Complete Chloroplast Genome of <i>Rhipsalis baccifera,</i> the only Cactus with Natural Distribution in the Old World: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies

<i>Rhipsalis baccifera</i> is the only cactus that naturally occurs in both the New World and the Old World, and has thus drawn the attention of most researchers. The complete chloroplast (cp) genome of <i>R. baccifera</i> is reported here for the first time. The cp genome of <i>R. baccifera</i> has 122, 333 base pairs (bp), with a large single-copy (LSC) region (81,459 bp), SSC (23,531 bp) and two inverted repeat (IR) regions each 8530 bp. The genome contains 110 genes, with 73 protein-coding genes, 31 tRNAs, 4 rRNAs and 2 pseudogenes. Twelve genes have introns, with loss of introns being observed in, <i>rpoc1</i><i>clpP</i> and <i>rps12</i> genes. 49 repeat sequences and 62 simple sequence repeats (SSRs) were found in the genome. Comparative analysis with eight species of the ACPT (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae) clade of the suborder Portulacineae species, showed that <i>R. baccifera</i> genome has higher number of rearrangements, with a 19 gene inversion in its LSC region representing the most significant structural change in terms of its size. Inversion of the SSC region seems common in subfamily Cactoideae, and another 6 kb gene inversion between <i>rbcL- trnM</i> was observed in <i>R. baccifera</i> and <i>Carnegiea gigantea</i>. The IRs of <i>R. baccifera</i> are contracted. The phylogenetic analysis among 36 complete chloroplast genomes of Caryophyllales species and two outgroup species supported monophyly of the families of the ACPT clade. <i>R. baccifera</i> occupied a basal position of the family Cactaceae clade in the tree. A high number of rearrangements in this cp genome suggests a larger number mutation events in the history of evolution of <i>R. baccifera</i>. These results provide important tools for future work on <i>R. baccifera</i> and in the evolutionary studies of the suborder Portulacineae.