Genome of beloved sea otter Gidget now available for browsing

MAY 13, 2020

by University of California - Santa Cruz

A sea otter genome browser—featuring the Monterey Bay Aquarium's beloved Gidget—is now available to the public. The visualizable genome for the Southern sea otter, Enhydra lutris nereis, comes following work by the National Center for Biotechnology Information (NCBI) and UC Santa Cruz software bioinformaticians to make available the first complete southern sea otter genome sequenced by researchers at the University of California Los Angeles.

The release of the sea otter genome on the UCSC Genome Browser is the result of a study by UCLA scientists and co-authors that examined the evolutionary history and genetic diversity of sea otters, and found that sea otters have low genetic diversity. In their investigations, the researchers sequenced Gidget's genetic code—her genome.

A genome assembly is the entirety of the species' genetic code, produced after chromosomes have been fragmented, the genetic code in those fragments has been written down—or sequenced—and the resulting sequences have been put back together—or assembled.

The sea otter's low level of genetic diversity is similar to other threatened species, such as the cheetah and Tasmanian devil, said investigator Annabel Beichman, a UCLA graduate student in ecology and evolutionary biology.

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Himalayan marmot genome offers clues to life at extremely high altitudes

December 20, 2018, Cell Press

Himalayan marmots can survive at altitudes up to 5,000 meters in the Himalayan regions of India, Nepal, and Pakistan and on the Qinghai-Tibetan Plateau of China, where many of them face extreme cold, little oxygen, and few other resources. Now, researchers have sequenced the first complete Himalayan marmot genome, which may help them to better explain how the marmots live in such extremes.

The findings, which appear December 20 in the journal iScience, hint at the genetic mechanisms underlying high-altitude adaptation and hibernation, the researchers say. They also serve as a valuable resource for researchers studying marmot evolution, highland disease, and cold adaptation.

"As one of the highest-altitude-dwelling mammals, the Himalayan marmot is chronically exposed to cold temperature, hypoxia, and intense UV radiation," said Enqi Liu of Xi'an Jiaotong University Health Science Center in China. "They also hibernate for more than six months during the wintertime."

Those striking biological features led Liu and his team, including first author Liang Bai, to consider the Himalayan marmot as an ideal animal model for studying the molecular mechanisms of adaptation to extreme environments. To begin, they sequenced and assembled a complete draft genome of a male Himalayan marmot. They also re-sequenced 20 other Himalayan marmots, including individuals living at high and low altitudes, and four other marmot species. Additionally, RNA sequencing was done to compare gene-expression differences between marmots in a state of torpor and awake marmots.

The DNA data show that the Himalayan marmot diverged from the Mongolian marmot about 2 million years ago. The researchers identified two genes, Slc25a14 and ψAamp (a processed pseudogene), that have been selected in different directions in marmots living at low versus high altitudes, suggesting they are related to survival in high-altitude populations under conditions of extremely low oxygen.

They further suggest that Slc25a14 may have an important neuroprotective role. The shift in ψAamp affects the stability of RNA encoding the gene Aamp, which may be a protective strategy to prevent the excess growth of new blood vessels under extremely low-oxygen conditions.

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First jellyfish genome reveals ancient beginnings of complex body plan

Date:  December 3, 2018

Source:  University of California - Davis

Jellyfish undergo an amazing metamorphosis, from tiny polyps growing on the seafloor to swimming medusae with stinging tentacles. This shape-shifting has served them well, shepherding jellyfish through more than 500 million years of mass extinctions on Earth.

"Whatever they're doing has really worked for them," said David Gold, an assistant professor of paleobiology in the UC Davis College of Letters and Science.

The first in-depth look at the genome of a jellyfish -- the moon jelly Aurelia aurita -- reveals the origins of this successful survival strategy. The Aurelia genome, published online Dec. 3 in the journal Nature Ecology and Evolution, indicates early jellyfish recycled existing genes to morph from polyp to medusa. The results suggest animals can radiate into new niches and forms fairly easily.

"These findings provide further evidence that evolution doesn't necessarily make the genetic code more complex," said Gold, a lead researcher on the genome study. "Jellyfish can build a big, complex life history using many of the same genes found in simpler animals."

The research team was led equally by Gold, who performed much of the work as a postdoctoral fellow at the California Institute of Technology, and by Takeo Katsuki, a project scientist at the Kavli Institute for Brain and Mind at UC San Diego.

The genome: a multi-use tool

Jellyfish come from one of the oldest branches on the animal family tree, the phylum Cnidaria, which includes corals and anemones. Jellyfish were probably the first muscle-powered swimmers in the open ocean. They appeared in the late Precambrian Era, a period of major geologic and ecological changes that preceded the Cambrian explosion of animal life.

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Tapeworm found living inside a patient's brain: Worm removed and sequenced

A genome of a rare species of tapeworm found living inside a patient's brain has been sequenced for the first time, in research published in the open access journal Genome Biology. The study provides insights into potential drug targets within the genome for future treatments.

Tapeworms are parasites that are most commonly found living in the gut, causing symptoms such as weakness, weight loss and abdominal pain. However, the larvae of some species of tapeworm are able to travel further afield to areas such as the eyes, the brain and spinal cord.

A 50-year-old man of Chinese ethnicity was admitted to hospital in the East of England after reporting symptoms of headaches, seizures, altered smell and memory impairment. The patient had lived in the UK for 20 years but visited his homeland often. After testing negative for a range of diseases and not presenting any other abnormalities, doctors began to take a series of MRI images of his brain. Over the course of four years, they noticed a lesion migrate at least 5 cm across his brain, and after taking a biopsy from his left thalamus, they discovered a 1 cm long ribbon-shaped larval worm. The patient, who remains anonymous, was cured of his infection by the operation and is now recovering.

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Fly genome could help improve health, environment

Date:

October 14, 2014

Source:

BioMed Central

Summary:

The house fly might be a worldwide pest, but its genome will provide information that could improve our lives. From insights into pathogen immunity, to pest control and decomposing waste, the 691 Mb genome has been sequenced and analyzed by a global consortium of scientists.

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African elephant genome suggests they are superior smellers

Date:

July 22, 2014

Source:

Cold Spring Harbor Laboratory

Summary:

Sense of smell is critical for survival in many mammals. In a new study, researchers examined the olfactory receptor repertoire encoded in 13 mammalian species and found that African elephants have the largest number of OR genes ever characterized; more than twice that found in dogs, and five times more than in humans.

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Rainbow trout genome sequenced

2 hours ago

Using fish bred at Washington State University, an international team of researchers has mapped the genetic profile of the rainbow trout, a versatile salmonid whose relatively recent genetic history opens a window into how vertebrates evolve.

The 30-person team, led by Yann Guiguen of the French National Institute for Agricultural Research, reports its findings this week in Nature Communications.

The investigators focused on the rate at which genes have evolved since a rare genome doubling event occurred in the rainbow trout approximately 100 million years ago. Unlike most evolutionary processes involving mutations and the selection of advantageous traits, a doubling event acts like the copied draft of a piece of writing that can be edited and recast without the risk of destroying the earlier version.

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Elephant Shark Genome Decoded: New Insights Gained Into Bone Formation and Immunity

Jan. 8, 2014 — An international team of researchers has sequenced the genome of the elephant shark, a curious-looking fish with a snout that resembles the end of an elephant's trunk.

The elephant shark and its cousins the sharks, rays, skates and chimaeras are the world's oldest-living jawed vertebrates. But their skeletons are made of cartilage rather than bone, making this group of vertebrates an oddity on the evolutionary tree.

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Genome for the King Cobra Sequenced

Dec. 3, 2013 — Researchers from LSTM, along with a team of international biologists who have recently sequenced the genome of the king cobra, say that their work reveals dynamic evolution and adaptation in the snake venom system, which seemingly occurs in response to an evolutionary arms race between venomous snakes and their prey.

A paper co-lead by Dr Nicholas Casewell, a NERC research Fellow at LSTM, and 34 co-authors from six countries, including the Director of the Alistair Reid Venom Unit at LSTM, Dr Robert Harrison, has been published in the Proceedings of the National Academy of Sciences (PNAS). Members of this team also analysed the genome of the Burmese python (Python molurus bivittatus) and used it for comparison with the king cobra (Ophiophagus Hannah). These papers represent the first complete and annotated snake genomes.

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How the attempt to sequence “Bigfoot’s genome” went badly off track

Humans interbred with an unknown hominin in Europe, then crossed the Bering Sea—say what?by John Timmer - July 7 2013, 10:00pm GMTDT

When we first looked at the report of the bigfoot genome, it was an odd mixture of things: standard methods and reasonable looking data thrown in with unusual approaches and data that should have raised warning flags for any biologist. We just couldn't figure out the logic of why certain things were done or the reasoning behind some of the conclusions the authors reached. So, we spent some time working with the reported genome sequences themselves and talked with the woman who helped put the analysis together, Dr. Melba Ketchum. While it didn't answer all of our questions, it gave us a clearer picture of how the work came to be.The biggest clarification made was what the team behind the results considered their scientific reasoning, which makes sense of how they ran past warning signs that they were badly off track. It provided an indication of what motivated them to push the results into a publication that they knew would cause them grief.

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'Living fossil' coelacanth genome sequenced

By Rebecca Morelle, Science reporter, BBC World Service

The genetic secrets of a "living fossil" have been revealed by scientists.

Researchers sequenced the genome of the coelacanth: a deep-sea fish that closely resembles its ancestors, which lived at least 300 million years ago.

The study found that some of the animal's genes evolved very slowly, giving it its primitive appearance.

The work also shed light on how the fish was related to the first land-based animals.

The coelacanth has four large, fleshy fins, which some scientists believe could have been the predecessors of limbs.

It had been suggested that this fish was closely related to early tetrapods - the first creatures to drag themselves out of the ocean, giving rise to life on land.

But the study, published in the journal Nature, suggested that another fish called the lungfish, which also has four limbs, had more genes in common with land-based animals.

Slow to change

The coelacanth can reach up to 2m-long and is found lurking in caves deep beneath the waves.

It was thought to have been extinct for millions of years, until it turned up in a trawlerman's net off the coast of Africa in 1938.

Its ancient appearance has earned it the title "living fossil" - but it is so elusive, that it has been hard to study.

Continued:  http://www.bbc.co.uk/news/science-environment-22184556

Genome of Mysterious Extinct Human Reveals Brown-Eyed Girl

The genome of a recently discovered branch of extinct humans known as the Denisovans that once interbred with us has been sequenced, scientists said today (Aug. 30).

Genetic analysis of the fossil revealed it apparently belonged to a little girl with dark skin, brown hair and brown eyes, researchers said. All in all, the scientists discovered about 100,000 recent changes in our genome that occurred after the split from the Denisovans. A number of these changes influence genes linked with brain function and nervous system development, leading to speculation that we may think differently from the Denisovans. Other changes are linked with the skin, eyes and teeth.

"This research will help [in] determining how it was that modern human populations came to expand dramatically in size as well as cultural complexity, while archaic humans eventually dwindled in numbers and became physically extinct," said researcher Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Continued:  http://www.livescience.com/22836-genome-extinct-humans-denisovans.html

Human-Chimp Genetic Differences: New Insights Into Why Humans Are More Susceptible to Cancer and Other Diseases

ScienceDaily (Aug. 23, 2012) — Ninety-six percent of a chimpanzee's genome is the same as a human's. It's the other 4 percent, and the vast differences, that pique the interest of Georgia Tech's Soojin Yi. For instance, why do humans have a high risk of cancer, even though chimps rarely develop the disease?

In research published in September's American Journal of Human Genetics, Yi looked at brain samples of each species. She found that differences in certain DNA modifications, called methylation, may contribute to phenotypic changes. The results also hint that DNA methylation plays an important role for some disease-related phenotypes in humans, including cancer and autism.

"Our study indicates that certain human diseases may have evolutionary epigenetic origins," says Yi, a faculty member in the School of Biology. "Such findings, in the long term, may help to develop better therapeutic targets or means for some human diseases. "

Read on:  http://www.sciencedaily.com/releases/2012/08/120823142735.htm

Why Some Animals Live Longer Than Others

ScienceDaily (Mar. 29, 2012) — Scientists at the University of Liverpool have developed a new method to detect proteins associated with longevity, which helps further our understanding into why some animals live longer than others.

The team looked at the genome of more than 30 mammalian species to identify proteins that evolve in connection with the longevity of a species. They found that a protein, important in responding to DNA damage, evolves and mutates in a non-random way in species that are longer-lived, suggesting that it is changing for a specific purpose. They found a similar pattern in proteins associated with metabolism, cholesterol and pathways involved in the recycling of proteins.

Findings show that if certain proteins are being selected by evolution to change in long-lived mammals like humans and elephants, then it is possible that these species have optimized pathways that repair molecular damage, compared to shorter-lived animals, such as mice.

Read on:  http://www.sciencedaily.com/releases/2012/03/120329112105.htm

Oetzi the Iceman's nuclear genome gives new insights

By Jason PalmerScience and technology reporter, BBC News

New clues have emerged in what could be described as the world's oldest murder case: that of Oetzi the "Iceman", whose 5,300-year-old body was discovered frozen in the Italian Alps in 1991.

Oetzi's full genome has now been reported in Nature Communications.

It reveals that he had brown eyes, "O" blood type, was lactose intolerant, and was predisposed to heart disease.

They also show him to be the first documented case of infection by a Lyme disease bacterium.

Analysis of series of anomalies in the Iceman's DNA also revealed him to be more closely related to modern inhabitants of Corsica and Sardinia than to populations in the Alps, where he was unearthed.

'Really exciting'

The study reveals the fuller genetic picture as laid out in the nuclei of Oetzi's cells.

This nuclear DNA is both rarer and typically less well-preserved than the DNA within mitochondria, the cell's "power plants", which also contain DNA.

Continued:  http://www.bbc.co.uk/news/science-environment-17191398

Big Pest, Small Genome: Two-Spotted Spider Mite Genome Decoded

ScienceDaily (Nov. 23, 2011) — A University of Utah biologist and an international research team decoded the genetic blueprint of the two-spotted spider mite, raising hope for new ways to attack the major pest, which resists pesticides and destroys crops and ornamental plants worldwide.

The voracious mites, which technically are not insects, can eat more than 1,100 plant species -- a rare trait. The mites' newly revealed and sequenced genome contains a variety of genes capable of detoxifying pesticides as well as toxins plants use to defend themselves, the scientists report in the Nov. 24 issue of the journal Nature.

"One key thing that makes spider mites unique is they can eat many, many different plant species," says Richard M. Clark, one of five main authors of the study and an assistant professor of biology at the University of Utah. "These mites are often house plant pests -- a major cause of people's house plants turning yellow and getting sick. They also are a major problem for agricultural nurseries and greenhouses, and for field crops."

Primary targets are tomatoes, peppers, cucumbers, strawberries, corn, soybeans, apples, grapes and citrus.

Clark says the new study's "importance is largely in understanding how animals eat plants, with the long-term goal of developing effective ways to prevent crop damage from mites and insects. If we can identify the biological pathways mites use to feed on plants, we can potentially identify chemical and biological methods to disrupt those pathways and stop the mites from feeding."

The two-spotted spider mite, which is no more than 1 millimeter long, "is a major global pest, and is predicted to be a growing concern in a warming climate because they multiply extremely fast at high temperatures -- 90 degrees Fahrenheit or more," he adds. "They do really well in hot and dry climates like Utah."

Yet, the two-spotted spider mite "has been found to rapidly develop resistance to multiple types of pesticides, often within a couple of years after a pesticide is introduced," says Clark. "It is resistant to many common pesticides used against insects."

The Nature study deciphering the genome of Tetranychus urticae, the two-spotted spider mite (which has two red spots), was conducted by an international research team of 55 scientists from North America, Europe and South America.

Besides Clark, the other primary authors are biologists Yves Van de Peer of Ghent University and the Flanders Institute for Biotechnology in Belgium; Miodrag Grbic of the University of Western Ontario, Canada; Thomas Van Leeuwen of Ghent University; and Rene Feyereisen of the University of Nice Sophia Antipolis in France.

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Tasmanian devil genome holds secret to survival (Via Dawn Holloway)

Scientists have sequenced the complete genomes of two Tasmanian devils in the hope of finding clues to preserving this highly endangered marsupial. Devil populations have been decimated by a highly contagious facial cancer that is transferred when these aggressive animals bite each other.

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Mapping the crocodile genome

The first ever genetic linkage map for a non-avian member of the Class Reptilia has been developed. Researchers writing in the open access journal BMC Genomics have constructed a first-generation genetic linkage map for the saltwater crocodile Crocodylus porosus.

Dr Lee Miles, from the University of Sydney, worked with a team of Australian and international researchers to study a population of saltwater crocodiles from the Darwin Crocodile Farm in the Northern Territory. He said, "This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry".

The researchers' map also provides a significant step towards the elucidation of the crocodilian genome, forming a scaffold for genome sequence assembly, and will be of intrinsic value to comparative mapping efforts aimed at understanding the molecular evolution of reptilian, as well as other amniote genomes. From an economic perspective, this new information should be able to assist in the breeding of farmed crocodiles with favourable growth rate, survival and skin quality by facilitating the systematic searches necessary to identify the genes that affect these traits.

Speaking about the map, Miles said, "The crocodile is a very charismatic organism, but with surprisingly very little genetic or genomic resources available prior to this map. As part of my PhD I was fortunate to have been involved in this collaboration between the University of Sydney, Darwin Crocodile Farm and the University of Georgia in the USA, and it is very satisfying to know that the outcomes of our research will be of value to both future research efforts, as well as industry. We've taken that first difficult step and I am certain that even more exciting research with follow."

http://www.eurekalert.org/pub_releases/2009-07/bc-mtc072709.php