Abstract
Theobroma is a plant genus included in tribe Theobromeae, subfamily Byttnerioideae Burnett and family Malvaceae. Discrepancies exist in taxonomy at family and genus level. Here, we compared structures of two previously reported chloroplast genomes of Theobroma cacao and Theobroma grandiflorum after correction of annotation and search for highly polymorphic regions which could be used to design molecular markers to investigate phylogenetic relationships among the genus. Both chloroplast genomes showed similar structure, gene content and organization. The correctly annotated genomes contained 130 genes including 8 ribosomal RNA, 37 tRNA genes and 85 protein-coding genes. The amino acids frequencies, codon usage, putative RNA editing sites, microsatellites and oligonucleotide repeats were alike in two genomes. Polymorphic hotspot regions were mostly observed in intergenic regions followed by intronic regions, as well as in coding sequences of few genes. We identified 30 polymorphic loci including trnH-psbA, ndhE-ndhG, rpl32-trnL, trnP-PsaJ, rpl33-rps18, trnQ-psbK, trnS-trnG, and ndhF-rpl32 that might be suitable for development of appropriate and suitable markers for inferring of genus Theobroma phylogeny. The inferring of phylogeny with the markers of these loci might be helpful to identify genetically compatible and closely related species to T. cacao and T. grandiflorum for breeding purposes to produce quality cultivars of these species for high quantity of fruit production and with high resistance towards the pathogens.