The complete chloroplast genome of Aconitum chiisanense Nakai (Ranunculaceae)

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. PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3360v1 | CC BY 4.0 Open Access | rec: 21 Oct 2017, publ: 21 Oct 2017 1 A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional 2 herbal medicinal genus 3 4 Abstract 25 The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the 26 earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. 27 subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences 28 were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. 29 Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship 30 and provide molecular information for utilization of Aconitum species particularly in Eastern 31 Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 32 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes 33 with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural 34 variation was detected in the LSC/IR/SSC boundaries. Five ps...

Complete chloroplast genome of medicinal plant Aconitum carmichaelii: genome characterization and phylogenetic analysis

“…The complete chloroplast genome of A. carmichaelii was 154,776 bp in size (GenBank accession number KY006977) with 38.1% overall GC content. The genome structure was highly similar to the reported chloroplast genome of closely related species A. chiisanense (Lim et al 2015), and contained 83 proteincoding genes, 35 tRNA genes, and 8 rRNA genes. The chloroplast genome was composed of a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions of 86,330bp, 15,986 bp and 26,193 bp, respectively.…”

“…Thirtythree genes (14 tRNA, 8 rRNA, and 11 protein-coding genes) were duplicated in two inverted repeat regions. As in the chloroplast genomes of other Ranunculaceae species reported (Lim et al 2015;Park et al 2015), the rpl32 gene was lost in A. carmichaelii.…”

The complete chloroplast genome of Aconitum austrokoreense Koidz. (Ranunculaceae), an endangered endemic species in Korea

“…A total of 22 genes (8 tRNA and 14 protein-coding genes) contained one or two introns. The maximum likelihood tree constructed using 79 non-redundant protein-coding genes in cpDNAs from 12 Ranunculaceae species and two outgroup species indicated that the cp genome of A. austrokoreense is closely related to the cp DNA of A. chiisanense that we reported recently (Lim et al 2015; Figure 1). Furthermore, sequence comparison identified several distinct sequence variations in proteincoding genes of Aconitum species.…”

Untitled

“…Lycoctonum as well as 10 species from the subg. Aconitum (Choi et al, 2016;Kim et al, unpublished;Lim et al, 2017;Yang, unpublished;Yang et al, unpublished) (Table 1). Altogether, 14 species and 2 varieties in both subgenera of Aconitum were used for annotation (Table 1).…”

“…hispidum, and A. barbatum var. puberulum were collected from China (Chen et al, 2015), A. reclinatum came from the United States (Kong et al, 2017a), while the remaining species were all sampled from Korea (Choi et al, 2016;Kim et al, unpublished;Lim et al, 2017;Yang, unpublished;Yang et al, unpublished). Chloroplast genome sequences of Aconitum species from Europe were not available in GenBank.…”