Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes

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.

Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria

“…Only seven hypervariable intergenic regions were selected as potential specific DNA barcode based on comparison of four Fritillaria cp genomes. Similar results existed in other studies [ 58 – 64 ], except that the number of highly variable regions was different. Unfortunately, none of the above regions have been verified by further experiments.…”

“…In order to find ideal molecular markers in Fritillaria , many studies tried to select highly variable regions based on cp genomes as genus-specific DNA barcodes for species identification [ 56 – 64 ]. Li et al [ 56 ] found eight genes which had abundant variations among species by comparing four Fritillaria cp genomes.…”

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

“…The extent and types of genetic polymorphisms in different regions of the cp genome vary. In most plants, the single copy regions (LSC and SSC regions) of the cp genome are more variable than that are the IR regions [ 16 , 41 , 42 ]. In our study, nucleotide diversity, as quantified by Pi values across the six Desmodieae cp genomes, for SSC and LSC was 0.02752 and 0.02146, respectively, both of which were significantly higher than the Pi value for the IR regions (0.00374).…”

“…In contrast with nuclear genomes, cp genomes in Fabaceae are uniparentally inherited and largely conserved in gene content, organization, and structure [ 13 , 14 ]. Due to its stable uniparental inheritance, the cp genome can be of great value for discriminating between closely related species and understanding their evolutionary relationships [ 15 , 16 , 17 ]. With the development of next-generation sequencing (NGS), complete plastome sequencing has increased dramatically.…”

Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences

“…Cp genomes are haploid, and most of them are maternally inherited. High conservation of gene content and genome structure makes cp genome an important resource for reconstructing the phylogenetic relationships among plant groups [13][14][15][16][17][18][19][20], which may suggest that the cp genome could be better to solve the relationships between species [21][22][23]. Additionally, the cp genome encodes many chloroplast-specific components, like photosynthesis genes, which play fundamental roles in the life of plant [24][25][26].…”