Comparative genomics identifies sequences involved in photosynthesis under reduced water conditions.
The Science
In Nature Communications, researchers sequenced and analyzed the genome of Kalanchoë fedtschenkoi (lavender scallops) to better understand how this plant transitioned from C3 to CAM photosynthesis. (Forest and Kim Starr, Flickr CC BY 2.0)
In the presence of sufficient water and light, most plants conduct photosynthesis through what is known as the C3 pathway. As plants spread out and adapted to live in a variety of environments, they developed alternate photosynthesis pathways, known as C4 and CAM, to make use of limited nutrients. To understand how many plant lineages have independently transitioned from C3 to CAM photosynthesis, researchers sequenced and analyzed the genome of Kalanchoë fedtschenkoi (lavender scallops). Comparing this plant’s genome to those of other plants that also conduct CAM photosynthesis allowed the team to identify the genes and protein sequences involved in its evolution to a flowering plant that efficiently uses limited water resources to conduct photosynthesis.
The Impact
Kalanchoë is a model plant for eudicots, a term applied to one of the largest group of flowering plants that includes coffee, bean and sunflower. As the first CAM eudicot to have its genome sequenced, Kalanchoë offers researchers a reference to trace the evolution of CAM photosynthesis in this group. Understanding how the CAM photosynthesis pathway evolved in plants would enable researchers to engineer a C3 to CAM photosynthesis pathway to improve crop yields for fuel or food applications on arid or marginal lands.
Summary
In the presence of abundant water and sunlight, most plants conduct photosynthesis using what is known as the C3 pathway. Some plants can conduct C4 photosynthesis in water-limited conditions; a different enzyme collects carbon dioxide from the air to form a 4-carbon chain that lends itself to the pathway name. In water-poor conditions, some plants collect and process carbon at night rather than during the day through crassulacean acid metabolism (CAM) photosynthesis, named for its discovery in succulents. In the December 1, 2017 issue of Nature Communications, a team led by Oak Ridge National Laboratory researchers and including scientists at the Joint Genome Institute, a DOE Office of Science User Facility, sequenced and analyzed the genome of Kalanchoë fedtschenkoi to better understand how this plant transitioned from C3 to CAM photosynthesis. CAM photosynthesis is found across 36 plant families and is thought to have evolved independently from multiple C3 lineages. As the first CAM eudicot to have its genome sequenced, K. fedtschenkoi offers researchers an emerging model to trace the evolution of CAM photosynthesis through these plant lineages.
Using recently sequenced genomes of related CAM plants – the pineapple and the moth orchid – the team identified sequences involved in the evolution of plant lineages. They found changes in protein sequences and in gene expression changes related to rescheduling a plant’s daily cycles that impact genes involved in traits such as when the leaf pores (stomata) open and heat stress response. Comparing the three CAM genomes, while they found convergent changes to either protein sequences or gene expression across genomes, they did not find the same changes in all three simultaneously.
Armed with the K. fedtschenkoi genome data, researchers can learn more about how CAM genes are regulated and functionally characterize CAM-related genes, such as by generating loss-of-function mutants. The information can help accelerate genetic improvement of plants to make them more tolerant of stresses such as drought and boost crop yields in non-CAM plants for fuel and food production on marginal lands.
BER Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov
PI Contacts
Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute
jschmutz@hudsonalpha.com
Jerry Tuskan
Chief Executive Officer, Center for Bioenergy Innovation
ORNL Corporate Fellow
Oak Ridge National Laboratory
tuskanga@ornl.gov
Funding
This research was supported by the U.S. Department of Energy, Office of Science, Genomic Science Program under Award Number DE-SC0008834. Additional support was provided by the UK Biotechnology and Biological Sciences Research Council (grant no. BB/F009313/1) and the Laboratory Directed Research and Development (LDRD) Program (Project ID: 7758) of Oak Ridge National Laboratory. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under Contract Number DE-AC05-00OR22725.
Publication
- Yang X et al. The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nat Commun. 2017 Dec 1. doi: 1038/s41467-017-01491-7.