Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification

Abstract

Background Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis. Results Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined. Conclusion The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.

Comparative chloroplast genomes provided insights into the evolution and species identification on the Datureae plants

“…Thus, a ratio of Ka/Ks < 1 indicates purifying selection, Ka/Ks > 1 denotes probable positive selection, and Ka/Ks values close to one indicate neutral evolution. In this study, the majority of the protein-coding genes of Datureae species were found to be under purifying selection by Ka/Ks analysis, which was conservative in plastid genomes of most angiosperms ( Gong et al., 2022 ). However, we found that 31 cp genes might be under positive selection during the evolution process; these genes are connected to proteins from ATP subunit, photosystem subunit, ribosome large subunit, NAD(P)H dehydrogenase complex, and other genes such as clp P, pet B, rbc L, rpo C1, ycf 4, and cem A.…”

Deciphering the Plastome and Molecular Identity of Six Medicinal Amomum Species

“…Previous studies have indicated that the single plastome fragment is not suitable for the identification of several medicinal plants within the genus Amomum [55,61,63,[73][74][75][76]. The complete plastomes have demonstrated a strong capability to differentiate species of Amomum [55].…”

“…Additionally, the matK gene and the psbA-trnH intergenic spacer exhibit high identification efficiency for A. tsao-ko and other Amomum species [57]. Among them, the barcodes that are more effective for molecular identification of Amomum are ITS [57][58][59], ITS1 [60,61], and ITS2 [61][62][63]. These research findings demonstrate the promising potential application of DNA barcoding technology in species identification and classification within Amomum.…”

Standardization of Euphorbia tithymaloides (L.) Poit. (Root) by Conventional and DNA Barcoding Methods

“…Some other aspects that are included in QC are physical examination, microscopical examination, chemical examination, microbiological examination, stability testing, toxicological examination, and a combination of the aforementioned techniques. 9 Despite these advances, adulteration and substitutions persist in the current period. These conventional pharmacognostic studies and techniques, even the use of modern hyphenated analytical systems, also failed to detect adulterants and substitutions.…”

“…On the other hand, molecular biology has had a significant impact on plant science research, allowing us to uncover many previously unknown genetic and behavioral traits in plants. These genetic traits are very helpful in identifying plants of particular species in cases of adulteration and substitution. , There are several techniques available, including conventional sequencing, non-Sanger sequencing, random amplifiable polymorphic DNA, DNA barcoding, amplifiable fragment length polymorphism, microsatellites, single nucleotide polymorphism, and others. The limitation with a few of these methods is that no ideal marker exists for all the species, and sometimes, it may mislead in identifying the taxonomy but could be highly beneficial in population genetics .…”