Complete chloroplast genome of the rare medicinal vegetable Allium hookeri.

Allium hookeri is a rare medicinal plant with unique flavor. In this study, the first complete chloroplast (cp) genome of A. hookeri was sequenced and assembled based on the next generation sequencing. The cp genome is 153,592 bp in length, including a large single-copy (LSC) region of 82,609 bp, a small single-copy (SSC) region of 17,487 bp, and a pair of inverted repeat (IR) regions of 26,748 bp each. The genome encodes 131 genes, including 86 protein-coding genes, 39 tRNA genes, and six rRNA genes. The GC content of whole genome is 36.99%. The phylogenetic analysis based on 24 complete cp sequences revealed that A. hookeri was at the base of the phylogenetic tree, indicating an older species in the Allium genus.

Characterization of the first chloroplast genome of Euchresta tubulosa Dunn and its phylogenetic analysis.

Euchresta tubulosa Dunn not only is a national second-level protected wild plant in China, but also has a long history as a source plant in traditional Chinese medicine. The chloroplast (cp) genome of E. tubulosa was 154,102 bp, consisting of a large single-copy region (LSC: 92,877 bp), a small single-copy region (SSC: 36,645 bp), and a pair of inverted repeat regions (IRb and Ira: 12,290 bp, respectively). These sequences encoded 123 genes, including 78 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that E. tubulosa is close to Lupinus species.

Characterization of the first chloroplast genome of Dichroa febrifuga and its phylogenetic analysis.

Dichroa febrifuga, seen as a medicinal plant, has a long history in traditional Chinese medicine. In this study, we adopted Illumina Hiseq sequencing technology in order to determine the first complete chloroplast (cp) genome of D. febrifuga. The cp genome was 157,647 bp in length, including a large single-copy (LSC) region of 86,728 bp, a small single-copy (SSC) region of 18,675 bp, and a pair of inverted repeat (IR) regions of 26,122 bp. The genome encoded 128 genes, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis based on 20 complete cp genome sequences revealed that D. febrifuga was the sister of the ancestor of the reported Hydrangeeae species. The findings of the study will serve as a stepping stone for follow-up researches regarding the development of the D. febrifuga species.

First complete chloroplast genome of the rare medicinal plant Schnabelia tetrodonta.

Schnabelia tetrodonta is a medicinal plant used in traditional Chinese medicine. However, the molecular biology data of the species was too scarce to bioprospect the medicinal species. In this study, the first complete chloroplast genome (cp) of S. tetrodonta was sequenced and assembled based on the next generation sequencing. The cp genome is 157,004 bp in length, including a large single-copy (LSC) region of 83,605 bp, a small single-copy (SSC) region of 36,899 bp, and a pair of inverted repeat (IR) regions of 18,250 bp each. The genome encodes 134 genes, including 90 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The GC content of whole genome is 37.80%. The phylogenetic analysis based on 20 complete cp sequences (19 genome sequences from the Teucrioideae of Lamiaceae and an outgroup of Ipomoea purpurea) revealed that S. tetrodonta was closely related to S. oligophylla.

DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae.

The genus Corydalis is recognized as one of the most taxonomically challenging plant taxa. It is mainly distributed in the Himalaya-Hengduan Mountains, a global biodiversity hotspot. To date, no effective solution for species discrimination and taxonomic assignment in Corydalis has been developed. In this study, five nuclear and chloroplast DNA regions, ITS, ITS2, matK, rbcL, and psbA-trnH, were preliminarily assessed based on their ability to discriminate Corydalis to eliminate inefficient regions, and the three regions showing good performance (ITS, ITS2 and matK) were then evaluated in 131 samples representing 28 species of 11 sections of four subgenera in Corydalis using three analytical methods (NJ, ML, MP tree; K2P-distance and BLAST). The results showed that the various approaches exhibit different species identification power and that BLAST shows the best performance among the tested approaches. A comparison of different barcodes indicated that among the single barcodes, ITS (65.2%) exhibited the highest identification success rate and that the combination of ITS + matK (69.6%) provided the highest species resolution among all single barcodes and their combinations. Three Pharmacopoeia-recorded medicinal plants and their materia medica were identified successfully based on the ITS and ITS2 regions. In the phylogenetic analysis, the sections Thalictrifoliae, Sophorocapnos, Racemosae, Aulacostigma, and Corydalis formed well-supported separate lineages. We thus hypothesize that the five sections should be classified as an independent subgenus and that the genus should be divided into three subgenera. In this study, DNA barcoding provided relatively high species discrimination power, indicating that it can be used for species discrimination in this taxonomically complicated genus and as a potential tool for the authentication of materia medica belonging to Corydalis.

Transcriptome-Guided Mining of Genes Involved in Crocin Biosynthesis.

Gardenia jasminoides is used in traditional Chinese medicine and has drawn attention as a rich source of crocin, a compound with reported activity against various cancers, depression and cardiovascular disease. However, genetic information on the crocin biosynthetic pathway of G. jasminoides is scarce. In this study, we performed a transcriptome analysis of the leaves, green fruits, and red fruits of G. jasminoides to identify and predict the genes that encode key enzymes responsible for crocin production, compared with Crocus sativus. Twenty-seven putative pathway genes were specifically expressed in the fruits, consistent with the distribution of crocin in G. jasminoides. Twenty-four of these genes were reported for the first time, and a novel CCD4a gene was predicted that encodes carotenoid cleavage dioxygenase leading to crocin synthesis, in contrast to CCD2 of C. sativus. In addition, 6 other candidate genes (ALDH12, ALDH14, UGT94U1, UGT86D1, UGT71H4, and UGT85K18) were predicted to be involved in crocin biosynthesis following phylogenetic analysis and different gene expression profiles. Identifying the genes that encode key enzymes should help elucidate the crocin biosynthesis pathway.

[Optimization for ISSR-PCR system of traditional Chinese medicine Lysimachia christinae by orthogonal design].

In order to establish the stable andreliable ISSR-PCR System of Lysimachia christinae, L16 (4(5)) orthogonal design, which based on 7 levels of single factor experiment, were used in this study. The variance analysis was carried out by SPSS 19.0, and 5 main factors affecting the reaction system were optimized in 4 levels. The best annealing temperature was selected by the optimized reaction system. And the stability and reliability of this system was tested by 23 samples from different origins. The results showed that the five factors (DNA template, primer, dNTP, Mg2+ and Taq enzyme) were the most impacts on the amplified results of ISSR-PCR of L. christinae. The order of the influence was: primer > Taq enzyme > DNA template > Mg2+ > dNTP. The optimal system, which was determined by multiple comparison on different levels of each factor, was total volume of 25 microL, including DNA template 60 ng, primer 0.3 micromol x L(-1), dNTP 0.2 mmol x L(-1), Mg2+ 1.8 mmol x L(-1), Taq enzyme 1.25 U. The optimal system was stable and reliable tested by 23 samples from different origins. This study lays the foundation for genetic diversity analysis, fine varieties selection and molecular identification of L. christinae, and provides reference for optimization on ISSR-PCR system of other speciesin future.