Comparative analysis of whole chloroplast genomes of Ligusticum sinense and L. jeholense, Umbelliferae

Abstract Background Gaoben has a long history of application as medicine. There are few records of Liaogaoben in ancient books. The varieties of Ligusticum in practical application are confused. Therefore, it is very important to identify Ligusticum accurately. The phylogenetic position of Ligusticum in Umbelliferae needs to be determined. It is also of great significance to analyze the phylogeny of Ligusticum in Umbelliferae the difference of somatic genome. Methods Chloroplast (cp) genomic DNA was extracted from two species of Ligusticum and sequenced on Hiseq4000 light source. The sequence was assembled into contrags by soapenovo 2.04, aligned with reference genome by blast, and then corrected manually. Genereanation is performed by online dogma tools. The general characteristics of cp genomes of two species were analyzed, and compared with the relative species. The DNA of chloroplasts of higher plants is double stranded covalently closed loop molecule, and its length varies with species. According to the assembly genome sequence of the sequenced samples, combined with the prediction results of the coding genes, the genome of the samples was displayed in circles. After alignment, the evolutionary tree was constructed based on the single nucleotide polymorphism (SNP) of cp genome in 31 species by ML method. Results The whole chloroplast genome of Gaoben and Liaogaoben is 148,515 bp and 148,493 bp, both of which contain IR (IRa and IRb) LSC and SSC. 127 genes have been annotated, including 83 protein coding genes, 8 tRNA and 36 rRNA of all species, and 28 coding genes in IR region. There are six genes in the ATPase subunit of photosynthesis gene group, and there are obvious differences in the types of introns in NADH dehydrogenase subunit between them. In the comparative analysis of Pi value, two significant gene variation points are petG gene and psaL-ycf4 gene. The phylogenetic tree of the whole cp genome of SNP Umbelliferae was constructed, including 28 Umbelliferae and 3 Ligusticum. Conclusions In this study, the cp genomic characteristics of Ligusticum sinense and L. jeholense were identified, which provided a theoretical basis and documentation for the identification and phylogenetic analysis of Ligusticum.