Daily Archives: May 2, 2017

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

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. ...

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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