Whole-genome resequencing analysis of the medicinal plant Gardenia jasminoides.

Background: Gardenia jasminoides is a species of Chinese medicinal plant, which has high medicinal and economic value and rich genetic diversity, but the study on its genetic diversity is far not enough. Methods: In this study, one wild and one cultivated gardenia materials were resequenced using IlluminaHiSeq sequencing platform and the data were evaluated to understand the genomic characteristics of G. jasminoides. Results: After data analysis, the results showed that clean data of 11.77G, Q30 reached 90.96%. The average comparison rate between the sample and reference genome was 96.08%, the average coverage depth was 15X, and the genome coverage was 85.93%. The SNPs of FD and YP1 were identified, and 3,087,176 and 3,241,416 SNPs were developed, respectively. In addition, SNP non-synonymous mutation, InDel mutation, SV mutation and CNV mutation were also detected between the sample and the reference genome, and KEGG, GO and COG database annotations were made for genes with DNA level variation. The structural gene variation in the biosynthetic pathway of crocin and gardenia, the main medicinal substance of G. jasminoides was further explored, which provided basic data for molecular breeding and genetic diversity of G. jasminoides in the future.

Complete chloroplast genome of Chloranthus henryi (chloranthaceae).

The complete chloroplast genome of Chloranthus henryi, an important traditional Chinese herbal medicine, was sequenced and characterized in this study. The genome size is 157,990 bp in length with 37.3% GC content. Two inverted repeats of 26,151 bp are separated by a large single-copy region (87,148 bp), and a small single-copy region (18,569 bp). A total of 131 genes were identified, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Eight plastome accessions from Chloranthales, Austrobaileyales, Nymphaeales, and Amborellales were selected to assess the phylogenetic placement of genus.

The complete chloroplast genome sequence of Euscaphis japonica (Staphyleaceae).

Euscaphis japonica is not only an ideal ornamental plant, but also a traditional medicinal plant, which is an extremely valuable species to study. We determined the complete chloroplast genome sequence for E. japonica using Illumina sequencing technology. The complete chloroplast sequence is 160,467 bp in length, including a large single-copy (LSC) region of 88,716 bp, a small single-copy (SSC) region of 18,614 bp, and a pair of invert repeats (IR) regions of 26,568 bp. Plastid genome contains 142 genes, 46 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 14 chloroplast genomes indicates that E. japonica forms an isolated clade and sisters to Glycosmis-Gossypium clade with strong support.