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

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.

DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes

“…Phylogenomic analysis supported the monophyly of the subgenus Fritillaria. More importantly, 23 species in the subgenus could be divided into four major clades (Clade I, II, III, and IV) with high support values (Figure 4), in accordance with the previous findings based on chloroplast regions and ITS (Day et al, 2014;Huang et al, 2018;Zhang et al, 2021). The four clades possessed obvious geographic structure except the last one (Figures 4, 7).…”

“…Among them, the first clade, distributed in southwest China, was undoubtedly the most complicated group probably due to its recent diversification. This work provided a comprehensive topological structure for the Fritillaria in China although the previous studies have revealed similar results based on limited samples and DNA markers (Park et al, 2017;Bi et al, 2018;Huang et al, 2018;Li et al, 2018;Zhang et al, 2021). Moreover, it is worth noting that of the suspicious species, "F. omeiensis" was not clustered into the same clade with F. crassicaulis, which was treated as a synonym for the latter in Flora of China (2000); similarly, "F. hupehensis" was also far from the F. monantha (Figure 4).…”

“…A series of studies revealed that universal barcodes (matK, rbcL, trnH-psbA, ITS) or plastid region (rpl16) could not afford efficient identification for such a complicated genus (Zhang et al, 2016;Huang et al, 2018;Chen et al, 2020). Until now, complete chloroplast genomes have been adopted to explore phylogeny of Fritillaria species, and showed unambiguous relationships with highly supportive values, especially for the related species (Park et al, 2017;Bi et al, 2018;Li et al, 2018;Chen et al, 2019;Wu et al, 2021;Zhang et al, 2021). But these studies generally only cover minority species with few samples, so they could not represent the species well.…”

Fritillaria cinsinin ve bu cinsin bir üyesi olan Aygül lalesi’nin (Fritillaria eduardii) dünü, bugünü ve yarını

“…Bununla birlikte, Zhang ve diğ [44]. yapmış olduğu araştırmada Fritillaria türlerinde tüm kloroplast (CP) genomlarını belirleyerek elde edilen ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI ve rps19 moleküler markırlarının taksonomik çalışmalarda yararlı olacağını rapor etmişlerdir[44].Zambakgiller ailesine ait Fritillaria cinsinin bir türü olan Aygül lalesinin bilimsel adı "Fritillaria eduardii"-Eduard çiçeğidir.…”

“…Bununla birlikte, Zhang ve diğ [44]. yapmış olduğu araştırmada Fritillaria türlerinde tüm kloroplast (CP) genomlarını belirleyerek elde edilen ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI ve rps19 moleküler markırlarının taksonomik çalışmalarda yararlı olacağını rapor etmişlerdir[44].Zambakgiller ailesine ait Fritillaria cinsinin bir türü olan Aygül lalesinin bilimsel adı "Fritillaria eduardii"-Eduard çiçeğidir. F. eduardii; karbonat içeren topraklarda, nemli, kireç ve taşlı toprağa sahip olan orman bölgelerinde, çalıların arasında, ağaçların altında, bazen çalıların ve ağaçların bulunmadığı açık alanlarda, dağların genelde batı ve kuzey kısımlarında deniz seviyesinden 700-2500 metre yükseklikte Eduard Regel tarafından bahsedilen kokususuz Fritillaria bitkilerinin de F. eduardii'nin biri Fritillaria eduardii var.…”