Chromosome-level baobab (Adansonia digitata) genome illuminates its evolutionary insights

AbstractBaobab, Adansonia digitata, is a long-lived tree endemic to Africa that holds great economic, ecological, and cultural value. However, our knowledge of its genomic features, evolutionary history, and diversity is limited, rendering it orphaned scientifically. We generated a haploid chromosome-level reference genome anchored into 42 chromosomes for A. digitata, as well as draft assemblies for a sibling tree, two trees from distinct locations in Africa, and a related species, A. za from Madagascar. Unlike any other plant to date, DNA transposable elements (TEs) make up 33% of the A. digitata genome compared to only 10% long terminal repeat retrotransposons (LTR-RTs), which are usually predominant in plant genomes. Baobab has undergone a whole genome duplication (WGD) shared with the Malvoideae [~]30 million years ago (MYA), as well as a confirmed autotetraplody event 3-4 million MYA that coincides with the most recent burst of TE insertions. Resequencing 25 A. digitata trees from Africa revealed three subpopulations that suggest gene flow through most of West Africa but separated from East Africa. Gene enrichment analysis for baobab-specific and high fixation index (Fst) suggested baobab may have retained multiple copies of circadian, light and growth genes to coordinate genome protection for longevity through the UV RESISTANCE LOCUS 8 (UVR8) and synchronizing flower development with pollinators. This study lays the groundwork for the creation of breeding resources and the conservation of baobab biodiversity.