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Genome sequence for sacred lotus reported

Sacred Lotus.  Image courtesy Flickr user WEAZ 73.

Sacred Lotus. Image courtesy Flickr user WEAZ 73.

Sacred lotus has cultural and religious importance as a symbol of purity, and it is also used as a food and in traditional medicines. It was domesticated in Asia about 7,000 years ago and has since been cultivated for its rhizomes and seeds. It is particularly noted for its 1,300-year seed longevity and for its leaves’ exceptional water repellence, known as the lotus effect.

The genome sequence for sacred lotus has now been reported in the journal Genome Biology. The international team of scientists was led by Dr. Ray Ming, a UH Mānoa graduate who is now a professor at the University of Illinois in Plant Biology; Professor Jane Shen-Miller at the University of California-Los Angeles; and Shaohua Li, Director of the Wuhan Botanical Garden at the Chinese Academy of Sciences.

Dr. Robert Paull and Dr. Nancy Chen of CTAHR’s Department of Tropical Plant and Soil Sciences were involved in this sequencing project. Their role was to analyze and annotate the predicted genes in cell wall metabolism and modification, and to determine their evolutionary relationships. This effort follows from their earlier collaborations on the papaya and Asian pear genomes, both of which efforts led to peer-reviewed articles in Nature and Genome Research.

The sequences revealed that sacred lotus bears the closest resemblance to the ancestor of all eudicots. “Eudicots” is a term used to refer to one of the two largest groups of angiosperms (flowering plants), constituting over 70% of angiosperm species. Common species include papaya, cabbages, cotton, soybean, grapes, and tomato. The other group is the monocots (grasses), which have a single seed leaf and include orchids, grasses, bamboo, and banana.

Sacred lotus forms a separate branch of the eudicot family tree because it lacks the characteristic triplication of the genome found in other eudicots. Whole-genome duplications and triplications with hybridization have been important events in plant evolution. The doubling of genes means some genes can retain their original function and others will gradually adapt to new functions. If the adaptation is not beneficial, they disappear from the genome. Many of our most important crops have evolved through genome duplication and hybridization, including many cereals (wheat, oats, rice), cotton, cabbage, sugarcane, tomato, papaya, coffee, and banana.

Though sacred lotus lacks the 100-million-year-old triplication that occurred in other eudicots, it did undergo a duplication in its own lineage about 65 million years ago. A high proportion of the duplicated genes (~40%) have been retained. For instance, the duplicated genes for wax formation (to repel water) and for plant survival in nutrient-poor watery habitats are retained. This gene retention was also seen in the cell wall genes in the analysis by Drs. Paull and Chen.

Drs. Paull and Chen, in collaboration with a colleague from the Lawrence Berkeley National Laboratory, have already submitted a follow-up paper from the sacred lotus genome paper to another peer-reviewed journal. This paper focuses on the genes involved in cell wall synthesis and modification. It is thought that the cell wall structure plays a crucial role in imparting longevity to the seeds.

Many scientific breakthroughs are expected from this sequencing and gene annotation effort. The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the ancestral plant genome. This slower substitution rate should therefore accelerate comparative analysis between eudicots and monocots. The divergence of the grasses (monocots) from other flowering plants (eudicots) about 200 million year ago was crucial to flowering plants’ diversity and adaptation to occupy nearly every habitat on Earth except for extreme environments.

This evolutionary analysis of the sacred lotus also fits with Drs. Paull and Chen’s interest in how fleshy fruit evolved. Fleshy fruit apparently evolved independently throughout the angiosperms, and the sacred lotus data gives leads as to how developmental controls are modified through evolution.

The paper, “Genome of the Long-Living Sacred Lotus (Nelumbo nucifera Gaertn.),” is available online at http://genomebiology.com/2013/14/5/R41/abstract.

Source:  A UH Manoa Press Release

 

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