Research

The scientific understanding of baobab ecology is continuously being furthered through active and ongoing research from several of the World’s leading scientist, researchers and organizations. References to previous research can be found below along with results and findings from the active projects that the Baobab Genome Project is associated with.

Ongoing Research

Preliminary Data

As part of the initial funding in the BGP from the Illumina Greater Good Initiative, PI Michael generated genomes for all eight Adansonia species, including a high-quality reference for A. digitata (Fig. 3). The reference genome, which is based on a tree in the USDA Germplasm Information Resource Network (GRIN) so that other researchers can readily access it, was sequenced with ONT long reads resulting in chromosome-resolved genome.

Population genomics provides first clues to robust genomic markers

The first phase of our ongoing GCRF-supported (to International Collaborator Dr. Yant) broadscale sequencing of >200 baobab trees across Africa has yielded a preliminary assessment of population structure. Illumina short read resequencing (>20x depth) from two dozen samples across sub-Saharan Africa (Fig. 4A) indicates that broad-scale structure recapitulates geographic structure tightly. The complete set of >200 baobab trees will be available by the start of this project and will inform our sampling strategy.

Direct DNA methylation (epigenome) detection with ONT reveals baobab markers

The long read ONT sequencing platform enables direct detection of DNA methylation (epigenome). Therefore, we now routinely call methylated bases when sequencing a genome; without any additional lab work, just additional computational time, we get a genome and epigenome.  The epigenomic patterns in baobab are similar to those found in other long-lived trees like oak, where these epigenomic patterns were used to evaluate adaptation to specific climates. This means that we will be able to get both genomic as well as epigenomic markers when we sample baobab in the field with the MinION sequencer.

Telomere length as a marker of plant age

In animals, telomere length and the rate of shortening, has been associated with longevity. However, it is currently unknown if there is a relationship between plant telomere length and longevity. Since we generated our reference A. digitata genome using ONT long read sequencing technology we were able to estimate the length of the telomeres. Telomere length is well documented in the model plant Arabidopsis thaliana to be 3-5 kilo bases (kb). In contrast the telomeres in A. digitata are greater than 30 kb, which is 10 times larger than A. thaliana, and similar to other long-lived trees that we evaluated. Our genome assembly was based on a one-month-old seedling, so leveraging long read sequence to look at the telomeres of different tissues and baobabs of different ages will also provide insight into the longevity of these trees as well as help define the role of telomere length in longevity in plants.

Stay tuned...

As results from the various research projects become available we will provide links to the data here.

Useful Baobab References

Below is a list of baobab related references if you would like to discover more about this amazing tree.