Researchers Document First Algal Pan-Genome

Leading a decade-long research initiative with a team of international scientists, Dr. Betsy Read from CSUSM has documented the first-ever algal pan-genome after sequencing 13 strains of the marine phytoplankter Emiliania huxleyi.Their findings address the alga’s ability to survive in diverse oceanic environments, which opens avenues for new research on climate change, global carbon cycling, biomineralization and the design of novel materials with biomedical applications, such as bone scaffolding, implants and periodontal structures. The phenomenon of a pan-genome, or family of species-specific genomes, is commonly seen in bacteria, but this is the first reported example in eukaryotic algae.Drs. Betsy Read, Xiaoyu Zhang and the late Tom Wahlund from CSUSM and Dr. Igor Grigoriev from the U.S. Department of Energy’s Joint Genome Institute (JGI) coordinated the project, which involved an international team of more than 75 research scientists from 12 countries. The team’s research, touted as filling a vital gap in the tree of life, was published in the renowned journal Nature on June 12, 2013.A Small but Mighty OrganismThe third most abundant phytoplanktonic species in the ocean, E. huxleyi is a single-celled organism enveloped by an elegantly sculpted calcium carbonate cell covering. Although it cannot be seen with the naked eye, E. huxleyi forms massive blooms that can be viewed by satellite imagery because of the remarkable light reflecting properties of its shell, which gives the water a milky turquoise tint. Arguably no other single living creature has such a striking impact on our planet as seen from outer space.While the chalky fossilized remains of E. huxleyi are prominently displayed in the White Cliffs of Dover, and blooms are often associated with southern coast of England, the microorganism can be found in almost all marine ecosystems. According to Dr. Read, E. huxleyi is in nearly every bucket of water pulled from the ocean, with the exception of the polar seas. As such, it is the basis of virtually all marine food systems.In addition, E. huxleyi influences climate processes. The light reflecting capabilities of its exterior push light and heat back into the atmosphere, ultimately lowering ocean temperatures. The alga is involved in marine carbon cycling and may serve as a “carbon sink” by taking up CO2 to produce energy and its calcium carbonate shell, and burying carbon in the sediments when it sinks to ocean floor. It may also influence cloud formation when an organosulfur compounds is released into the water, and evaporates into the atmosphereMaking the DiscoveryThe genome of E. huxleyi is unlike any other group of algae and sequencing its DNA proved difficult due to the inherent complexities and size. An organism’s genome is the sum total of its DNA, including genes and other information needed to function and maintain itself.Researchers found that the tiny unicellular organism, which can only been seen using a microscope, contains approximately 30,000 genes and 141.7 million DNA bases -- comparable to that of a multi-cellular terrestrial plant.As researchers worked to annotate the sequences, they discovered the genomes from the 13 E. huxleyi strains, collected from different regions of the ocean, give rise to a pan-genome. A pan-genome is characterized as being a family of genomes that have a core set of genes, as well as genes that are unique or strain specific, and genes that are shared by two or more strains. Documenting the genetic variability of E. huxleyi helps explain the alga’s competitive advantage to thrive in almost all oceanic environments, from the tropic to the subarctic seas. “The high morphological, physiological, and ecological diversity within this species indicates that a single strain is unlikely to be typical -- or representative of all strains,” the team noted. “Future sequencing of phytoplankton isolates will reveal whether this discovery is a unique or more common feature in the microalgae. Together, the physiological capacity and genomic plasticity of E. huxleyi make it a powerful model for studying speciation and adaptations to global climate change.”Researchers believe the unusually large amount of repetitive sequence in the genome may have contributed to the genetic and morphological diversity of the organism. The ability to rapidly evolve enables E. huxleyi to respond and quickly adapt to changing environmental conditions.The CSUSM Research TeamWhile the international project was led by Dr. Read, vital contributions were also made by CSUSM Professor Xiaoyu Zhang and two students from Dr. Read’s lab.Dr. Zhang, an associate professor of computer science, worked closely with bioinformaticians at JGI and was involved in nearly every aspect of the genome analysis.  He was instrumental in unraveling the pan-genome story. Dr. Zhang compared the genomes of 13 different strains of E. huxleyi and was the first to note that the number and kinds of genes varied considerably across the isolates. According to Dr. Read, he was “the tour de force, and without his efforts and the unwavering commitment on both his part and those at JGI, the project would not have been realized.”CSUSM student researchers also made contributions to the project. Biological sciences undergraduate Analissa Sarno teamed with graduate student Karina Gonzalez, and together they analyzed a unique complement of proteins know as selenoproteins and their associated biosynthetic machinery. They also assisted with the data organization and editing of the manuscript.“This type of project exemplifies the importance of collaboration and cooperation by scientists around the globe,” said Sarno. “There is an immense amount of work that goes on behind the scenes… and I was fortunate enough to have an active role that really opened my eyes to the difficulty and complexity of scientific writing.”Where Researchers are Headed NextEmbedded in the genetic code are clues about the cellular processes that enable E. huxleyi to produce the remarkably elaborate shell-like scales that surround the cell. Identifying genes and proteins involved in this process could lead to the design of new composite materials and devices for applications related to bone replacement, periodontal reconstruction, sensing systems, optoelectronic devices and the treatment of diseases.“We have some clues,” Dr. Read said, “but what makes this more difficult is that proteins involved in calcification are not conserved across biomineralizing species. What we desperately need in order to identify the genes involved in biomineralization, is a genetic transformation system. Several labs -- including my own -- are aggressively working on this.”To fully exploit the sequence information and to achieve a complete understanding of E. huxleyi, its biological significance and impact on society and the environment, Dr. Read and her colleagues will next begin to study the products of the genome and define the role of each and every gene, how they interrelate and come together in synergistic networks to accomplish complex functions.