Category Archives: Genome

May 1, 2017 by Sandra Avant ARS research helps catfish producers, like these in Mississippi, improve fish quality and quantity. Credit: Stephen Ausmus

A fish named "Coco" is at the center of the first genome sequence for any catfish species.

Catfish is an important dietary protein source and is the third most commonly farmed fish worldwide. While more than 2,500 species of catfish are known to exist, the channel catfish dominates U.S. aquaculture, accounting for more than 60 percent of fish and seafood production. In 2015, production sales for U.S. catfish growers totaled $361 million, up 3 percent from the previous year, according to USDA's National Agricultural Statistics Service.

Research at the Agricultural Research Service (ARS) Warmwater Aquaculture Research Unit (WARU) in Stoneville, Mississippi, helps catfish producers improve the quality and quantity of their products. Recently, a team led by WARU molecular biologist Geoff Waldbieser and Auburn University scientist John Liu produced the first genome-sequence assembly for the channel catfish. It's also the first for any type of catfish.

The total complement of DNA in the cell is called the "genome," and the catfish genome, like an instruction manual, contains the information needed to make and "operate" each fish. The catfish genome-sequence assembly gives scientists the ability to read the instruction manual for each individual catfish and look for differences that make some animals grow faster or resist disease better.

Waldbieser used a special breeding technique called "gynogenesis" to produce the genome donor, Coco, so that she contained two copies of DNAlike other animalsexcept that both copies were completely identical.

"I named her after Coco Chanel, because she's Channel No. 1," Waldbieser says.

Collaborating with ARS scientists at the Genomics and Bioinformatics Research Unit in Stoneville and the Bovine Functional Genomics Laboratory in Beltsville, Maryland, Waldbieser produced about 800 million DNA sequences from Coco's DNA.

"Those sequences were like puzzle pieces. It took 2 months on a 64-processor computer workstation to align them and produce the genome assembly," Waldbieser says.

Waldbieser and WARU geneticist Brian Bosworth recently used Coco's genome to identify variation in DNA sequences between individual catfish within the Delta Select linean improved catfish line being developed at WARU for use by farmers. "Now that we know where the genetic variations in the DNA sequences are located, we will be able to analyze different parts of the genome inherited by different individual catfish," Waldbieser says. "We can identify those segments, propagate them to our fish population, and improve meat production and production efficiency for farmers."

This is important, because improving catfish growth rate, fillet yield, meat quality, and disease resistance will greatly benefit fish farmers, Waldbieser adds.

Explore further: Breeding hybrid catfish

More information: Qifan Zeng et al. Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence, Scientific Reports (2017). DOI: 10.1038/srep40347

In the catfish industry, it's well-known that hybrid catfisha cross of the channel catfish with the blue catfishgenerally have better growth, higher survival rates and better meat yield than purebred channel catfish. ...

Researchers in the Philippines are studying the genetics of local catfish to help protect them from becoming endangered.

The aquaculture industry is taking notice of U.S. Department of Agriculture (USDA) research that gives the precise levels of dissolved oxygen needed to keep pond-raised catfish alive and growing.

During a survey of the freshwater fishes of the Mali Hka River drainage in the Hponkanrazi Wildlife Sanctuary, Myanmar, scientists Xiao-Yong Chen, Tao Qin and Zhi-Ying Chen, from the Chinese Academy of Sciences (CAS), identified ...

Large catfish in a desert river in the Pilbara are eating native mice when available, Murdoch University researchers have found.

(Phys.org)A research team in the southern Indian state of Kerala has discovered a new species of blind catfish living in a deep well. The newly discovered fish was named Horaglanis abdulkalami in honor of a former president ...

Viruses are notorious for taking over their host's operations and using them to their own advantage. But few human viruses make themselves quite as cozy as the Epstein-Barr virus, which can be found in an estimated nine out ...

Chickens were domesticated from Asian jungle fowl around 6000 years ago. Since domestication they have acquired a number of traits that are valuable to humans, including those concerning appearance, reduced aggression and ...

On a research dive in 2011 off the Aegean Sea coast of the fishing village e?mealt?, Turkey, a lucky pair of graduate students bore accidental witness to a phenomenon scientists have otherwise only ever seen in the lab: ...

A hormone called FGF21 that is secreted by the liver after eating sweets may determine who has a sweet tooth and who doesn't, according to a study in Cell Metabolism published May 2. Researchers at the Novo Nordisk Foundation ...

Young mongooses may conceal their identityeven from their own parentsto survive.

William Shakespeare wrote with a quill, Helen Keller liked her typewriter, and the oval squid prefers to use its body, when it comes to expressing love. But unlike these famous authors, the romanticisms of Sepioteuthis lessoniana ...

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The first sequencing of a channel catfish genome - Phys.Org

From a single species of plant comes many teas. The tea tree, a shrub called Camellia sinensis,produces white, green, black and oolong teas. The tea's destiny is a matter of variables. The final drink reflects the tea cultivar, the growing environment and how the leaves areprocessed dried, crushed, steamed, blended. Farmers pluck baby leaves, as one Snapple commercial put it in the mid-2000s, to begin makingwhite tea.

And yet scientists in China, South Korea and the United States say there is another way to further tea's potential, beyond altering the dirt or the stages of harvest or processing.

DNA analysis could lead toa more diversified set of tea flavors by tracing the genes responsible for taste, according to Lizhi Gao, a botany professor at the Chinese Academy of Sciences' Kunming Institute of Botany. Heand colleagues have completed the first high-quality genome of thetea tree shrub, published this week in the journal Molecular Plant.

The plant took five years to analyze, thanks to the sheer numberof DNA sequences involved. The tea tree genome is extremely large, Gao wrote in an email to The Washington Post counting 3 billion base pairs, about four times the size of coffee's genome.

Of hot and invigorating drinks, coffee getsmost of the buzz, at least in the United States: This country is home to140 million daily coffee drinkersand the StarbucksUnicorn Frappuccino, and Americans consume more coffee than people anywhere else. Researchers sequenced thegenome of robustacoffee in 2014, hinting at a future of genetically modified coffees, as The Post reported at the time. Scientists followed up with the arabica coffee genomein January.

Monday markedthe tea tree's turn. It was a long time coming. Dried plants, recently found in a Chinese mausoleum, revealed that emperors in the Han Dynasty enjoyed tea2,100 years ago, possibly as part of a soup. Thesovereigns were onto something. Today, 3 billion people drink tea, and by one estimate, for everymug of coffee consumed on the planet, humans drinkthree cups of tea.

Gao and hiscolleagues had to churn through the tea tree's huge levels of retrotransposons. These repeated DNA sequences, about 80 percent of the tea genome, duplicated themselves into the genome again and again over 50 million years of tea tree evolution.It is a mystery why retrotransposon sequences are abundant in this plant but not in another, Gao said.

But the researchers were most interested not in size but in the waytea produces tastymolecules. The tea-processing industries in tea-drinking countries, especially in China, have developed numerous tea products with diverse tea flavor, Gao said. But processing techniques alone aren't enough, he said. Tea also depends ondeveloping new plantvarieties, containing unique combinations of flavorful molecules.

Three types of chemicals are most responsible for tea's taste. One is an amino acidonly found in tea, called l-theanine, whichin the last decade has been added todrinks that promote focus andconcentration. (Such focus drinks are of dubious efficacyand lack supporting research.)

The second type of chemical is a class of flavonoid, or plant pigment molecule, called catechins.The third is caffeine, which evolvedin tea independently of cacao and coffee, akin to the way both sea turtles and dolphins evolved flippers separately.

There are several theories as to why plants produce caffeine. Caffeine at high doses is a natural pesticide. Butat low doses, as in some nectars, it may be giving insects a memorable jolt.Caffeine was one tool in tea's repertoire ofdisease defense and environmental stress tolerance methods to help it adapt globally to diverse habitats, Gao said.

The tea genome answered a question the scientist had long pondered: Why can't we make tea from closeCamelliasinensis cousins, such as the tea oil plantCamellia oleifera?

It turns out thatC. oleifera and its 100 other Camelliarelatives do not produce high amounts of the caffeine or catechin family of genes.(Caffeine and catechins are not proteins but secondary metabolites, which means manygenes are required to constructthem.) Put another way, Gao said, the expression levels of caffeine- and catechin-related genes determines the tea processing suitability.

The chief horticulturist at Britain's Royal Horticultural Society, Guy Barter, said plant breeders would welcome this work. Once you understand the basis for the flavors and the processing quality of the tea, you can then have genetic markers that breeders can look for when trying to produce new varieties, he told the BBC.

Read more:

Bees love caffeine, too and tricky flowers take advantage

Genetically modified coffee could be just around the corner

The European Space Agency sent Kombucha into space for science and stuff

Read the rest here:
The tea plant has a whopper genome, four times that of coffee, scientists find - Washington Post

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Now that scientists have mapped the barley genome, better beer could be the result - Digital Trends

Gatersleben, Germany A group of researchers has mapped the entire genome of barley.

Sci-News.com (Science News) reports that the International Barley Sequencing Consortium (IBSC) announced the news in late April.

Barley, says Sci-News.com, is the worlds fourth most important cereal crop after wheat, rice and

Image: ThinkStock

maize. IBSC has published its work in the journal Nature.

Barley, says the story on Sci-News.com April 27, 2017, is cultivated in all temperate regions from the Arctic Circle to the tropics. Its known for its tolerance to cold, drought, alkali and salinity.

Barley is found in breakfast cereals and all-purpose flour and it helps bread rise, says Sci-News.com. Malted barley also gives beer its colour, body, protein and the natural sugars needed for fermentation.

In a statement, the IBSC says the mapping of barleys genome can lead to higher yields, improved pest and disease resistance and enhanced nutritional value.

It will also facilitate the development of new and better barley varieties able to cope with the demands of climate change. It should also help in the fight against cereal crop diseases, which cause millions in losses every year.

Barley, says IBSC, was first cultivated more than 15,000 years ago. It belongs to the Triticeae family, which includes wheat and rye, and that together provides around 30 per cent of the calories consumed worldwide.

In the statement, IBSC writes the sequencing will accelerate research in barley and its close relative wheat. Armed with this information breeders and scientists will be much better placed to deal with the challenge of effectively addressing the food security agenda under the constraints of a rapidly changing environment.

For more on barley and IBSC, click here.

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Researchers unravel barley's genome - food in canada

As for thesis 3 discussed beginning on pp. 124ff. namely that God orders creation into a temple, I have a hard time finding this theme in Gen. 1-3. God rests or ceases from his work and admires it. This is all about Gods activity. There is nothing said at all about worshipping by the human beings of God, nothing about sacrifices either. None of the language of Biblical worship shows up in these chapters. Instead, we hear about what Adam and Eve are supposed to do as jobs, as their work. Nothing is said about how they should relate to, adore, worship, sing praises of God, unless very indirectly in the sense that doing your job right glorifies God (see my book on Work. A Kingdom Perspective).

Here again I think we have a case of over-reading ANE accounts into the Genesis account. Adam and Eve are not presented as priests here, Kings maybe, but not priests. And since there is as yet no sin, there is as yet no need for a sacrifice in a temple. I do however take the point that earth is the footstool of God, and that one can say that the heavenly sanctuary can extend down to and include the earthly one (which is what Isaiah 6 is about). Isaiah 6 is a proper worship scene, rather like Rev. 4 and 5. Gen. 1-2 is not. The place where Adam and Eve dwell is called a park or a garden, not a palace or a temple, and notice that in Revelation while there is a garden and Eden motif, John sees no need for a temple in the new creation. It is unwise to read later Israelite literature from the monarchy when there was a temple, such as Ps. 132.7-8 back into Gen. 1-3, written probably during a time when there wasnt such a Jewish temple. And even less convincing is an appeal to Ezek. 43.7 from the exilic period!

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Adam and the Genome Part Fourteen - Patheos (blog)

Science Daily

Barley genome sequenced Science Daily "This takes the level of completeness of the barley genome up a huge notch," said Timothy Close, a professor of genetics at UC Riverside. "It makes it much easier for researchers working with barley to be focused on attainable objectives, ranging from ... You Want Better Beer? Good. Here's a Better Barley GenomeWIRED Researchers Sequence Barley GenomeSci-News.com Reference Barley Genome Assembled Using Chromosome Conformation Capture MappingGenomeWeb ZME Science -The West Australian all 13 news articles »

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Barley genome sequenced - Science Daily

Forbes

How Domestication Altered The Horse Genome Forbes Human influence is captured in the genomes of modern horses in a number of ways: (i) extreme diversity in mitochondrial genomes, which contrasts sharply with a Y-chromosome that is virtually identical in all modern domestic horses; (ii) higher ... Scythian horse breeding unveiled: Lessons for animal domestication ...Science Daily Ancient Ritually Sacrificed Stallions Reveal How Humans Changed ...Motherboard Long-frozen DNA shows how humans made horses faster and more likely to get sickWashington Post all 7 news articles »

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How Domestication Altered The Horse Genome - Forbes

Science Daily

How Domestication Altered The Horse Genome - Forbes Forbes A new study published today reveals the suite of traits that ancient nomadic peoples selected to develop the type of horse that best fit their purposes. Scythian horse breeding unveiled: Lessons for animal domestication ...Science Daily Ancient Ritually Sacrificed Stallions Reveal How Humans Changed ...Motherboard all 7 news articles »

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How Domestication Altered The Horse Genome - Forbes - Forbes

After 10 years of study, the barley genome has been fully sequenced, which could lead to better beer and single malt Scotch whiskey (Credit: aaron007/Depositphotos)

Sequencing the entire genome of an organism is no easy feat, but the benefits can be as important as saving species from the brink of extinction, fighting cancer, getting rid of pests and now, brewing better booze. After a decade of study, an international team of scientists has finally unraveled the genome of barley, an achievement that could not only lead to tastier beer and whiskey, but a better understanding of other staple food crops.

Showing up in your cereal in the morning, your sandwich at lunch, and your beers or single malt Scotch whiskey after work, the humble barley grain is one of the most widely grown and consumed crops on Earth. Its importance stretches back as far as 10,000 years, and improving our understanding of it means we can grow varieties more selectively to help feed (and intoxicate) the growing population.

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While it might look like a pretty simple organism, barley has some 39,000 genes to its name almost twice as many as there are in the human genome. To make the job even more challenging, 80 percent of the genes are arranged in highly repetitive sequences, which makes pinning down their precise locations in the genome extremely difficult.

As a result, it took 10 years for a team of 77 scientists to piece together the plant's entire sequence. Spearheaded by the International Barley Genome Sequencing Consortium, the project involved researchers from across the globe, including the US, UK, Australia, Germany, China, Czech Republic, Denmark, Finland, Sweden and Switzerland.

Many barley products rely on the grains being malted first, which means they're soaked in water to start the germination process, then interrupted and dried out. The amylase proteins that brings out then convert starch into sugars, which yeast can feed on to ferment the mix into alcohol.

To their surprise, the researchers found that there were far more genes that encoded for amylase than they expected. The completed sequence can also help improve the overall quality of barley crops, by identifying parts of the genome that might be holding breeders back, and showing them which genes they should be selecting for. The study could also prove to be a solid foundation to better understand related crops, like rice and wheat.

"This takes the level of completeness of the barley genome up a huge notch," says Timothy Close, one of the study's many authors. "It makes it much easier for researchers working with barley to be focused on attainable objectives, ranging from new variety development through breeding to mechanistic studies of genes."

The research was published in the journal Nature.

Source: University of California, Riverside

Originally posted here:
With the barley genome sequenced, better beer and whiskey is on ... - New Atlas

By historical Adam and Eve I simply mean real people in space and time, the progenitors of Gods people who were the sinners in question that set in motion the train of murder and death and iniquity that followed, no sooner than they stepped outside the garden (see the story of Cain and Abel). I do not think it is adequate to suggest that the writers of the NT or for that matter of the intertestamental period were simply referring to Adam and Eve as archetypal or literary figures in a story.

No, they believed these folks actually existed on planet earth long long ago. Indeed, so much did they take that for granted, that they argued from that basis to be able to say other things about Adam and Eve. I find weird the argument of John Walton cited on p. 109 that says because Christ is called the last Adam, since he was not the last biological specimen, one cannot conclude that when Paul refers to the first Adam he means the first biological specimen. Paul is talking about two founders of the race of Gods people the first one, who is the progenitor of Gods people and the last one who will also be the progenitor of Gods people. Biology is neither implied nor denied by this rhetorical comparison, for either Adam.

The chapter about the Twelve major theses, which begins on p. 111 makes up the bulk of Scots main argument. It begins with a very ironic quote from Walter Brueggemann on p. 112. Speaking about the theologians who wrote Gen. 1-11 he says of them they resist a scientific view of creation which assumes the world contains its own mysteries and can be understood in terms of itself without any transcendent referent. Indeed its a pity that the first half of this book didnt approach the matter more like the writers of Gen. 1-11. This quote accurately describes what we find in this book in the discussion on genetics.

See the article here:
Adam and the Genome Part Twelve - Patheos (blog)