Assembling the puzzle: Complete chloroplast genome sequences of Discocactus bahiensis Britton & Rose and Melocactus ernestii Vaupel (Cactaceae) and their evolutionary significance

Abstract

Discocactus and Melocactus are representatives of Core Cactoideae II BCT clade (Browningieae, Cereeae and Trichocereeae clade) and consist of 14 and 50 species, respectively. Both genera occur in South America, but Melocactus distribution extends through Central America and the West Indies. Although the Cactaceae family stands out for having highly rearranged plastomes, with particular gene organization, small or divergent inverted repeats (IRs) and IR loss, the plastome variation in the BCT clade is unknown. In this study, we assembled plastomes of Discocactus bahiensis and Melocactus ernestii and compared them with other available plastomes of Cactoideae (Carnegiea gigantea, and species of the genera Mammillaria and Rhipsalis) as well as with canonical plastomes of members of the order Caryophyllales (Portulaca oleracea and Spinacea oleracea). The plastomes of D. bahiensis (128,733-bp) and M. ernestii (130,703-bp) showed a quadripartite structure with 17 rearrangements when compared to those of P. oleracea and S. oleracea. Thus, twenty-eight genes were transferred from the LSC (large single copy) region to the IRs and 12 genes from the IRs to the LSC or SSC (small single copy) regions. Twenty-seven syntenic blocks were identified, evidencing a large number of rearrangements within the subfamily Cactoideae. These rearrangements could not be explained by the absence of IR regions nor the number of repeats. By comparing plastomes of D. bahiensis and M. ernestii, we propose new regions for phylogenetic inferences for the subfamily Cactoideae, for Discocactus and Melocactus, and for related groups.