Abstract

Bomarea ovallei (Phil.) Ravenna (2n=2x=18) is an endangered endemic species that inhabits only a small part of the coast of the Atacamaregion. We describe the structure, gene composition and phylogeny of the complete chloroplast sequence of this elusive species. Thechloroplast genome consists of 155,018 bp, with typical quadripartite structures: a large single copy region (LSC) of 84,132 bp, a smallsingle copy region (SSC) of 17,794 bp, and two inverted repeat regions (IRs) contain 26,546 bp. One hundred and thirty-four genes wereidentified out of which 84 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. B. ovallei chloroplast resembles chloroplasts from sevenspecies of the order Liliales in length and structure and is most similar to Bomarea edulis (BP=100). The average nucleotide variability(Pi) of 0.00254 between these two Bomarea species is moderate. Nine loci with increased variability were identified: rps16-trnQ, atpF,trnL, ndhC-trnV, rbcL, psbJ, rpl32-trnL, ndhD and ycf1. These loci could be used as DNA markers for classification and evaluation studiesin Bomarea populations.