Abstract
Aconitum pseudolaeve Nakai and Aconitum longecassidatum Nakai, which belong to the Aconitum subgenus Lycoctonum, are distributed in East Asia and Korea. Aconitum species are used in herbal medicine and contain highly toxic components, including aconitine. A. pseudolaeve, an endemic species of Korea, is a commercially valuable material that has been used in the manufacture of cosmetics and perfumes. Although Aconitum species are important plant resources, they have not been extensively studied, and genomic information is limited. Within the subgenus Lycoctonum, which includes A. pseudolaeve and A. longecassidatum, a complete chloroplast (CP) genome is available for only one species, Aconitum barbatum Patrin ex Pers. Therefore, we sequenced the complete CP genomes of two Aconitum species, A. pseudolaeve and A. longecassidatum, which are 155,628 and 155,524 bp in length, respectively. Both genomes have a quadripartite structure consisting of a pair of inverted repeated regions (51,854 and 52,108 bp, respectively) separated by large single-copy (86,683 and 86,466 bp) and small single-copy (17,091 and 16,950 bp) regions similar to those in other Aconitum CP genomes. Both CP genomes consist of 112 unique genes, 78 protein-coding genes, 4 ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes. We identified 268 and 277 simple sequence repeats (SSRs) in A. pseudolaeve and A. longecassidatum, respectively. We also identified potential 36 species-specific SSRs, 53 indels, and 62 single-nucleotide polymorphisms (SNPs) between the two CP genomes. Furthermore, a comparison of the three Aconitum CP genomes from the subgenus Lycoctonum revealed highly divergent regions, including trnK-trnQ, ycf1-ndhF, and ycf4-cemA. Based on this finding, we developed indel markers using indel sequences in trnK-trnQ and ycf1-ndhF. A. pseudolaeve, A. longecassidatum, and A. barbatum could be clearly distinguished using the novel indel markers AcoTT (Aconitum trnK-trnQ) and AcoYN (Aconitum ycf1-ndhF). These two new complete CP genomes provide useful genomic information for species identification and evolutionary studies of the Aconitum subgenus Lycoctonum.
Highlights
Chloroplasts (CPs) play important functional roles in photosynthesis, biosynthesis, and metabolism of starch and fatty acids throughout the plant life cycle [1]
The angiosperm CP genome is a circular molecule with a quadripartite structure consisting of large single-copy (LSC) and small single-copy (SSC) regions and two copies of an inverted repeat (IR) region
Seven and six initial CP contigs of A. pseudolaeve and A. longecassidatum, respectively, were de novo assembled from low-coverage whole-genome sequence
Summary
Chloroplasts (CPs) play important functional roles in photosynthesis, biosynthesis, and metabolism of starch and fatty acids throughout the plant life cycle [1]. The CP genome is more highly conserved than the nuclear genome, it frequently contains insertions/deletions (indels) and single-nucleotide polymorphisms (SNPs) [9,10] These variations have been used to estimate divergence times among evolutionarily-related species [11,12,13]. Several studies report the use of indels and SNP mutations from complete CP genomes for species identification in Panax ginseng, buckwheat, Aconitum, and other genera [7,14,15]. Indel and SNP mutations provide useful information for identification of species, phylogenic tree analysis, and population studies Such markers can overcome the limits of universal DNA barcodes. Of A. pseudolaeve, A. longecassidatum, and A. barbatum Patrin ex Pers., we developed indel markers to distinguish three species of the subgenus Lycoctonum based on divergent regions of the CP genome. Lycoctonum, and will inform genomic resources for evolutionary studies of these plants
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