Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny

Abstract

AbstractBackgroundThe cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect.Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect.Arachisis the biggest taxonomic section within genusArachisand its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of theArachisspecies need first to be better understood.ResultsHere, in this study, we have sequenced and/or assembled twelveArachiscomplete chloroplast (cp) genomes (eleven from Sect.Arachis). These cp genome sequences enriched the publishedArachiscp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect.Arachisspecies into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts andA.monticolathat are the only tetraploid (AABB) species withinArachisare nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species.ConclusionIn summary, we have acquired sequences of twelve completeArachiscp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.