Unraveling genetic relationships among Arachis species (Fabaceae) with a basic chromosome number of x = 9 through complete chloroplast genome analysis

Abstract

Arachis L. (Fabaceae) is a highly diverse genus comprising 84 diploid (x = 10, 9) and tetraploid (x = 10) species, classified into nine taxonomic sections. This genus is particularly important as it includes the cultivated peanut, A. hypogaea, one of the most significant oilseed crops grown in warm regions worldwide. Previous genetic and genomic investigations have mainly focused on diploid and tetraploid species with x = 10; therefore, the genomic composition and the interspecific relationships of x = 9 Arachis species remain poorly understood. Here we performed a comparative plastome analysis of all x = 9 Arachis species: A. decora, A. praecox, and A. palustris from section Arachis, and A. porphyrocalyx from section Erectoides. The plastome lengths ranged from 156,272 bp to 156,391 bp, containing 76 protein-coding genes, 29 tRNA genes, and four rRNA genes, with an average GC content of 36.4%. The sequences were characterized by the presence of 94 to 101 simple sequence repeats and a high degree of conservation in the SC/IR boundaries and protein-coding genes. The phylogenetic tree confirmed the monophyly of x = 9 species of section Arachis and their close relationship with non-A-genome species of section Arachis. Interestingly, A. porphyrocalyx clustered more closely with A-genome species of section Arachis than with its expected relatives from section Erectoides. These results improve the understanding of interspecific relationships among Arachis species with distinct basic chromosome numbers and provide genomic information for germplasm characterization and conservation.