Comparison of two African rice species through a new pan-genomic approach on massive data

Abstract

Pangenome theory implies that individuals from a given group/species share only a given part of their genome (core-genome), the remaining part being the dispensable one. Domestication process implies a small number of founder individuals, and thus a large core-genome compared to dispensable at the first steps of domestication. We sequenced at high depth 120 cultivated African rice Oryza glaberrima and of 74 wild relatives O. barthii, and mapped them on the external reference from Asian rice O. sativa. We then use a novel DepthOfCoverage approach to identif missing genes. After comparing the two species, we shown that the cultivated species has a smaller core-genome than the wild one, as well as an expected smaller dispensable one. This unexpected output however replaces in perspective the inadequacy of cultivated crops to wilderness.