It seems that every day, another species of plant or animal is being sequenced. How do scientists choose which species should have its genome sequenced?
For some, such as African rice, the main consideration is whether the genome sequence will allow for improvement of agriculturally important crops. For others, including the marmoset, the interest lies mainly in the connection to human evolution.
Now, Zhong-Jian Liu at the National Orchid Conservation Center of China and colleagues from around the world have sequenced the genome of the orchid Phalaenopsis equestris. Besides being a popular ornamental plant (and therefore a commercially important plant) with gorgeous flowers, the orchid has another unique claim to fame. This species uses a type of photosynthesis that is different from all other plant species sequenced to date.
Orchids use a photosynthesis strategy called crassulacean acid metabolism (CAM). CAM plants make up approximately 7% of plant species. Other notable CAM plants include cacti (such as the saguaro—a native of my home state, Arizona), agave (where tequila comes from), aloe vera and pineapple.
Most plants use the C3 metabolic pathway to turn carbon dioxide (CO2) into energy (there is also a third pathway, called C4, used by about 3% of plant species). All plants use sunlight and water to incorporate the carbons from CO2 into sugar, producing oxygen as a byproduct. When it is very hot or dry, C3 plants are at a disadvantage because they cannot efficiently use carbon due to a process called photorespiration. CAM plants are specifically adapted to these extreme environments. Their specialized leaves chemically store the carbon from CO2 acquired during the night and use it for photosynthesis during the day (when their stomata are closed, to prevent water loss) .
Many orchids, such as the species sequenced in the new paper, are epiphytes, meaning that they do not get their water from roots in the soil, but rather from the air or rain. They would therefore need to budget their water supply. This adaptation is likely related to their use of CAM instead of C3 metabolism.
In the genome paper, the authors identified genes important for CAM and analyzed their evolutionary history. They also analyzed genes involved in flower development, to better understand how orchids develop their spectacular flowers. The paper is certain to be an important resource for future studies of plant evolution and adaptation.
We asked one of the senior authors of the paper, Zhong-Jian Liu, to tell us a little bit more about the background of this study.
Can you tell us a little about the National Orchid Conservation Center of China?
The National Orchid Conservation Center of China was established in 2006 and is located beside Wutong Shan Mountain and Shenzhen reservoir, which is a very good location for the growth of orchids. The center is aimed at conducting the conservation of Orchidaceae germplasm, improving the level of orchid protection and advancing the cause of orchid conservation in China.
The center now owns the most endangered orchid species in China and there are more than 1,000 Chinese orchids belonging to international and national first and second-class protective orchids. There is a herbarium, tissue culture room and special library for orchids at the center. The herbarium has 3,835 specimens and 110 type specimens of orchids, and 243 animal and plant fossil specimens related to orchid evolution, which is the most in China. More than 1,800 books and 20,000 audio-visual documents are stored in the library. In academic research, 187 papers and 14 monographs have been published in China and abroad. “Pollination: Self-fertilization strategy in an orchid” was published in Nature and summarized by Year in Review 2006 and included in Book of the Year 2007 by Encyclopaedia Britannica.
The orchid genome represents the first genome sequence of a CAM plant. Why do you think this is so significant and how will it affect plant research in the future?
The CAM pathway for photosynthesis is indeed of importance. It not only leads to more efficient power conversion, but also strengthens the adaptation to harsh environments, especially drought, in comparison with C3 plants. Meanwhile, research of CAM can provide new directions for breeding programs to produce neo-species with drought resistance.
In our manuscript, we found gene duplication and loss events in four of the six key gene families in the CAM pathway. These events are important to the adaptation and evolution of orchids.
What was the most surprising result of the study and why?
We consider the finding that Orchidaceae has undergone an orchid-specific whole-genome duplication (WGD) event to be the most intriguing result. WGD can trigger a tremendous burst in gene diversification within quite a short period, which provides extensive gene material for neo-functionalization, sub-functionalization or dosage strengthening. All of these outcomes can give rise to diversity in morphology, metabolism, live style, etc. that can finally result in tremendous species radiation. We think the WGD event may be linked to the success of the orchid family. There are more than 20,000 species of orchid within 880 genera.
What was the most difficult part of the study?
The unexpectedly high heterozygosity rate in the orchid genome was the most challenging aspect for us. It is extremely difficult to assemble its genome using the raw reads. But we finally overcame this difficulty via the use of diverse assembly software packages, optimization of their core parameters and verification with the complement of the BAC sequences. Finally, we accomplished a very accurate, complete genome assembly.
There have been other genomes published with a similar level of heterozygosity to our genome, but we were able to achieve a much more accurate and complete assembly than was the case with those genomes.
Do you have a personal favorite type or color of orchid?
I love all the species and colors of orchids very much. If there was one for me to choose, it would be Paphiopedilum armeniacum. I like its beautiful pale yellow flowers, which I have sometimes thought symbolize a yellow Chinese dream.