Complete Chloroplast Genome Analysis And Phylogenetic Study Of Rhipsalis Baccifera

The family Cactaceae is an important component of the New World's flora and a popular family in horticulture.Almost all cacti are native exclusively to the New World,with the sole exception of Rhipsalis baccifera.R.baccifera,commonly known as the mistletoe cactus,is the only species in Cactaceae that is native in both the New World and the Old World.The success of this species occupying the largest ranges in Cactaceae remains puzzling.Although Cactaceae has been proved as monophyletic in previous studies by morphological synapomorphies and molecular data,phylogenetic relationships within the family remain insufficiently understood.In addition,Cactaceae is placed in the ACPT(acronym from Anacampseroteae,Cactaceae,Portulaca,Talinum)clade of suborder Portulacineae of order Caryophyllales,while relationship between members of the clade is also unclear.Chloroplast genome of land plants is highly conserved in nucleotide sequence as well as gene content and order and its relatively slow rate of evolution makes it excellent for phylogenetic and evolutionary studies.However,there are still very few representatives from Cactaceae and suborder Portulacineae with sequenced chloroplast genomes and the phylogenetic resolution using such data in those interesting taxa is still unclear.In this study,the complete chloroplast genome of Rhipsalis baccifera was sequenced and analyzed for the first time.The chloroplast genome of R.baccifera contains 122,333 bp.It displays a typical quadripartite structure with a LSC region of 81,459 bp in length,separated from the SSC region of 23,531 bp,by two inverted repeat(IR)regions both 8,530 bp long.The gene contents and order in the structure of the cp genome of R.baccifera displays several structural changes such as rearrangements,gene loss,and loss of introns of genes,contraction of the inverted repeat(IR)regions,inversions and translocations of some genes.Rhipsalis baccifera displays a large rearrangement in the LSC region,involving 19 genes:ndhJ-trnF-trnL-trnT-rps4-trnS-ycf3-psaA-psaB-rpsl4-trnfM-trnG-psbZ-trnS-psbC-psbD-trnT-trnE-trnY.which is observed for the first time in order Caryophyllales.This study has also revealed the inversion of the SSC region of subfamily Cactoideae species.The 6 kb gene inversion between genes rbcl-trnM seems to be another commonly shared characteristic of the cp genomes of Cactaceae.Some genes in the chloroplast genome of R.baccifera have lost introns,such as the clpP gene.In R.baccifera,the rps12 gene has also lost one intron but unlike in other angiosperm genomes where one intron is found in the LSC region and two other introns are duplicated in the IR regions,one is found in the LSC region and the other in the SSC region.In comparison to other cp genomes of suborder Portulacineae studied,the cp genome of R.baccifera seems to be the most rearranged and this is evident by the fact that this genome contains the highest number of repeat sequences with larger sizes>100bp which has been correlated in previous studies with large number of rearrangements in the cp genomes.Phylogenetic analysis using the whole chloroplast genome sequences confirmed the relationships among Cactaceae,Talinum and Portulaca.Interestingly,Rhipsalis baccifera is located a basal position within Cactaceae and has the longest branch length in the phylogenetic tree,suggesting long evolution history of this species.This therefore supports previous studies that suggested that the wide distribution of this species to be a result of longer history of evolution.In conclusion,Rhipsalis baccifera has the longest evolution history compared to other groups in Cactaceae and this is an important reason for its wide geological expansion in the world.This study will contribute to future work on cacti phylogeny and evolution and also shed more light on the explanation as to why this species is the only cacti that naturally occurs outside the New World.It is recommended that more indepth phylogeographical analyses of R.baccifera using both chloroplast genomic and nuclear genomic data with representative samplings from the New World and Old World regions to reveal the details of the biogeographical expansion history of this amazing species.