Short and long reads chloroplast genome assemblies and phylogenomics of Artemisia tangutica (Asteraceae)

The accurate chloroplast genome is the basis of its utilization in phylogeny, species evolution, and resource conservation. Here, the chloroplast genome of Artemisia tangutica Pamp. was sequenced and assembled with Illumina and PacBio. After PCR verification, the hybrid assembly result produced the most accurate chloroplast genome, assembly results of only short reads and only long reads were showed different blemishes. The chloroplast genome of A. tangutica was 151, 140 bp, including a large single copy (LSC, 82, 885 bp), a small single copy (SSC, 18, 337 bp), and a pair of reverse repeat regions (IRs, 24, 959 bp). Total 115 genes and 20 duplicate genes were annotated, including 80 protein-coding genes, four rRNA genes, and 37 tRNA genes. We observed 78 long repeat sequences and 201 simple repeat sequences, and their distribution in the genome was different to some extent. Genome comparative analysis indicated that the coding regions of chloroplast genomes of six species in Artemisia showed a high degree of sequence similarity, while the intergenic spacers showed variations. The photosystems II (PSA) and large subunit of ribosome (RPS) gene of Artemisia have a high nucleotide substitution rate. Phylogenetic relationship including 34 species of Artemisia and 12 outgroups recovered Sect. Viscidipubes , embedded in Sect. Artemisia . The subgenus Artemisia revealed a polyphyletic nature, however, the subgenus Dracunculus is monophyletic. This study provides a better understanding of species identification and phylogeny of Artemisia .