The complete chloroplast genome sequence of Lithospermum erythrorhizon: Insights into the phylogenetic relationship among Boraginaceae species and the maternal lineages of purple gromwells

In Japan, Lithospermum erythrorhizon grows in the wild, and its roots are traditionally used for dyeing and medicinal purposes. However, due to excessive harvesting and changes in the natural environment, the population of this species has significantly declined over the past decades. To conserve the domestic varieties, it is important to obtain genomic information that accurately represents their pure lineage. The objective of this study was to characterize the chloroplast genome, which serves as a valuable phylogenetic marker, using next-generation sequencing. The results revealed that the DNA has a typical quadripartite structure, spanning 150,478 bp with a GC content of 35.5%. A total of 113 unique genes are encoded, including 80 protein-coding genes, 4 ribosomal RNA genes, and 29 transfer RNA genes. Comparative plastome analyses involving 13 Boraginaceae species, including L. erythrorhizon, showed high similarities in the gene order and codon usage, while an accelerated substitution rate was observed in matK. Phylogenetic analyses using this gene and 71 common protein-coding genes indicated a close evolutional relationship between L. erythrorhizon and Glandora prostrata. Furthermore, when comparing the chloroplast genome assembly data of a Chinese variety, a total of 44 structural variants were identified. Most of these variants were mononucleotide or dinucleotide in size, but a 70 bp insertion/deletion was identified in the intergenic region flanked by the accD and psaI genes. The presence of this relatively substantial structural variant indicates that the maternal lineages of the Japanese and Chinese varieties examined in this study are distinctly different.