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

Abstract

BackgroundThe 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. Arachis is the biggest taxonomic section within genus Arachis and its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of the Arachis species need first to be better understood.ResultsHere, in this study, we have sequenced and/or assembled twelve Arachis complete chloroplast (cp) genomes (eleven from Sect. Arachis). These cp genome sequences enriched the published Arachis cp 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. Arachis species 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 and A. monticola that are the only tetraploid (AABB) species within Arachis are 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 complete Arachis cp 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.

Interspecific Hybrids Between Pelargonium × hortorum and Species From P. Section Ciconium Reveal Biparental Plastid Inheritance and Multi-Locus Cyto-Nuclear Incompatibility

“…The insight from this study further open up possibilities for breeding of currently available Pelargonium cultivars with their crop wild relatives. Now we could conceivably start breeding in plastids that, for instance, perform better in warmer/colder/dryer climates allowing for the adjustment of cultivars to different climates (Deng et al, 2004;Cortés and Blair, 2018;Westerbergh et al, 2018) and other abiotic factors (Mezghani et al, 2019;Wang et al, 2019;Ribera et al, 2020;Singh et al, 2020). Especially, photosynthesis would be an interesting trait to focus on as differences between the species are, likely, more dramatic than those observed between the different populations of A. thaliana which has been the focus so far when studying the effects of plastid types and photosynthetic efficiency (Flood et al, 2011;Cruz et al, 2016;Flood et al, 2020).…”

Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes

“…2 and 3). For other land plant species, such as peanuts, cherries and radishes, the cp genome size and structure, as well as the gene content and order, are highly conserved among the cultivated and wild species [29][30][31].…”

Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes

“…2 & 3). For other land plant species, such as peanuts, cherries and radishes, the cp genome size and structure, as well as the gene content and order, are highly conserved among the cultivated and wild species [29][30][31].…”