Comparison and Phylogenetic Analysis of Chloroplast Genomes of Three Medicinal and Edible Amomum Species

Abstract

Amomum villosum is an important medicinal and edible plant with several pharmacologically active volatile oils. However, identifying A. villosum from A. villosum var. xanthioides and A. longiligulare which exhibit similar morphological characteristics to A. villosum, is difficult. The main goal of this study, therefore, is to mine genetic resources and improve molecular methods that could be used to distinguish these species. A total of eight complete chloroplasts (cp) genomes of these Amomum species which were collected from the main producing areas in China were determined to be 163,608–164,069 bp in size. All genomes displayed a typical quadripartite structure with a pair of inverted repeat (IR) regions (29,820–29,959 bp) that separated a large single copy (LSC) region (88,680–88,857 bp) from a small single copy (SSC) region (15,288–15,369 bp). Each genome encodes 113 different genes with 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. More than 150 SSRs were identified in the entire cp genomes of these three species. The Sanger sequencing results based on 32 Amomum samples indicated that five highly divergent regions screened from cp genomes could not be used to distinguish Amomum species. Phylogenetic analysis showed that the cp genomes could not only accurately identify Amomum species, but also provide a solid foundation for the establishment of phylogenetic relationships of Amomum species. The availability of cp genome resources and the comparative analysis is beneficial for species authentication and phylogenetic analysis in Amomum.

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…The most abundant were mononucleotide repeats, located in non-coding regions, and contributed to AT richness ( Figure 3). These results are consistent with most reported angiosperms [23][24][25][26][28][29][30]. The total number of SSRs was 237 in A. katsumadai, 244 in A. oxyphylla sampled from Guangdong, 247 in A. pumila, 236 in A. zerumbet, and 241 in A. oxyphylla sampled from Hainan ( Figure 3A).…”

“…Additionally, the AT content was the highest (70.18-70.38%) in the SSC region, the lowest (50.48%-50.79%) in the IR regions, and moderate (66.14%-66.18%) in the LSC region (Table S1). These genomic structures were consistent with most other published chloroplast genomes of family Zingiberaceae, such as two Kaempferia species [23], three Amomum species [24], Zingiber officinale [25], Stahlianthus involucratus [31], Hedychium coronarium [32] and Curcuma longa [33].…”

“…The complete chloroplast genome of A. oxyphylla sampled from Guangdong was 59 bp longer than that of A. oxyphylla sampled from Hainan ( Table 1). The lengths of the IR regions of the five chloroplast genomes, ranging from 26,917 to 29,707 bp (Table 1), were shorter than those of the three species of Amomum, which varied from 29,820 to 29,959 bp [24]. In addition, 86 protein-coding genes were identified in the A. zerumbet chloroplast genome, and 87 were identified in the other four accessions.…”

“…Typical chloroplast genomes of angiosperms have a generally conserved quadripartite circular structure, which consists of a large single copy (LSC) region, a small single copy (SSC) region, and two copies of inverted repeats (IRs) [16][17][18]. With the rapid development of high-throughput sequencing technologies, such as Illumina and PacBio sequencing platforms, it is now convenient to acquire complete chloroplast genome sequences [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. The chloroplast genomes have been widely utilized for species identification, the reconstruction of phylogenetic relationships, the resolution of origin problems, and the development of molecular markers [19][20][21][22][23][24][25][26][27][28][29][30].…”

Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses

“…Comparative plastome studies provide the opportunity to explore sequence variation and the molecular evolutionary patterns associated with genome rearrangements (e.g., Knox, 2014;Weng et al, 2014;Rabah et al, 2019;Shrestha et al, 2019) as well as gene loss, duplication, and transfer events (e.g., Downie and Jansen, 2015;Wu and Chaw, 2016;Sun et al, 2017), while also detecting signatures of positive selection in plastid genes facilitating our understanding of plants adapting to extreme environments (e.g., alpine areas) (Bock et al, 2014;Jiang et al, 2018;Liu et al, 2018). Highly divergent regions and simple sequence repeats (SSRs) obtained from whole plastome sequence hold promise as efficient molecular markers implemented in species delimitation and population genetics Cui et al, 2019). Use of these markers as DNA barcodes for herbal medicine is promising for the authentication and identification of specimens for quality assurance (Sgamma et al, 2017;Wang et al, 2017;Kreuzer et al, 2019).…”