David Alvarez-Ponce understands evolution in a way few people do, from the inside out. The assistant professor of biology has studied the genomes of different plant and animal species, but as a contributor to a paper published Feb. 6 in Nature Ecology and Evolution, he recently applied his specialized skills to understanding a group of creatures entirely new to him, carnivorous plants.
"I analyze genomic data, the genomes from different species, and I compare them to learn things about their evolution," he said. "This is my first time working with carnivorous plants."
The cephalotus, also known as the Australian pitcher plant, is duplicitous by nature. Its alluring mix of greens and reds make it appear quite lovely. It produces a pleasant odor and promises a hearty meal to any insects that might stop by to drink its nectar. When they land, however, insects slip and fall into its pitcher shaped leaves and are digested by the enzymes inside. It is like something out of a horror film.
The plant is also host to an intriguing genetic duality. While the tube-shaped leaves of the cephalotus may be the things of insect nightmares, it has other leaves designed for photosynthesis. These two leaves live alongside each other on the same plant. Those contrasts drew researchers, including Alvarez-Ponce, to study the plant.
Alvarez-Ponce's contribution to the project included studying the cephalotus' genetic data under the lenses of Evolution and Network Biology. What he found was fascinating. In comparing the cephalotus' genome with the genomes of eight other plants, 1,896 genes were found across all nine that were "single-copy," meaning that each plant contained only one copy of the gene, and more intriguingly, that these single copies had remained unchanged since the plants first diversified. Alvarez-Ponce observed that these genes were expressed at particularly high levels and in a broader range of plant tissues, and that they exhibited a particularly high number of interactions with other genes. To establish this, he used techniques borrowed from Graph Theory, the branch of Mathematics dealing with Networks.
"My observations indicate that these genes are somehow special, encoding key functions for plant life," Alvarez-Ponce said.
More than 30 researchers collaborated as part of a team led by Mitsuyasu Hasebe of the National Institute for Basic Biology in Japan and SOKENDAI (The Graduate University for Advanced Studies) in Japan; Kenji Fukushima of the same institutions and the University of Colorado School of Medicine; Shuaicheng Li of BGI-Shenzhen in China; and Victor Albert, professor of biological sciences in the University at Buffalo's College of Arts and Sciences. It was Albert who asked Alvarez-Ponce to join the study and was his primary contact throughout.
"We had been working before on different projects that involved network analysis, analysis of networks of interacting proteins," Alvarez-Ponce said. "That is why he approached me, because he wanted to incorporate a network analysis into this work."
There are Australian, Asian and American variations of the plant, though all three varieties appear strikingly similar, and, from a genetics standpoint, seem to have evolved along the same lines.
"We compared the set of genes that we found in this plant to other carnivorous plants," Alvarez-Ponce said. "The key point is that carnivory has emerged multiple times. So, we looked for the genes that were involved in carnivory in our plant genomes and compared them to the genes that were involved with carnivory in other species, and many of the genes we found were the same. That is one of the most striking or important results from this paper. It shows that carnivory, which we knew already had evolved multiple times, has evolved each time using, to a great extent, the same genes. Other species that are not carnivorous as well have the same genes, but they serve other functions. They are not used for carnivory. They are not used to digest insects or any of this. What this shows is that repeatedly the same genes have been recruited and repurposed to do these functions."
In addition to studying genetic variations between plants, the paper endeavored to understand the reasons for the Jekyll and Hyde nature of the plant's two types of leaves.
"These plants are interesting because they have two types of leaves and, depending on the temperature, one or the other tends to appear more," Alvarez-Ponce said. "There were important differences in the RNAs, or genes expressed, in both kinds of leaves. The genes expressed in the carnivorous leaves were enriched for genes with functions related to carnivory, such as prey attraction, capture, digestion and nutrient absorption."
Genetic research like that performed on the cephalotus is vital not only because it is interesting, but because understanding how a simple plant evolved to be a fly's worst nightmare can help humanity in many ways.
"The more genomes you have, the easier it gets to obtain more genomes. Each new genome has a multiplicative impact in the area of genomics," Alvarez-Ponce said. "We humans are evolving things. Pathogens are evolving. Animals and plants are evolving things too. So, understanding evolution is going to help us in agriculture, stockbreeding, medicine, and other areas. For instance, understanding how different plants become carnivorous independently has a lot to do with understanding how different pathogens can become resistant to antibiotics."