Complete chloroplast genome analysis based study on origins of cultivated Radix Aconitum Vilmoriniani

Abstract

To study the influencing factors on the quality of cultivated varieties of Radix Aconitum Vilmoriniani, a toxic medicinal material for traumatology in Yunnan Province, the chloroplast genomes of samples from 10 different cultivation bases were sequenced by Illumina HiSeq 4000 high-throughput sequencing platform. Then the sequencing data were assembled and annotated followed by analysis of the characteristics of the chloroplast genomes by bioinformatics tools and construction of the phylogenetic trees. The results were as follows: (1) The full length of chloroplast genome of the 10 cultivated varieties from different regions were 155 744-155 937 bp, the large single copy region (LSC) and small single copy region (SSC) were 86 363-86 548 bp and 16 921-17 007 bp, respectively, the size of the inverted repeat region (IR) was 26 170-26 236 bp. The GC content of chloroplast genome of 10 cultivated varieties was 38.1%, with obvious AT preference, and 131 genes were annotated, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. (2) These sequences identified 60-73 SSR sites, and genome comparative analysis found that the length of chloroplast genome of 10 cultivated varieties ranged from 155 744 to 155 937 bp with moderate expansion. Some variation hot spots were found, such as trnK-UUU-trnQ-UUG, trnY-GUA-trnE-UUC, trnC-GCA-trnT-GGU, ycf4-cemA, ycf1 and ndhF, etc. (3) Phylogenetic analysis based on the two datasets showed that JS-1-4, QJ-1-2, LX-1-3, LJ-3-2 were closely related to Aconitum vilmorinianum and LQ-1-3, GJ-1-3, NL-1-3, DC-2-2 were closely related to A. austroyunnanense. In the phylogenetic tree, which was constructed based on the complete chloroplast genomes, LJ-4-3 was closely related to A. delavayi and LJ-1-2 was closely related to A. duclouxii; while in the phylogenetic tree which was constructed based on the protein coding gene sequences (PCGs), LJ-4-3 was closely related to A. episcopale and LJ-1-2 was closely related to A. contortum. In summary, the hybrid origins of cultivation of Radix Aconitum Vilmoriniani include at least the two original plants: A. vilmorinianum and A. austroyunnanense, and other species of Aconitum even existed in individual cultivation bases. The mixed origins of cultivation may be one of the influencing factors on instability of the quality of Radix Aconitum Vilmoriniani.

Keywords

• cultivated radix aconitum vilmoriniani
• chloroplast genome
• sequence characteristics
• phylogenetic analysis
• species identification