The first complete chloroplast genome of Vicatia thibetica de Boiss.: genome features, comparative analysis, and phylogenetic relationships

• Published in: Physiology and molecular biology of plants Vol. 28; no. 2; pp. 439 - 454
• Main Authors: Guan, Yun-hui, Liu, Wen-wen, Duan, Bao-zhong, Zhang, Hai-zhu, Chen, Xu-bing, Wang, Ying, Xia, Cong-long
• Format: Journal Article
• Language: English
• Published: New Delhi Springer India 01.02.2022; Springer Nature B.V
• Subjects: Annotations; Apiaceae; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Cell Biology; Chloroplasts; Comparative analysis; Genera; Genes; Genetics; Genomes; Inverted repeat; Life Sciences; Medicinal plants; Minority & ethnic groups; Next-generation sequencing; Nucleotide sequence; Phylogenetics; Phylogeny; Plant Physiology; Plant Sciences; Population genetics; Research Article; rRNA; Sequence analysis; Species; Comparative analysis; Apiaceae; Chloroplast genome; Phylogenomics; Vicatia thibetica
• ISSN: 0971-5894; 0974-0430
• DOI: 10.1007/s12298-022-01154-y

Vicatia thibetica  de Boiss.: a herb in the family Apiaceae, has been used for over a hundred years as an essential medicinal and edible plant in the Bai ethnic group of Dali City. However, due to the lack of study on plastid genomes of V. thibetica , studies of comparison and phylogeny with other related species remain scarce. In the current study, we assembled, annotated, and characterized the entire chloroplast (cp) genome of V. thibetica through high-throughput sequencing for the first time, compared with published whole chloroplast genomes from the same family. A phylogenetic analysis of the chloroplast genome has also been performed. The whole chloroplast genome of V. thibetica was 145,796 in size and consisted of a large single-copy region (LSC; 92,186 bp), a small single-copy region (SSC; 17,452 bp), and a pair of inverted repeat regions (IRs; 18,079 bp) forming a circular quadripartite structure. Annotation resulted in 128 genes, including 84 protein-coding genes (PCGs), 35 transfer RNA genes (tRNAs), eight ribosomal genes (rRNAs), and one pseudogene. Repeat sequence analysis displayed V. thibetica plastid genome contains 75 simple repeats, 37 long repeats, and 29 tandem repeats. Compared with the cp genome of other Apiaceae species, a common feature was that the IR regions of the genome were more conservative compared to the LSC and SSC regions. Highly variable hotspots included rps16 , ndhC-trnV-UAC , clpP , ycf1 , and ndhB in the genomes, which supply valuable molecular markers for phylogeny, identification, and classification in the Apiaceae family. The results of phylogenetic analysis strongly supported the genus Vicatia as an independent genus in the family Apiaceae, in which the closest affinities to the related species of Angelica , Peucedanum , and Ligusticum were observed. In conclusion, the first chloroplast genome of Vicatia reported in this study may  improve our understanding of phylogenetic relationship of different genera of Apiaceae. In addition, the current data will be valuable as chloroplast genomic resource for species identification and population genetics.