Characteristics and phylogenetic analysis of chloroplast genome in Berberis diaphana Maxim.

Abstract

Abstract [Objective] In order to examine the structural features of the chloroplast genome of Berberis diaphana and the phylogenetic relationship with the taxa of the same genus, we analyzed its chloroplast genome structure and performed phylogenetic analysis. [Methods] Sequencing was performed by Illumina Hiseq X Ten technology. The chloroplast genome characteristics of B. diaphana were analyzed by using CPGview, CodonW, MISA, Reputer, IRscope, and mVISTA. Phylogenetic tree was constructed by ML method in MEGA7 software. [Results] The chloroplast genome of B. diaphana showed a length of 166 225 bp, with a typical quadripartite structure and the GC content of the whole genome was 38.07%. A total of 144 genes were annotated, including 99 protein coding genes, 37 tRNA genes, and 8 rRNA genes. Among them, 23 genes contained introns, and 32 genes were present in duplicate copies, with preference for codons ending in A/U. A total of 98 SSR loci and 150 scattered repeat sequences were detected, and most SSR loci composed of A/T bases. The degree of variation in the SSC and IR regions was higher than that in the LSC region. Phylogenetic analysis revealed that B. diaphana was most closely related to B. weiningensis. [Conclusion] The chloroplast genome structure of B. diaphana is similar to other species of berberis, providing a theoretical basis for molecular identification and evolutionary relationship of this genus.

Keywords

• berberis diaphana
• chloroplast genome
• sequence characterization
• phylogenetic analysis