Sacred Lotus Genome May Hold Key To The Secrets Of Aging
| |A team of international scientists report today that they have sequenced and annotated the genome of the sacred lotus (Nelumbo nucifera), which is thought to have a powerful genetic system.
The team, which includes researchers from the US, China, Australia and Japan, have sequenced nearly 90 percent of the plant’s 27,000 genes.
The sacred lotus, which is a symbol of spiritual purity and longevity, has the ability to repair genetic defects, and may hold a key to the secrets of aging; the seeds of the lotus can survive up to 1,300 years.
The petals and leaves of the plant also repel dirt and water and the flower can generate its own heat to attract pollinators.
Through sequencing, the researchers have found that the lotus bears the closest resemblance to the ancestor of all eudicots, than of any other plant that has been successfully sequenced to date.
Eudicots are a group of flowering plants that include apple, coffee, peanut, soybean, tobacco, tomato, and countless others.
Publishing the paper in the journal Genome Biology, the team noted that the results of the sequencing offer insight into the heart of many of the plant’s mysteries.
The research was co-led by Ray Ming, a plant biology professor at University of Illinois’ Institute for Genomic Biology (IGB); Jane Shen-Miller, a plant biology professor at UCLA; and Shaohua Li, director of the Wuhan Botanical Garden (WBG) at the Chinese Academy of Sciences.
“The lotus genome is an ancient one, and we now know its ABCs,” said Shen-Miller, who works out of the UCLA’s Center for the Study of Evolution and the Origin of Life.
“Molecular biologists can now more easily study how its genes are turned on and off during times of stress and why this plant’s seeds can live for 1,300 years. This is a step toward learning what anti-aging secrets the sacred lotus plant may offer.”
Shen-Miller said the plant’s genetic repair mechanisms could be very useful if researchers could find a way to transfer them to crops that have seeds that generally only have life spans of a few years. They could even prove significant if transferable to human health.
“If our genes could repair disease as well as the lotus’ genes, we would have healthier aging. We need to learn about its repair mechanisms, and about its biochemical, physiological and molecular properties, but the lotus genome is now open to everybody,” she said.
Study co-author Crysten Blaby-Haas, a UCLA postdoctoral scholar in chemistry and biochemistry, explained that understanding how the lotus repair mechanism works is a three-step process.
“Knowing the genome sequence was step one. Step two would be identifying which of these genes contributes to longevity and repairing genetic damage.
Step three would be potential applications for human health, if we find and characterize those genes. The genome sequence will aid in future analysis,” she said.
“The next question is what are these genes doing, and the biggest question is how they contribute to the longevity of the lotus plant and its other interesting attributes,” Blaby-Haas said.
“Before this, when scientists studied the lotus, it’s almost as if they were blind; now they can see.
Once you know the repertoire of genes, you have a foundation to study their functions.”
The lineage that includes the sacred lotus forms a separate branch of the eudicot family tree and lacks a signature triplication of the genome that is seen in most members of this particular family, Ming explained.
“Whole-genome duplications — the doubling or tripling of an organism’s entire genetic endowment — are important events in plant evolution,” Ming said in a statement. “Some of the duplicated genes retain their original structure and function, and others gradually adapt and take on new functions.
If those changes are beneficial, the genes persist; if they’re harmful, they disappear from the genome.”
Study coauthor Robert VanBuren, a graduate student in Ming’s lab, said that many crops, such as watermelon, sugar cane, and wheat, benefit from genome duplication.
The genome of most other eudicots triplicated 100 million years ago, but the lotus experienced a separate, whole-genome duplication about 65 million years ago.
Researchers who study aging and stress could be eager to learn more about the genetics of the lotus, said Shen-Miller.
“The lotus can age for 1,000 years, and even survives freezing weather,” she noted. “Its genetic makeup can combat stress. Most crops don’t have a very long shelf life.
But starches and proteins in lotus seeds remain palatable and actively promote seed germination, even after centuries of aging.”
The unusual genetics of the lotus give the plant a unique set of survival skills. Not only does the plant produce its own heat to attract pollinators, but the fruit of the lotus is covered with antibiotics and wax that ensure the viability of the seed inside.
The sacred lotus is known from the geologic record as early as 135 million years ago, noted Shen-Miller.
The plant has been grown in China for at least the last 4,000 years, and has long been used there for food and medicine.
Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance.
It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop.
It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect.
The latter property is due to the nanoscopic closely-packed protuberances on its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan.
The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101x and 5.2x.
The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size.
The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication.
The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape.
Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has sixteen COG2132 multi-copper oxidase family proteins with root specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment.
The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.