Chloroplast Genomic Analysis of Pyrrosia assimilis / 中国实验方剂学杂志

Objective::The complete chloroplast genome of Pyrrosia assimilis was sequenced, its sequence characteristics was analyzed and herbgenomics of P. assimilis was discussed. Method::Its complete chloroplast genome sequence was determined through high-throughput sequencing technology, and its structural characteristics and phylogenetic relationships were analyzed by bioinformatics. Result::The chloroplast genome of P. assimilis was a circular double-chain structure with a total length of 154 964 bp, and the total content of guanine and cytosine (GC) was 41.2%. A total of 131 genes were annotated, including 88 protein-coding genes, 35 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. A total of 43 dispersed repetitive sequences and 56 simple sequence repeats (SSRs) were detected. The frequency of codon encoding leucine was the highest, while the number of codon encoding tryptophan was the lowest. Five highly divergent regions (psbA, rrn16, petA-psbJ, ndhC-trnM, and psbM-petN) were screened, phylogenetic analysis showed that P. assimilis was closely related to P. bonii. Conclusion::Comparative analysis of the complete chloroplast genome of P. assimilis reveals that non-coding regions exhibited a higher divergence than the coding regions, the large single copy region (LSC) and small single copy region (SSC) are more divergent than the reverse repeat region (IR), the selected five highly variable regions can be used as specific DNA barcodes for identification of Pyrrosia species. Study on the chloroplast genome of P. assimilis can provide a reference for the molecular identification, genetic transformation, expression of resistance protein and secondary metabolism pathway analysis of other Pyrrosia medicinal plants.

Chloroplast Genome Analysis of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang / 中国实验方剂学杂志

Objective::To determine the chloroplast genomes of Liriope spicata var. prolifera, Ophiopogon japonicus in Sichuan and Zhejiang, analyze their sequence characteristics and complete the screening of specific DNA barcodes. Method::The chloroplast genomes of L. spicata var. prolifera, O. japonicus in Sichuan and Zhejiang were sequenced, spliced and annotated through high-throughtput sequencing technology, and the structural characteristics and phylogenetic relationships of chloroplast genomes were analyzed by bioinformatics. Result::The total length of chloroplast genome of L. spicata var. prolifera was 155 998 bp, the total content of guanine and cytosine (GC) was 37.7%, and 85 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes were successfully annotated, a total of 274 simple sequence repeats (SSRs) were detected, the number of codons encoding leucine was the most, while the number of codons encoding tryptophan was the least. The total length of chloroplast genome of O. japonicus in Sichuan province was 156 078 bp, the total content of GC was 37.8%, and 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were successfully annotated, a total of 265 SSRs were detected, the number of codons encoding leucine was the most, while the number of codons encoding tryptophan was the least. The total length of chloroplast genome of O. japonicus in Zhejiang province was 156 207 bp, the total content of GC was 37.7%, and 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes were successfully annotated, a total of 274 SSRs were detected with the highest number of codons encoding leucine and the lowest number of codons encoding tryptophan. Conclusion::The phylogenetic trees show that compared with O. japonicus in Sichuan province, L. spicata var. prolifera is more closely related to O. japonicus in Zhejiang province. The variation of non-coding regions of L. spicata var. prolifera, O. japonicus in Zhejiang and Sichuan is greater than that in the coding region. The entire chloroplast genome can be used as a super barcode for identifying species of Ophiopogon and Liriope.

Molecular structure and phylogenetic analyses of the complete chloroplast genomes of three original species of Pyrrosiae Folium / 中国天然药物

Pyrrosia petiolosa, Pyrrosia lingua and Pyrrosia sheareri are recorded as original plants of Pyrrosiae Folium (PF) and commonly used as Chinese herbal medicines. Due to the similar morphological features of PF and its adulterants, common DNA barcodes cannot accurately distinguish PF species. Knowledge of the chloroplast (cp) genome is widely used in species identification, molecular marker and phylogenetic analyses. Herein, we determined the complete cp genomes of three original species of PF via high-throughput sequencing technologies. The three cp genomes exhibited a typical quadripartite structure with sizes ranging from 158 165 to 163 026 bp. The cp genomes of P. petiolosa and P. lingua encoded 130 genes, whilst that of P. sheareri encoded 131 genes. The complete cp genomes were compared, and five highly divergent regions of petA-psbJ, matK-rps16, ndhC-trnM, psbM-petN and psaC-ndhE were screened as potential DNA barcodes for identification of Pyrrosia genus species. The phylogenetic tree we obtained indicated that P. petiolosa and P. lingua are clustered in a single clade and, thus, share a close relationship. This study provides invaluable information for further studies on the species identification, taxonomy and phylogeny of Pyrrosia genus species.