Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics

Tian Zhang; Sipei Huang; Simin Song; Meng Zou; Tiechui Yang; Weiwei Wang; Jiayu Zhou; Hai Liao

doi:10.7717/peerj.12612

Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics

PeerJ. 2021 Dec 16:9:e12612. doi: 10.7717/peerj.12612. eCollection 2021.

Authors

Tian Zhang¹, Sipei Huang¹, Simin Song¹, Meng Zou¹, Tiechui Yang², Weiwei Wang¹, Jiayu Zhou¹, Hai Liao¹

Affiliations

¹ School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China.
² Qinghai lvkang Biological Development Co., Ltd, Xining, Qinghai, China.

Abstract

The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.

Keywords: Chloroplast genomic; DNA markers; Fritillaria; Phylogenetic analysis; Species-specific identification.

Associated data

figshare/10.6084/m9.figshare.14531937

Grants and funding

This work was co-supported by the National Natural Science Foundation of China (No. 31500276), the Sichuan Science and Technology Program (No. 2018SZ0061 and 2021ZHFP0170), the Sichuan Administration of TCM program (No. 2021MS116), and the Fundamental Research Funds for the Central Universities (No. 2682021ZTPY017). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.