Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation

Our study delves into the evolutionary history of the baobab tree, one of Earth's oldest non-clonal plants. Motivated by FDA recognition of baobab for food use and reports of historic tree deaths, we sought to provide genome-based insights. We began with skim sequencing and genome size estimation for all eight baobab species. Using Illumina and Oxford Nanopore Technologies, we created two chromosome-scale haploid Adansonia digitata assemblies and several long-read contig assemblies for baobabs from Namibia, Sudan, and Madagascar. Additionally, we collected leaf samples from 25 Adansonia digitata specimens across Africa for population genetics analyses. Despite challenges in seed germination and DNA extraction, we refined our methods to obtain high-quality DNA and RNA.

Our research unveiled that Adansonia digitata is autotetraploid, unlike the other seven diploid species, and highlighted a proliferation of DNA transposable elements over long terminal repeat retrotransposons. We identified a whole-genome duplication event about 30 million years ago, leading to up to 16 copies of genes related to flower development, chromatin/transcription, and exocytosis. We hypothesize that genes associated with UV-B light perception and chromatin regulation contribute to the baobab's longevity. Additionally, our study revealed distinct baobab populations in Namibia linked to specific watersheds, suggesting geographical barriers to gene flow. These findings enhance our understanding of baobab diversity and inform breeding strategies.

By sequencing and providing quality genomic data, we aim to advance conservation efforts and understanding of the baobab's evolutionary trajectory amidst climate change. Our chromosome-resolved genome assembly for Adansonia digitata represents a significant improvement over previous fragmented assemblies.