Monthly Archives: May 2013

May 10, 2013 The sacred lotus (Nelumbo nucifera) is a symbol of spiritual purity and longevity. Its seeds can survive up to 1,300 years, its petals and leaves repel grime and water, and its flowers generate heat to attract pollinators.

Now researchers report in the journal Genome Biology that they have sequenced the lotus genome, and the results offer insight into the heart of some of its mysteries. The sequence reveals that of all the plants sequenced so far -- and there are dozens -- sacred lotus bears the closest resemblance to the ancestor of all eudicots, a broad category of flowering plants that includes apple, cabbage, cactus, coffee, cotton, grape, melon, peanut, poplar, soybean, sunflower, tobacco and tomato.

The plant lineage that includes the sacred lotus forms a separate branch of the eudicot family tree, and so lacks a signature triplication of the genome seen in most other members of this family, said University of Illinois plant biology and Institute for Genomic Biology professor Ray Ming, who led the analysis with Jane Shen-Miller, a plant and biology professor at the University of California at Los Angeles (who germinated a 1,300-year-old sacred lotus seed); and Shaohua Li, the director of the Wuhan Botanical Garden at the Chinese Academy of Sciences.

"Whole-genome duplications -- the doubling, tripling (or more) of an organism's entire genetic endowment -- are important events in plant evolution," Ming said. Some of the duplicated genes retain their original structure and function, and so produce more of a given gene product -- a protein, for example, he said. Some gradually adapt new forms to take on new functions. If those changes are beneficial, the genes persist; if they're harmful, they disappear from the genome.

Many agricultural crops benefit from genome duplications, including banana, papaya, strawberry, sugarcane, watermelon and wheat, said Robert VanBuren, a graduate student in Ming's lab and collaborator on the study.

Although it lacks the 100 million-year-old triplication of its genome seen in most other eudicots, sacred lotus experienced a separate, whole-genome duplication about 65 million years ago, the researchers found. A large proportion of the duplicated genes (about 40 percent) have been retained, they report.

"A neat thing about the duplication is that we can look at the genes that were retained and see if they are in specific pathways," VanBuren said. The researchers found evidence that duplicated genes related to wax formation (which allows the plant to repel water and remain clean) and survival in a mineral-starved watery habitat were retained, for example.

By looking at changes in the duplicated genes, the researchers found that lotus has a slow mutation rate relative to other plants, Ming said.

These traits make lotus an ideal reference plant for the study of other eudicots, the researchers said.

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Sacred lotus genome sequence enlightens scientists

The results of an avian genome project conducted by a team of Texas A&M researchers were published this month in a scientific journal.

Spearheaded by Christopher Seabury and Ian Tizard at the Schubot Exotic Bird Health Center, which is part of the Texas A&M College of Veterinary Medicine and Biomedical Sciences, the team studied the DNA of a Scarlet Macaw named "Neblina" in producing the first genome sequence of the breed.

The macaw is a rare type of parrot known for its intelligence, ability to fly long distances and their long lives, with some living up to 75 years, according to Tizard.

Because of their unique characteristics, affectionate demeanor and colorful feathers, the Scarlet Macaw is coveted by illegal pet traders. Neblina, who lives in a Iowa zoo, is believed to be from Brazil and was recovered during a raid on illegally imported exotic birds.

Seabury said the project is significant for several reasons. It's one of just a handful of avian genomes that's been assembled and published in a peer-reviewed scientific journal.

Additionally, the techniques used by the team have the potential to lead the way in future avian genome research.

"We demonstrated that genome projects like this are absolutely feasible for small scientific groups," Seabury said.

He added that by studying the Scarlet Macaw genome in comparison to other known bird genomes, scientists can gain a better understanding of avian biology.

"The Scarlet Macaw Genome Project opens a variety of doors ranging from modern forensics to determining how the macaws utilize their natural habitat and landscape, as inferred from variable genetic markers," Seabury said.

The research also helps define genetic components that influence traits commonly found in parrots such as longevity and intelligence.

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Texas A&M researchers uncover genome sequence of Scarlet Macaw