A Novel Inversion in the Chloroplast Genome of Marama (Tylosema esculentum)

Marama bean (Tylosema esculentum (Burchell) A. Schreiber: Caesalpinioideae) is a perennial non-nodulating legume of southern Africa (Namibia, Botswana and South Africa), growing in poor, arid soils surrounding the western, southern and eastern Kalahari and is being developed as a possible crop for resource poor farmers in arid regions of Southern Africa. Marama produces large (2.5 g per seed without shell), protein- and oil-rich edible seeds, and extremely large (up to 200 kg) tubers, containing protein and carbohydrate. Whole genome sequencing using both Illumina and PacBio platforms have yielded a nuclear genome assembly and a complete chloroplast molecule. The chloroplast genome has been assembled from next generation sequencing using both Illumina and Pac-Bio data. The genome is of typical organization with a large single copy and a small single copy region separated by a pair of inverted repeats and covers 161,537 base pairs. The inverted repeat is expanded compared with other legumes and the small single copy region reduced. However, the marama chloroplast genome contains a unique inversion not present in any other legumes, even in the closest relatives for which the complete chloroplast genome is available, and two complete copies of the ycf1 gene. The sequencing of multiple individuals has identified variation in the chloroplast genomes of marama. The genomes from individuals collected in South Africa differ from those collected from Namibia. There is a more limited variation among the Namibian samples, than that between the South African and Namibian samples, but that which does occur appears appears to be geographically restricted.