Comparative Analysis of Chloroplast Genomes of Dalbergia Species for Identification and Phylogenetic Analysis

Abstract

<i>Dalbergia</i> L.f. is a pantropical genus consisting of 269 species of trees, shrubs, and woody lianas. This genus is listed in <i>CITES</i> Appendices because of illegal logging and trafficking driven by the high economic value of its heartwood. Some species are also used medicinally. Species identification of <i>Dalbergia</i> timber and herbs is challenging but essential for <i>CITES</i> implementation. Molecular methods had been developed for some timber species, mostly from Madagascar and Southeast Asia, but medicinal species in south China were usually not included in those studies. Here, we sequenced and assembled the chloroplast genomes of five <i>Dalbergia</i> species native to Hong Kong, four of which are medicinal plants. Our aim is to find potential genetic markers for the identification of medicinal <i>Dalbergia</i> species based on divergence hotspots detected in chloroplast genomes after comparative and phylogenetic analysis. <i>Dalbergia</i> chloroplast genomes displayed the typical quadripartite structure, with the 50 kb inversion found in most Papilionoideae lineages. Their sizes and gene content are well conserved. Phylogenetic tree of <i>Dalbergia</i> chloroplast genomes showed an overall topology similar to that of <i>ITS</i> sequences. Four divergence hotspots (<i>trnL</i>(UAA)-<i>trnT</i>(UGU), <i>ndhG-ndhI</i>, <i>ycf1a</i> and <i>ycf1b</i>) were identified and candidate markers for identification of several <i>Dalbergia</i> species were suggested.