day 10 years ago. Whose genome was sequenced? And why would anyone want to know the genome sequence of some random person? Arent we all unique?

The idea all along was not to sequence a persons genome, but to develop a resource. It would be the sequence of a hypothetical genome, a reference genome. It was meant to represent humanity.

What does that mean? You used human DNA, right? Why was the genome hypothetical?

The way it was done then, we were reading out the letters of the genome, one page at a time, and at the end of the day different pages came from different people. Each page was a stretch of DNA, about 100,000 bases long out of the total 3 billion bases (the four chemicals that make up DNA).

The genome of one person, an anonymous blood donor in Buffalo, was the majority because the guy who was the expert at making a big DNA library the equivalent of those pages was at Roswell Park Cancer Institute, which is in Buffalo.

But if that hypothetical genome was made up of bits and pieces of DNA sequences from lots of different people, what good was it?

It was a reference that could be used for further research. People differ in only one out of 1,000 bases, so that reference genome is 99.9 per cent identical to any persons genome. We used that tool to build sort of a highway map. We could go through it and add information about what was important.

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A decade later, thanking the genome project

NEW YORK--(BUSINESS WIRE)--

The New York Genome Center (NYGC) and Roswell Park Cancer Institute (RPCI) today announced that RPCI, a nationally-designated Comprehensive Cancer Center in Buffalo, NY, is joining the organization as an Associate Member. This unique collaboration is designed to accelerate the clinical applications for genome sequencing in oncology.

We are thrilled by Roswell Park Cancer Institutes decision to join the NYGC collaboration, said Robert B. Darnell, President and Scientific Director of NYGC. Its unique, specialized focus on cancer research, prevention and treatment will contribute significantly toward our knowledge of disease, furthering our mission of achieving personalized medicine.

RPCI, founded by Dr. Roswell Park in 1898, is Americas first cancer center and is one of only three existing institutions in New York State to hold the National Cancer Institutes comprehensive cancer center designation. As one of the few freestanding comprehensive cancer centers in the US, RPCI has sustained its role as a national and international leader in cancer research, clinical care and education, establishing an exemplary reputation based on the combined strength of its basic and translational research, educational programs, and multidisciplinary and compassionate patient care. It also brings additional resources such as its Genomics Shared Resource, a Pathology Resource Network, Bioinformatics Shared Resource, and Data Bank and BioRepository (DBBR).

The bio banking facility at RPCI will be a tremendous resource to learn about genetic origins and new treatments for cancer patients, and it will expand the possibilities for important large-scale cancer genomic studies conducted at NYGC and with our collaborating member institutions, Darnell said.

The resources RPCI brings include the Institutes priority to understand cancer health disparities within its geographic target and develop appropriate research initiatives around the needs of those populations.

We are enthusiastic about the potential this collaboration brings to our cancer research capabilities and what it will mean for future treatment options, said Donald Trump, MD, President and CEO of Roswell Park Cancer Institute. This partnership enhances our opportunities to extend collaborations with our colleagues throughout New York, including the New York City cancer centers, thus allowing us to bring the latest discoveries in genome science to our work to understand, prevent and cure cancer and other diseases.

In December 2012, NYGC received $1.5 million from New York State as part of the Regional Economic Development Council Initiative (RDC) to assist with construction of its new 170,000 sf facility in Manhattan and to ramp up its staffing in the critical areas of bioinformatics, sequencing, and research computing; and in April 2012, RPCI received $5.1 million from the New York State Economic Development Council to extend its genomic capabilities.

Both NYGC and RPCI have already leveraged their respective investments from the states RDC to forge stronger collaborations between institutions across New York State, enhancing the impact of these investments throughout New York, Darnell said. This partnership will spur development of exciting new research opportunities and clinical breakthroughs that will lead to improvements in the health of all New Yorkers.

About Roswell Park Cancer Institute

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New York Genome Center Announces Roswell Park Cancer Institute as Associate Member

Apr. 17, 2013 An international team of researchers has decoded the genome of a creature whose evolutionary history is both enigmatic and illuminating: the African coelacanth. A sea-cave dwelling, five-foot long fish with limb-like fins, the coelacanth was once thought to be extinct. A living coelacanth was discovered off the African coast in 1938, and since then, questions about these ancient-looking fish -- popularly known as "living fossils" -- have loomed large. Coelacanths today closely resemble the fossilized skeletons of their more than 300-million-year-old ancestors. Its genome confirms what many researchers had long suspected: genes in coelacanths are evolving more slowly than in other organisms.

"We found that the genes overall are evolving significantly slower than in every other fish and land vertebrate that we looked at," said Jessica Alfldi, a research scientist at the Broad Institute and co-first author of a paper on the coelacanth genome, which appears in Nature this week. "This is the first time that we've had a big enough gene set to really see that."

Researchers hypothesize that this slow rate of change may be because coelacanths simply have not needed to change: they live primarily off of the Eastern African coast (a second coelacanth species lives off the coast of Indonesia), at ocean depths where relatively little has changed over the millennia.

"We often talk about how species have changed over time," said Kerstin Lindblad-Toh, scientific director of the Broad Institute's vertebrate genome biology group and senior author. "But there are still a few places on Earth where organisms don't have to change, and this is one of them. Coelacanths are likely very specialized to such a specific, non-changing, extreme environment -- it is ideally suited to the deep sea just the way it is."

Because of their resemblance to fossils dating back millions of years, coelacanths today are often referred to as "living fossils" -- a term coined by Charles Darwin. But the coelacanth is not a relic of the past brought back to life: it is a species that has survived, reproduced, but changed very little in appearance for millions of years. "It's not a living fossil; it's a living organism," said Alfldi. "It doesn't live in a time bubble; it lives in our world, which is why it's so fascinating to find out that its genes are evolving more slowly than ours."

The coelacanth genome has also allowed scientists to test other long-debated questions. For example, coelacanths possess some features that look oddly similar to those seen only in animals that dwell on land, including "lobed" fins, which resemble the limbs of four-legged land animals (known as tetrapods). Another odd-looking group of fish known as lungfish possesses lobed fins too. It is likely that one of the ancestral lobed-finned fish species gave rise to the first four-legged amphibious creatures to climb out of the water and up on to land, but until now, researchers could not determine which of the two is the more likely candidate.

In addition to sequencing the full genome -- nearly 3 billion "letters" of DNA -- from the coelacanth, the researchers also looked at RNA content from coelacanth (both the African and Indonesian species) and from the lungfish. This information allowed them to compare genes in use in the brain, kidneys, liver, spleen and gut of lungfish with gene sets from coelacanth and 20 other vertebrate species. Their results suggested that tetrapods are more closely related to lungfish than to the coelacanth.

However, the coelacanth is still a critical organism to study in order to understand what is often called the water-to-land transition. Lungfish may be more closely related to land animals, but its genome remains inscrutable: at 100 billion letters in length, the lungfish genome is simply too unwieldy for scientists to sequence, assemble, and analyze. The coelacanth's more modest-sized genome (comparable in length to our own) is yielding valuable clues about the genetic changes that may have allowed tetrapods to flourish on land.

By looking at what genes were lost when vertebrates came on land as well as what regulatory elements -- parts of the genome that govern where, when, and to what degree genes are active -- were gained, the researchers made several unusual discoveries:

The coelacanth genome may hold other clues for researchers investigating the evolution of tetrapods. "This is just the beginning of many analyses on what the coelacanth can teach us about the emergence of land vertebrates, including humans, and, combined with modern empirical approaches, can lend insights into the mechanisms that have contributed to major evolutionary innovations," said Chris Amemiya, a member of the Benaroya Research Institute and co-first author of the Nature paper. Amemiya is also a professor at the University of Washington.

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Coelacanth genome surfaces: Unexpected insights from a fish with a 300-million-year-old fossil record

The Human genome - who owns your DNA? - Truthloader Investigates
The Human genome project is ten years old in 2013, so we take a look at the background, impact and potential pitfalls of the project, including patents that ...

By: Truthloader

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The Human genome - who owns your DNA? - Truthloader Investigates - Video

A coelacanth head at the Smithsonian Museum of Natural History.

The coelacanth was discovered in 1938, but scientists already knew what the organism looked like. It's the lone representative of a lineage that we knew from fossils, the last of which were preserved while the dinosaurs still roamed the earth. Thus, the coelacanth earned the nickname of "living fossil," but that's a bit misleading. Although it looks similar, we have no real idea of how much or how little the organism has changed during those millions of years. After all, on the DNA level, the tuatara (the last representative of a lineage that originated in the Triassic) is the fastest evolving creature we know of.

Still, the coelacanth is interesting to scientists. It, along with the lungfish, is representative of a group called lobe-finned fishes, which have four limb-like fins. A series of fossils have revealed that these fins gradually transformed into the four limbs of modern tetrapods such as reptiles, birds, amphibians, and mammals. So, the coelacanth could tell us something about the base state that our limbs started out in. To find out, researchers have now sequenced its genome, and they found that genes essential to constructing our limbs were already active in the fins of the coelacanth.

The genome itself is just another example of all we can do with the massive DNA sequencing capacity that we've built up. Things only get interesting when you compare the coelacanth's genome to the genomes of other species. These tests do show that the coelacanth lives up to its dinosaur-era reputation, as its proteins are changing at the lowest rate of any vertebrate we've looked at. The new genome also makes it clear that the lungfish is more closely related to tetrapods than the coelacanth.

Tetrapods evolved some specialized genes to adapt to living on land, but the coelacanth genome shows that a number of genes controlling the development of fish-specific features have been lost. More than 50 genes shared by all fish are no longer present in tetrapods, many of them key developmental regulators (BMP, wnt, and FGF signaling networks are all affected). Among the organs that normally express the missing genes in fish are the ear, kidney, tail, and fin. This is about what you'd expect.

What can we tell about the transition of fins to limbs? Work in other organisms has demonstrated that a cluster of genes (called a Hox cluster, for the homeobox genes it encodes) is key to establishing the identity of all the bones that make up our limbs. The genes themselves are identical in almost all vertebrates (including the coelacanth), which suggests that the location and timing of their activity is key. And these factors are controlled by regulatory DNA sequences outside the ones that encode proteins.

Despite the hundreds of millions of years of time that separate us, the authors were able to compare the coelacanth genome with that of limbed vertebrates and pick out regulatory DNA near the Hox cluster. When placed into a mouse, the fish DNA was able to drive expression of genes in the areas of the limb normally seen in tetrapods. This means the genetic tools to make a complex limb were in place long before there was anything other than a fin being built. Tetrapods have since added a number of additional regulatory sequences in the region that probably refine the gene activity.

Thecoelacanth wasn't the only fish genome completed this week. In the same edition of Nature, researchers announced the completion of the zebrafish genome, a project that was started more than a decade ago. Although it's mostly found in home aquariums, the zebrafish has also made its way into genetics labs. Here, the zebrafish's small size and transparent embryo make it useful for studying development. As such, like mice and flies, its genome was an obvious target for sequencing.

Unfortunately, the project turned out to be much harder than expected. Part of problem was that the group the zebrafish belongs to, the teleosts, ended up with a duplication of its genome at some point in its evolutionary past. Most of the extra DNA has since been lost, but some of it has evolved new functions or specializations. This means many genes have extra copies relative to other vertebrates (with more than 26,000 genes, the fish has the most genes of any vertebrate we've looked at).

As if sorting all the extra genes out wasn't enough of a problem, the zebrafish also has the most repetitive DNA yet seen in a vertebrate. A lot of this is what's commonly called junkdead viruses, mobile genetic parasites, and more. Since many of these genes are similar to each other, it can make figuring out where any particular DNA sequence is supposed to reside rather challenging.

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Scientists get the coelacanth genome and a hint of the origin of limbs

Sonic Entity - Genome Evolution
2013 - Sonic Entity - The Rainmaker EP.

By: PsychedelicPower

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Sonic Entity - Genome Evolution - Video

Apr. 19, 2013 A new genome-wide association study of more than 6,000 people has identified seven new genetic regions associated with pulmonary fibrosis. In findings published online in Nature Genetics on April 14, 2013, researchers at National Jewish Health, the University of Colorado and several other institutions found a number of genes associated with host defense, cell-cell adhesion and DNA repair, which provide clues to possible mechanisms underlying this currently untreatable disease.

"This research gives us several new targets for investigation of pulmonary fibrosis," said David Schwartz, MD, senior author on the paper, Professor of Medicine at National Jewish Health and Chair of Medicine the University of Colorado School of Medicine. "We believe that there are several relatively common genetic risk factors, which combine with repeated lung injury to cause this devastating lung disease."

Pulmonary fibrosis is a potentially deadly scarring of lung tissue. Although there are a number of known contributors to its development, most cases have no known cause. Without an approved medical therapy, patients with the most common form, idiopathic pulmonary fibrosis, survive an average of only two to three years after diagnosis.

"Pulmonary fibrosis has resisted our attempts to find a clearly beneficial treatment," said co-author Kevin K. Brown, MD, Vice Chair of Medicine at National Jewish Health. "This study gives us new insights into how the disease develops. By better understanding this, we can better focus future therapies."

Researchers from more than 20 institutions, led by National Jewish Health and the University of Colorado, confirmed three previously reported genetic risk factors and identified seven new ones, which together account for about one-third of the disease risk.

The team's findings confirmed the risk associated with specific changes in MUC5B, a gene that produces a protein in mucus. Researchers believe variations in this gene may lead to pulmonary fibrosis by interfering with mucosal defense, repair of lung alveoli or direct toxicity to cells.

The researchers also found stronger evidence for the role of telomeres, a protective section of DNA located at the tips of chromosomes. Shorter telomeres are associated with a reduced ability to divide and premature cell death. Previously, two rare genetic mutations had been associated with some forms of pulmonary fibrosis. The research team found common variants in and near those two genes, and a common variant in another gene.

The researchers also identified three genes associated with connections that hold adjoining cells together, known as cell-cell adhesion. Impaired cell-cell adhesion can lead to lost tissue integrity.

These findings support the researchers' belief that pulmonary fibrosis may be influenced by different genes in different people. Careful genotyping could identify different forms of the disease, allowing for more effective, individualized therapy.

The research was supported by the National Heart, Lung and Blood Institute (NHLBI). "In addition to expanding the library of genetic changes that can underlie pulmonary fibrosis, this study's findings demonstrate that both rare and common genetic variants contribute significantly to pulmonary fibrosis risk," said James Kiley, PhD, Director of NHLBI's Division of Lung Diseases. "A key next step for research is figuring out how these genetic variants work with environmental factors in the development of the disease."

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Genome study suggests new strategies for understanding and treating pulmonary fibrosis