A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus

Abstract

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58–62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

“…A total of 23 substitutions and 6 indels ranging from 1 to 13 bp in length occurs in ΨinfA ( Figure 2 ; Table 2 ). The pseudogenized ΨinfA gene has also been frequently found in other angiosperm chloroplast genomes as well [ 40 , 41 , 42 ]. The pseudogenized ΨaccD gene is present in all species except T. indica and M. cucullatum , with a length of 1473 bp in both C. chuniana and C. canadensis and with length ranging from 1395 to 1500 bp in the other three species.…”

­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)

“…The nucleotide variability found among Brunellia species is also one of the lowest reported. In general, the π values in trees tend to be lower than in herbs; for example, in trees: Machilus (π = 0.00154, Song et al, 2015) and Juglans (π = 0.00219, Hu, Woeste & Zhao, 2017); in herbs: Nicotiana (π = 0.00321, Asaf et al, 2016), Aconitum (π = 0.00549, Kong et al, 2017) and Papaver (π = 0.00895, Zhou et al, 2018). Discrepancies in the rate of molecular substitutions can be explained by variations of generation time, size and habit, the age of the clade, and molecular mechanisms of DNA repair, among others (e.g., Lanfear et al, 2013;Smith & Donoghue, 2008).…”

Comparative Analysis of the Complete Chloroplast Genomes of Four Aconitum Medicinal Species

“…At present, many species are well-known herbs and mainly used for analgesia and anti-inflammatory purposes [ 12 ]. To date, the cp genomes of 17 Aconitum species have been reported [ 13 , 14 ].…”