Abstract
Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.
Highlights
Fritillaria L. is one of the most important genera in Liliaceae, which includes approximately 140 species of perennial herbaceous plants (Day et al, 2014; Teksen, Aytac & Pınar, 2010)
Nucleotide sequences of the eight Fritillaria chloroplast genomes ranged from 151,083 bp in F. unibracteata to 152,064 bp in F. sinica and shared the typical quadripartite structure, composed of a pair of inverted repeats (IRs) (26,090-26,364 bp) separated by the large single copy region (LSC) (81,339-81,827 bp) and ptrsnbZG-UCC
Variable loci and divergent regions were identified as possible ways to develop genetic markers which could be used for further study on population genetics
Summary
Fritillaria L. is one of the most important genera in Liliaceae, which includes approximately 140 species of perennial herbaceous plants (Day et al, 2014; Teksen, Aytac & Pınar, 2010). F. cirrhosa is one of the major original plants of Fritillariae Cirrhosae bulbus, a famous traditional Chinese medicine, which is used to relieve cough and eliminate phlegm (National Pharmacopoeia Committee, 2015) It is mainly found in areas of high altitude in the southwest of China and grows in moist environments near bushes, meadows, and other similar habitats (Chen & Helen, 2000). Luo & Chen (1996) had proposed the concept of a ‘‘complex group of F. cirrhosa’’ which was composed of four species, namely F. cirrhosa, F. sichuanica, F. taipaiensis and F. yuzhongensis, based on uncertain morphological characteristics and geographical distributions They pointed out that F. sichuanica was possibly a hybrid among F. cirrhosa, F. przewalskii and F. unibracteata. This posits the question of whether the theory is reasonable and what would be the phylogenetic relationships of the species in the so-called ‘‘complex group of F. cirrhosa’’ and their close relatives
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