Supercomputers at the Frontline of Climate-Resilient Forests

When he was introduced to forest genetics as a 23-year-old researcher in India, Dr. Om Rajora became obsessed and devoted to forest genetics research. “Sometimes, even at the cost of my health,” he says, laughing.

Decades later and half a world away, he is still going at it, and busier than ever. He heads the forest genetics and genomics lab and is a professor of Forest Genetics and Genomics at the University of New Brunswick, where he joined as the Tier 1 Canada Research Chair in Forest and Conservation Genomics and Biotechnology. He also coordinates the Population, Ecological and Conservation Genetics research unit at the International Union of Forest Research Organizations, and he developed and published a pioneering book series called Population Genomics. 

Through his work, Rajora seeks to reveal the secrets hidden within the genes of our woodlands, offering unprecedented insights into resilience, adaptability, and the preservation of biodiversity (genetic diversity) in the face of a rapidly changing world. His research has encompassed a wide range of forest genetic and genomics topics and fields, which besides contributing to basic science, can be used for conservation of genetic resources and sustainable forest management.

One of those areas involves analyzing the genes, gene expression, and metabolic pathways of trees under ambient and changing climate conditions. This in turn gives hints to how forests respond to environmental changes. By sequencing and analyzing the genes expressed under different scenarios, Rajora aims to identify the genes, biological processes and molecular functions affected by climate change, including those related to photosynthesis and stress response. “For example,” he explains, “this could provide us information about what traits could be affected with elevated levels of CO2.”

Rajora’s research obsession and a strong work ethic have their limits, however, and today’s rapid gene sequencing techniques have created the need for advanced methods of data analysis and storage. 

In a recent project, Rajora and his post-doctoral fellow, Dr. Rajni Parmar, needed to undertake extensive genetic analysis of the red spruce transcriptome and chloroplast genome, and identification and characterization of genes and pathways expressed differentially in response to climate change conditions. This required significant computational resources. In the past, they relied on personal computers for certain analyses, but the advent of next-generation sequencing—rapid DNA/RNA sequencing techniques—and the accumulation of massive amounts of data necessitated the use of supercomputers or computer clusters. ACENET and the Digital Research Alliance of Canada have been instrumental in providing these capabilities.

Dr. Serguei Vassiliev, a research consultant with ACENET, played a pivotal role in the study. He delved into the project, learning the fundamentals of computational bioinformatics, installing software, and creating parallelization schemes to process large problems simultaneously. He also trained the group in essential computational techniques, including genome assembly and annotation, transcriptome construction, statistical analysis of gene expression, and protein interaction network identification.

The outcomes were remarkable: computation time was slashed from weeks to hours, the group acquired advanced computational skills, and they published an article in the International Journal of Molecular Science, with another in progress. Vassiliev's significant contribution earned him co-authorship on the publication.

“The knowledge provided by this research is beneficial to the global plant genomics community,” explains Rajora. The variations found in gene expression clue scientists into what genes may allow forests to survive adverse conditions. Through international collaboration, scientists can pool their resources, data, and insights to develop innovative solutions that can be applied globally in the face of climate change.

Spring, 2023