Abstract
BackgroundAlthough molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species.MethodsWe here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species.ResultsThe cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level.ConclusionsThis study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification.
Highlights
Molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive
The rps12 is a trans-spliced gene in which two 3′ end residues are located within the Inverted repeats regions (IRs) region and the 5′ end is located within the Large single-copy regions (LSC) region
Our results showed that phylogenetic trees constructed by the entire cp genome presented a high discrimination power for the Fritillaria species, and different individuals in each species were resolved as a monophyletic clade
Summary
Molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species. The entire cp genome contains approximately as much information as does the COI gene used in animals and it has the potential to provide distinguishing differences that can help molecularly identify closely related species [7]. With advances in high-throughput sequencing, achieving cp genome is acquirable at a large-scale with lower costs. This has promoted studies of systematics using cp genome in Epimedium [8], Paris [9] and Sanguisorba [10]. Because of the low discrimination power of general molecular markers in plants and their closely related species, researchers have proposed the entire cp genome as a super-barcode to discriminate closely related species [11]
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