When a global pandemic forced former graduate student Devon Boland, Ph.D., out of the lab and onto the computer, he discovered a world of difference hidden in the long-studied species Botryoccocus braunii — and discovered that it isn’t. One kind, but three.
Botryococcus braunii was first discovered in the mid-19th century. Technically, it is a plant that undergoes photosynthesis and, most interestingly for researchers, produces large amounts of hydrocarbons that can be used as a renewable fuel source.
It was previously believed to be a single species with three varieties: A, B and L, each producing slightly different types of oils. But after discovering a dramatic 20-30% genetic difference between each breed, a team of Texas A&M AgriLife researchers proposed a new classification – completing every biologist’s dream of making species a to name.
“As a graduate student you read articles that all say the same thing: that this is a single species with three chemical races, and you internalize it,” says Boland, first author of the study showing the genomic comparisons. ‘You start to think that it must be so. No one has discovered anything different, and all those scientists have had much longer careers than me – I’m just a kid.
“But ultimately I got to propose names for a species that was accepted for publication, something I never thought would happen.”
Half necessity, half circumstance
Before coming to Texas A&M, Boland spent his undergraduate research on “bread and butter” biochemical research in areas such as protein engineering. His thesis was to focus on the production process that Botryococcus braunii uses to synthesize its unique hydrocarbons.
But when the COVID-19 pandemic hit, Boland worried that he would lose time on his dissertation and that it might delay his graduation.
In response, Tim Devarenne, Ph.D., associate professor of undergraduate programs and associate professor in the Department of Biochemistry and Biophysics at the Texas A&M College of Agriculture and Life Sciences, suggested that Boland take the opportunity to delve into genetic data and bioinformatics. .
“Mapping the genome of the organism you are interested in is always ideal in research because it makes it easier to find genes and work to determine their functions,” Devarenne said.
Another former graduate student in the lab, Daniel Browne, had done some sequencing and assembled the genome of the B race. During one of Devarenne and Boland’s weekly meetings, Devarenne suggested they try the same with the A and L races.
“It had a double benefit,” Boland said. “We were able to do something that hadn’t been done before, and it could help us better understand hydrocarbon biosynthesis.”
Although the breeds are virtually indistinguishable under the microscope, Boland said there had been some debate over whether these were different species. They were interested to know whether a genomic study could shed light on this question.
Along with Devarenne, Boland and Browne, the research team included Ivette Cornejo Corona, Ph.D., postdoctoral researcher in Devarenne’s laboratory; John Mullet, Ph.D., another researcher and professor in the Department of Biochemistry and Biophysics; Rebecca Murphy, Ph.D., a former graduate student in Mullet’s laboratory; and Shigeru Okada, Ph.D., a professor at the University of Tokyo in Japan, who have been collaborating on Botryococcus studies for many years.
Tim Devarenne, Ph.D., studies the biofuel properties of a common green microalga called Botryococcus braunii in his laboratory in the Department of Biochemistry and Biophysics. (Tim Devarenne, Kathleen Phillips/Texas A&M AgriLife)
Genetic analysis
Although Botryococcus is often studied for its hydrocarbon production, sequencing its genome has proven difficult.
Devon Boland, Ph.D., a former graduate researcher in Tim Devarenne’s lab, first discovered his love for bioinformatics when the COVID-19 pandemic forced him out of the lab. He now uses bioinformatics every day in his role at the Texas A&M Institute for Genome Sciences and Society. (Texas A&M Foundation)
Boland, now an assistant research scientist at the Texas A&M Institute for Genome Sciences and Society, said the thick, oily medium in which the cells live makes extracting and isolating the DNA a challenge.
Nevertheless, the team was determined to analyze the genomes to see the similarity between the genes and proteins involved in each variety’s biofuel production processes.
But after assembling the genomes and using the supercomputers at the Texas A&M High Performance Research Computing Center to perform genomic comparisons, Boland says it became clear that these organisms were not the same species.
“It was like everywhere we looked, things were different,” he said.
Ultimately, the researchers said that about one in five genes was unique to each of the Botryococcus varieties. To put that 20% difference into perspective, the genetic difference between humans and chimpanzees, our closest evolutionary relative, is less than 2%.
After a few more validations, Boland and Devarenne set out to reclassify the Botryococcus varieties. Boland said the team spent months coming up with different names.
They retained race B with the original name Botryococcus braunii to preserve its history and renamed race A to Botryococcus alkenealis and race L to Botryococcus lycopadienor, indicating the type of hydrocarbons each produces.
What makes a species
In the recent past, biologists have given more weight to genes and genomes when it comes to classifying organisms.
But even with all the evidence that these Botryococcus algae can be considered separate species, Devarenne said what makes a species real is its general acceptance by the scientific community.
After publishing their peer-reviewed research in PLOS OneDevarenne shared the team’s findings with more than 100 other researchers studying the organisms in their own laboratories.
“How we define individual species may not change much in how these organisms are used in research,” he said. “But it is important to the scientific understanding of how we think about the ways in which these organisms are related to each other and to all other species.”
Boland said he and Devarenne published in an open access journal so other scientists could build on their work. The complete genomes of the species are also available on the National Center for Biotechnology Information website.
“It was important to us that the information was publicly available when it was ready to be released,” he said. “Science is community-driven. The end goal is always to advance our collective knowledge, and I think that’s what we’ve accomplished here.”
