The Chloroplast Genome Sequence Characteristics Analysis of Berberis diaphana Maxim

Abstract

Berberis diaphana Maxim (B. diaphana), an important medicinal deciduous shrub, is narrowly endemic to China. In the present study, the complete chloroplast (cp) genome of B. diaphana was sequenced and analyzed. The complete cp genome of B. diaphana is 166, 225 bp in length, presenting a quadripartite structure comprising a large single copy region (LSC 73, 596 bp), a small single copy region (SSC 18, 656 bp), and a pair of inverted repeats regions (IRa/ IRb: 36, 954 bp each). The genomewide GC content was 38.07%, LSC made up 32.59%, SSC made up 32.59%, and IR made up 41.02%. The genome encodes 144 genes, including 99 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 98 simple sequence repeats (SSRs) was identified. Codon usage analysis showed that the genome tended to use codon ending in A/U. Phylogenetic relationships of 20 species inferred that B. diaphana is sister to Berberis weiningensis. The genome comparison revealed that there is a wide variability of the junction sites, and there is higher divergence in the SSC and IRa/ IRb regions than in LSC regions. This study identified the unique characteristics of the B. diaphana cp genome, which will provide valuable information for further studies as well as molecular identification approaches for this important medicinal plant.