Synchronous dissection of chloroplast and mitochondrial genomes clarifies the intra- and inter-genus phylogeny for the agriculturally important genus Brassica

Abstract

Background : The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being extensively studied, the origination of B. napus and the detailed interspecific relationships within Brassica genus remains unresolved and somewhere confused. By synchronous sequencing of both the chloroplast DNA and mitochondrial DNA, the whole Brassica phylogeny and the origination of the predominant nap -type B. napus have been clarified based on a large plant population, which maximally integrated the known Brassica species. Results : The phylogenetic analyses based on a data set including 72 de novo assembled whole chloroplast genomes, delineated a comprehensive evolutional atlas inside and around Brassica genus. Different from the monophyletical maternal origin of B. juncea and B. carinata from cam-type B. rapa and B. nigra , respectively, the natural B. napus has multiplex maternal origins. It contains three major cytoplasmic haplotypes: the cam -type which directly inherited from B. rapa , polima -type which is close to cam -type as a sister, and the predominant nap -type. Intriguingly, nap -type seems phylogenetically integrated with certain sparse C-genome wild species , thus implying that which may have primarily contributed the cytoplasm and the corresponding C subgenome to B. napus . Human breeding creation of the B. napus cytoplasmic male sterile lines (e.g., mori and nsa ) have dramatically disturbed the concurrent inheritance between mtDNA and cpDNA. Strong parallel evolution among genera Raphanus , Sinapis, Eruca , Moricandia with Brassica indicates their uncomplete divergence from each other. Conclusions : The elaborated phylogenetic relationships and overall variation data obtained herein can substantially facilitate to develop novel Brassica germplasms and to improve the Brassica crops.