Abstract
BACKGROUD: Sophora L. is a medicinally significant genus within Papilionoideae (Fabaceae), renowned for its medicinal, ecological, and economic importance. However, taxonomic and phylogenetic uncertainties persist within this genus, especially in China, due to limited genetic data and the lack of effective molecular markers. This study aimed to address these limitations by sequencing and analyzing chloroplast (cp.) genomes from six Sophora species endemic to China, thereby enriching genetic resources for future research. RESULT: Here, we reported and characterized six chloroplast (cp.) genomes of Sophora species (Sophora xanthantha, Sophora davidii, Sophora moocroftiana, Sophora tonkinensis, Sophora velutina, and Sophora velutina var. cavaleriei) from China, sequenced using the Illumina HiSeq platform. Comparative analyses of these newly generated cp. genomes, alongside previously published Sophora cp. genomes, revealed that the Sophora cp. genomes exhibited a size range of 151,270 - 154,378 bp (excluding S. japonica and S. xanthantha). We observed expansions of the inverted repeat (IR) regions in Sophora, leading to the translocation of rpl2 into the large single-copy (LSC) region, pseudogenization of ycf1, and absence of trnH in some species. Comparative genome analysis revealed a ~ 24-kb inversion between trnC-GCA and trnF-GAA within the genus, a phenomenon first observed to involve at least three rearrangements. Furthermore, we identified three valuable molecular markers (trnT-UGU - trnL-UAA, psbE - petL, and rps11 - rpl36) that are suitable for phylogenetic inference within Sophora. CONCLUSIONS: Phylogenetic analyses based on the chloroplast genomes robustly supported the monophyly of sect. Pseudosophora. Importantly, our phylogenetic results suggested that S. japonica and S. xanthantha should not be classified within the genus Sophora. These findings contribute significantly to the chloroplast genomic data of Sophora and provide valuable genetic resources and molecular markers for resolving taxonomic ambiguities and advancing future phylogenetic, evolutionary, and taxonomic investigations of Sophora.