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.

可可瘤是属于Theobromeae，Byttnerioideideae Burnett亚科和Malvaceae家族的植物属。在家庭和属级别的分类法中存在差异。在这里，我们比较了可可豆和可可豆两个先前报道的叶绿体基因组的结构在校正注解并搜索高度多态性区域后，可用于设计分子标记来研究属间的系统发生关系。两个叶绿体基因组均显示相似的结构，基因含量和组织。正确注释的基因组包含130个基因，包括8个核糖体RNA，37个tRNA基因和85个蛋白质编码基因。在两个基因组中，氨基酸频率，密码子使用，推定的RNA编辑位点，微卫星和寡核苷酸重复是相似的。多态性热点区域多见于基因间区域，随后是内含子区域，以及少数基因的编码序列。我们确定了30个多态性位点，包括trnH - psbA，ndhE - ndhG，RPL32 - trnL，TRNP - PsaJ，rpl33 - rps18，trnQ - psbK，TRNS - TRNG和ndhF - RPL32可能对属推断适合的适地适标记发展的可可系统发育。用这些基因座的标记来推断系统发育可能有助于鉴定与可可豆和大花麦草的遗传相容和密切相关的物种。 为了育种目的而生产这些种类的优质品种，以大量生产水果，并对病原体具有高度抵抗力。