When a global pandemic compelled former graduate student Devon Boland, Ph.D., to transition from laboratory work to computer research, he uncovered significant differences in the widely-explored species Botryococcus braunii — realizing that this was not just a single species, but three distinct ones.
During a global pandemic, Devon Boland, Ph.D., a former graduate student, had to shift from lab work to computer-based research. Through this change, he discovered that the well-researched species Botryococcus braunii is actually not one species but three different ones.
Botryococcus braunii was initially identified in the mid-1800s. It is classified as a plant due to its capabilities for photosynthesis, and it notably generates substantial amounts of hydrocarbons that can serve as a renewable energy source.
Previously, it was assumed to be a singular species consisting of three ‘races’: A, B, and L, which were known to produce slightly varying types of oils. However, a team of researchers from Texas A&M AgriLife discovered a significant genetic divergence of 20-30% between these races, prompting them to suggest a new classification and fulfill a dream for biologists to name new species.
“As a graduate student, I read countless papers claiming that this was a single species with three chemical races, and I started to believe it,” Boland shared, as he was the lead author of the genomic comparison study. “You get influenced by the established wisdom, especially when you see that those scientists have spent years in their careers, while I felt like just a kid.”
“Ultimately, I was able to propose names for the new species that were officially accepted for publication, which was something I never anticipated.”
Driven by necessity and circumstance
Before joining Texas A&M, Boland focused on fundamental biochemistry topics, such as protein engineering, during his undergraduate research. His graduate thesis was originally intended to explore the process through which Botryococcus braunii creates its unique hydrocarbons.
However, with the onset of the COVID-19 pandemic, Boland was concerned that he would lose valuable time on his thesis, which could postpone his graduation.
Tim Devarenne, Ph.D., associate head of undergraduate programs and an associate professor in the Department of Biochemistry and Biophysics at Texas A&M, encouraged Boland to utilize this opportunity to explore genetic data and bioinformatics.
“Having the genome of your research organism mapped is always advantageous as it helps locate specific genes and understand their functions,” explained Devarenne.
Another graduate student from the lab, Daniel Browne, had previously sequenced and assembled the genome for race B. During one of their regular discussions, Devarenne suggested they attempt to do the same for races A and L.
“This approach was beneficial in two ways,” Boland remarked. “We were tackling something unprecedented while also enhancing our understanding of hydrocarbon biosynthesis.”
Despite the races being nearly indistinguishable when viewed under a microscope, Boland mentioned there had been discussions over whether these could be classified as separate species. They were eager to see if genomic research could clarify this issue.
Along with Devarenne, the research team comprised Ivette Cornejo Corona, Ph.D., postdoctoral researcher in Devarenne’s lab; John Mullet, Ph.D., another researcher and professor in the Department of Biochemistry and Biophysics; Rebecca Murphy, Ph.D., a former graduate student from Mullet’s lab; and Shigeru Okada, Ph.D., a professor at the University of Tokyo, a long-standing collaborator on Botryococcus studies.
Tim Devarenne, Ph.D., investigates the biofuel characteristics of the green microalga Botryococcus braunii in his lab in the Department of Biochemistry and Biophysics. (Tim Devarenne, Kathleen Phillips/Texas A&M AgriLife)
Genetic Evaluation
Although Botryococcus is frequently investigated for its hydrocarbon generation, sequencing its genome has been quite challenging.
Boland, now an assistant research scientist at the Texas A&M Institute for Genome Sciences and Society, developed a passion for bioinformatics during the pandemic transition. He now employs bioinformatics daily in his current role. (Texas A&M Foundation)
Boland mentioned that the thick, oily environment in which the cells reside complicates DNA extraction and isolation, yet the team was eager to examine the genomes to identify similarities in the genes and proteins associated with each race’s biofuel production.
However, as they pieced the genomes together and executed genomic comparisons using supercomputers at the Texas A&M High Performance Research Computing Center, Boland noted that it became apparent these organisms were distinctly different species.
“It was as if every aspect we examined revealed differences,” he said.
Ultimately, the researchers identified that approximately one in every five genes was unique to each Botryococcus race. To provide context, the genetic disparity between humans and chimpanzees, our closest evolutionary relatives, is less than 2%.
Following further validations, Boland and Devarenne embarked on reclassifying the Botryococcus races. The team spent several months brainstorming different names.
They retained race B’s original name of Botryococcus braunii to honor its historical significance while renaming race A to Botryococcus alkenealis and race L to Botryococcus lycopadienor, reflecting the types of hydrocarbons produced by each race.
Defining a Species
Recently, biologists have increasingly relied on genetic and genomic data to classify organisms. Despite the solid evidence indicating that these Botryococcus algae should be recognized as separate species, Devarenne noted that what ultimately defines a species is the consensus within the scientific community.
After their study was published in the peer-reviewed journal PLOS One, Devarenne shared their findings with more than 100 researchers who examine these organisms in their labs.
“The criteria we use to define separate species may not alter how these organisms are utilized in research,” he clarified. “Nonetheless, it is crucial for scientific understanding and reshaping our perspective on how these organisms relate to one another and to all other species.”
Boland emphasized that he and Devarenne published their work in an open-access journal to enable other scientists to build upon their findings. The complete genomes of these species are also accessible on the National Center for Biotechnology Information website.
“We wanted the information to be publicly accessible by the time we published,” he explained. “Science thrives on community engagement. Our ultimate objective is to enhance collective knowledge, which is precisely what we achieved.”
