Woolly mammoths genome mapped

woolly mammoth genome

woolly mammoth genome

An international team of researchers has sequenced the nearly complete genome of two Siberian woolly mammoths — revealing the most complete picture to date — including new information about the species’ evolutionary history and the conditions that led to its mass extinction at the end of the Ice Age.

“This discovery means that recreating extinct species is a much more real possibility, one we could in theory realize within decades,” says evolutionary geneticist Hendrik Poinar, director of the Ancient DNA Centre at McMaster University and a researcher at the Institute for Infectious Disease Research, the senior Canadian scientist on the project.

“With a complete genome and this kind of data, we can now begin to understand what made a mammoth a mammoth — when compared to an elephant — and some of the underlying causes of their extinction which is an exceptionally difficult and complex puzzle to solve,” he says.

While scientists have long argued that climate change and human hunting were major factors behind the mammoth’s extinction, the new data suggests multiple factors were at play over their long evolutionary history.

Researchers from McMaster, Harvard Medical School, the Swedish Museum of Natural History, Stockholm University and others produced high-quality genomes from specimens taken from the remains of two male woolly mammoths, which lived about 40,000 years apart.

One had lived in northeastern Siberia and is estimated to be nearly 45,000 years old. The other -believed to be from one of the last surviving mammoth populations — lived approximately 4,300 years ago on Russia’s Wrangel Island, located in the Arctic Ocean.

“We found that the genome from one of the world’s last mammoths displayed low genetic variation and a signature consistent with inbreeding, likely due to the small number of mammoths that managed to survive on Wrangel Island during the last 5,000 years of the species’ existence,” says Love Dalén, an associate professor of Bioinformatics and Genetics at the Swedish Museum of Natural History.

Scientists used sophisticated technology to tease bits and pieces of highly fragmented DNA from the ancient specimens, which they then used to sequence the genomes. Through careful analysis, they determined the animal populations had suffered and recovered from a significant setback roughly 250,000 to 300,000 years ago. However, say researchers, another severe decline occurred in the final days of the Ice Age, marking the end.

“The dates on these current samples suggest that when Egyptians were building pyramids, there were still mammoths living on these islands,” says Poinar. “Having this quality of data can help with our understanding of the evolutionary dynamics of elephants in general and possible efforts at de-extinction.”

The latest research is the continuation of the pioneering work Poinar and his team began in 2006, when they first mapped a partial mammoth genome, using DNA extracted from carcasses found in permafrost in the Yukon and Siberia.

 

Source:  Sciencedaily.com

Humans Bred with Unknown Species

Humans Bred with Unknown Species

Humans Bred with Unknown Species

A new study presented to the Royal Society meeting on ancient DNA in London last week has revealed a dramatic finding – the genome of one of our ancient ancestors, the Denisovans, contains a segment of DNA that seems to have come from another species that is currently unknown to science. The discovery suggests that there was rampant interbreeding between ancient human species in Europe and Asia more than 30,000 years ago. But, far more significant was the finding that they also mated with a mystery species from Asia – one that is neither human nor Neanderthal. 

Scientists launched into a flurry of discussion and debate upon hearing the study results and immediately began speculating about what this unknown species could be.  Some have suggested that a group may have branched off to Asia from the Homo heidelbernensis, who resided in Africa about half a million years ago. They are believed to be the ancestors of Europe’s Neanderthals. 

However others, such as Chris Stringer, a paleoanthropologist at the London Natural History Museum, admitted that they “don’t have the faintest idea” what the mystery species could be.

Traces of the unknown new genome were detected in two teeth and a finger bone of a Denisovan, which was discovered in a Siberian cave. There is not much data available about the appearance of Denisovans due to lack of their fossils’ availability, but the geneticists and researchers succeeded in arranging their entire genome very precisely.

“What it begins to suggest is that we’re looking at a ‘Lord of the Rings’-type world – that there were many hominid populations,” Mark Thomas, an evolutionary geneticist at University College London.

The question is now: who were these mystery people that the Denisovans were breeding with?

 

Source:  ancient-origins.net

Cancer-resistant blind mole rat

 

Cancer-resistant blind mole rat gets genome sequence

Cancer-resistant blind mole rat gets genome sequence

Scientists have sequenced the genome of the blind mole rat, a mammal that digs with its teeth, has skin over its eyes and lives for more than 20 years.

Its underground lifestyle means coping with no light, very little oxygen and an awful lot of dirt.

It is also resistant to cancer, like its distant cousin the naked mole rat.

The new work, published in the journal Nature Communications, will help unpick those secrets and the wider adaptation of animals to difficult environments.

Among the results were what the researchers believe are the genetic signatures of the mole rat’s complete loss of vision and its impressive tolerance of low oxygen (or “hypoxia”).

They also discovered how its special cancer-fighting mechanism might have evolved.

One of the study’s lead authors, Prof Eviatar Nevo from the University of Haifa in Israel, has studied blind mole rats for more than 50 years. In all of that time, a spontaneous tumour has never been discovered.

Even when treated with carcinogenic chemicals, these remarkable rodents were incredibly resistant to cancer.

Most animals rely on cells detecting a cancerous malfunction and shutting themselves down (programmed cell death or “apoptosis”), but the blind mole rat’s immune system attacks tumours and causes “necrosis” instead. The new study reports that genes involved in this immune defence have been favoured by evolution, and some have been expanded or duplicated.

All this may have happened because one of the key mediators of the normal cell-shutdown defence, a protein called p53, is mutated in the mole rats as part of their adaptation to low oxygen.

The mole rat spends its entire life under the ground, where oxygen is scarce. In other animals this would send p53 into overdrive.

“When there is low oxygen, in other species, [normal p53] would mean that some cells would die from apoptosis – but not in blind mole rats, because that would be a disaster,” said Dr Denis Larkin from the Royal Veterinary College in London, one of the study’s authors.

So the mole rats have evolved a unique trade-off, weakening p53 and boosting the immune system’s necrotic defence, which “the cancer doesn’t know how to deal with,” Dr Larkin told BBC News.

The genome study was carried out by a large team of researchers that also spanned China, Israel, the US and Denmark. Dr Larkin was involved in piecing together the evolution of the animal’s chromosomes, having done similar work on other genomes ranging from the pig to the yak.

He told the BBC the findings would shift the blind mole rat to “a new level” in the research community. “When you have the whole genome… you can more efficiently use the species as a model – for cancer resistance, or adaptation to hypoxia, or other medical challenges.”

The naked mole rat, also studied for its cancer resistance, is a distant relative of the blind mole rat

Dr Philippa Brice, from the genomics think-tank PHG Foundation at the University of Cambridge, told BBC News the mole rats and their “really unusual lifestyle” had already been valuable to scientists studying cancer resistance. She agreed that the genome sequence would mean more rapid progress.

“Now that their complete genome is available, it will make it much easier to probe their unique genetic features, with potential applications for human medical research,” Dr Brice said.

The blind mole rat (the newly sequenced species is Spalax galili) is only distantly related to the naked mole rat (Heterocephalus glaber), another unusual, subterranean critter with remarkable cancer resistance.

Their evolutionary histories diverged over 70 million years ago, according to calculations in the new study, and the two mole rats adapted completely separately to life underground.

In fact, the furry-but-blind Spalax is a closer cousin to the common house mouse than to the “sabre-toothed sausage” lookalike Heterocephalus.

 

Chinese scientists crack another genome of cotton

Chinese scientists crack the genome of another diploid cotton Gossypium arboreum:

 

Chinese scientists crack the genome of another diploid cotton Gossypium arboreum

Chinese scientists crack the genome of another diploid cotton Gossypium arboreum

 

Chinese scientists from Chinese Academy of Agricultural Sciences and BGI successfully deciphered the genome sequence of another diploid cotton– Gossypium arboreum (AA) after the completed sequencing of G. raimondii (DD) in 2012. G. arboreum, a cultivated cotton, is a putative contributor for the A subgenome of cotton. Its completed genome will play a vital contribution to the future molecular breeding and genetic improvement of cotton and its close relatives. The latest study today was published online in Nature Genetics.

As one of the most important economic crops in the world, cotton also serves as an excellent model system for studying polyploidization, cell elongation and cell wall biosynthesis. However, breeders and geneticists remain little knowledge on the genetic mechanisms underlying its complex allotetraploid nature of the cotton genome (AADD). It has been proposed that all diploid cotton species present may have evolved from a common ancestor, and all tetraploid cotton species came from interspecific hybridization between the cultivated species G. arboreum and the non-cultivated species G. raimondii.

After the completed sequencing of G. raimondii in 2012, researchers started the work on decoding the genome of G. arboreum. In this study, they sequenced and assembled the G. arboreum genome using whole-genome shotgun approach, yielding a draft cotton genome with the size of 1,694 Mb. About 90.4% of the G. arboretum assembled scaffolds were anchored and oriented on 13 pseudochromosomes.

Furthermore, researchers found the long terminal repeat (LTR) retrotransposons insertions and expansions of LTR families contributed significantly to forming the double-sized G. arboreum genome relative to that of G. raimondii. Further molecular phylogenetic analyses suggested that G. arboreum and G. raimondii diverged about 5 million years ago, and the protein-coding capacities of these two species remained largely unchanged.

To investigate the plant morphology mechanisms of cotton species, a series of comparative transcriptome studies were performed. Results suggested that NBS-encoding subfamilies played an essential role on the immune to Verticillium dahliae. The resistance of G. raimondii on Verticillium dahliae was caused by expansion and contraction in the numbers of NBS-encoding genes, accordingly the loss in the genome of G. arboreum was responsible to their susceptible.

Another interesting finding of this study is the cotton fiber cell growth, and they found the 1-aminocyclo-propane-1-carboxylic acid oxidase (ACO) gene was a key modulator. Researchers suggest the overproduction of ACO maybe the reason why G. raimondii have a poor production of spinnable fiber, while the inactivation of ACO in G. arboreum might benefit its fiber development.

The G. arboreum genome will be an essential reference for the assembly of tetraploid cotton genomes and for evolutionary studies of Gossypium species. It also provides an essential tool for the identification, isolation and manipulation of important cotton genes conferring agronomic traits for molecular breeding and genetic improvement.

 

Source:  eurekalert.org

New light on how Genes turn off and on

New insights into how genes turn on and off:

New insights into how genes turn on and off

New insights into how genes turn on and off

 

Researchers at UC Davis and the University of British Columbia have shed new light on methylation, a critical process that helps control how genes are expressed. Working with placentas, the team discovered that 37 percent of the placental genome has regions of lower methylation, called partially methylated domains (PMDs), in which gene expression is turned off. This differs from most human tissues, in which 70 percent of the genome is highly methylated.

While PMDs have been identified in cell lines, this is the first time they have been found in regular human tissue. In addition to enhancing our understanding of epigenetics, this work could influence cancer research and help illuminate how environmental toxins affect fetal development. .

Since it was unraveled more than ten years ago, the human genome has been the focus of both popular interest and intense scientific focus. But the genome doesn’t act alone; there are many factors that influence whether genes are turned on or off. One of these is an epigenetic process called methylation, in which a group of carbon and hydrogen atoms (a methyl group) attaches to DNA, adjusting how genes are expressed.

“I like to think of epigenetics as a layer on top of your genetic code,” said senior author Janine LaSalle, professor of medical microbiology and immunology. “It’s not the DNA sequence but it layers on top of that — and methylation is the first layer. Those layers provide a lot of information to the cells on where and when to turn on the genes.”

How and when genes are activated (or inactivated) can have a profound impact on human development, cancer and the biological legacy of environmental toxins. Prior to this research, PMDs had only been found in cultured cell lines, which led some scientists to wonder if they existed outside the test tube. This study confirms they exist in placental tissue, a critically important window into fetal development.

“The placenta is the interface between mother and fetus,” said LaSalle, who is a researcher affiliated with the UC Davis MIND Institute. “It’s a time capsule from when a lot of important methylation events occurred.”

In addition, placental tissue was interesting to study because it has a number of invasive characteristics often associated with cancer. In fact, a number of cancers, such as breast and colon, have widespread PMDs. LaSalle notes that anti-cancer epigenetic therapies that adjust methylation could be refined based on this improved understanding of PMDs.

This work could also enhance our ability to detect genetic defects. Methylation, and other epigenetic data, provides information that cannot be found in the genome alone. For example, the vast majority of cells in the body contain identical genetic code. However, the added information provided by methylation allows scientists to determine where specific DNA came from.

“Methylation patterns are like fingerprints, showing which tissue that DNA is derived from,” LaSalle said. “You can’t get that information from just the DNA sequence. As a result, methylation studies could be a very rich source for biomarkers.”

In the study, PMDs encompassed 37 percent of the placental genome, including 3,815 genes, around 17 percent of all genes. When found in low-methylation regions, these genes were less likely to be transcribed into proteins. Researchers also found that PMDs also contain more highly methylated CpG islands (genomic areas with large numbers of cytosine-guanine pairs), which are often associated with gene transcriptional silencing of promoters.

Because the placental PMDs contained many genes associated with neuronal development, and specifically autism, LaSalle notes that future research could investigate how epigenetics impacts autism genes at birth.

“We are looking for biomarkers that predict neurodevelopmental outcomes,” LaSalle said. “Now we have a series of snap shots from a critical period where we think environmental factors are playing a role in the developing brain.”