Complete chloroplast genome data of Isatis indigotica Fort, an important medicinal plant species

<i>Isatis indigotica</i> Fort. is a biennial herbaceous plant belonging to the Isatis genus of the Brassicaceae family, with significant medicinal value. The entire genome of the chloroplast of <i>Isatis indigotica</i> was sequenced using the Illumina high-throughput sequencing platform, the Illumina NovaSeq 6000.The circular genome is 153,823 bp in size and includes two 26,271 bp inverted repeat sequences (IRs), an 83,575 bp large single copy region (LSC), and a 17,706 bp small single copy region (SSC).A total of 87 genes were annotated, including 41 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. Based on the whole chloroplast genome and PCG sequences, a phylogenetic tree of nine species of <i>Isatis indigotica</i> in Cruciferae was constructed, with Thlaspi arvense L. as the outgroup.Phylogenetic results indicate that Isatis cappadocica is closely related to the Isatis species studied in this research. These data enrich the genetic knowledge of Isatis species in the Cruciferae family and provide a basis for further research in molecular breeding, genetic breeding, and other related fields.