The family Aristolochiaceae, comprising about 600 species of eight genera, is a unique plant family containing aristolochic acids (AAs). The complete chloroplast genome sequences of Aristolochia debilis and Aristolochia contorta are reported here. The results show that the complete chloroplast genomes of A. debilis and A. contorta comprise circular 159,793 and 160,576 bp-long molecules, respectively and have typical quadripartite structures. The GC contents of both species were 38.3% each. A total of 131 genes were identified in each genome including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene (ycf1). The simple-sequence repeat sequences mainly comprise A/T mononucletide repeats. Phylogenetic analyses using maximum parsimony (MP) revealed that A. debilis and A. contorta had a close phylogenetic relationship with species of the family Piperaceae, as well as Laurales and Magnoliales. The data obtained in this study will be beneficial for further investigations on A. debilis and A. contorta from the aspect of evolution, and chloroplast genetic engineering.

More than 30 Ligularia Cass. (Asteraceae) species have long been used in folk medicine in China. Morphological features and common DNA regions are both not ideal to identify Ligularia species. As some Ligularia species contain pyrrolizidine alkaloids, which are hazardous to human and animal health and are involved in metabolic toxification in the liver, it is important to find a better way to distinguish these species. Here, we report complete chloroplast (CP) genomes of six Ligularia species, L. intermedia, L. jaluensis, L. mongolica, L. hodgsonii, L. veitchiana, and L. fischeri, obtained through high-throughput Illumina sequencing technology. These CP genomes showed typical circular tetramerous structure and their sizes range from 151,118 to 151,253 bp. The GC content of each CP genome is 37.5%. Every CP genome contains 134 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and two pseudogenes (ycf1 and rps19). From the mVISTA, there were no potential coding or non-coding regions to distinguish these six Ligularia species, but the maximum likelihood tree of the six Ligularia species and other related species showed that the whole CP genome can be used as a super-barcode to identify these six Ligularia species. This study provides invaluable data for species identification, allowing for future studies on phylogenetic evolution and safe medical applications of Ligularia.

Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum.