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.
Highlights
Amomum villosum Lour., which belongs to the monophyletic Zingiberaceae family, is a valuable medicinal plant in China with a history of more than 1300 years [1]
The high GC content of the inverted repeat (IR) region could be due to the four ribosomal RNA genes with a reduced number of duplicated AT nucleotides [25] and may be one of the important factors that cause the IR region to be more conservative than the large single copy (LSC) and small single copy (SSC) regions [26]
The results showed that trnD-trnY and trnI-ycf2 could not distinguish these eight Amomum species. accD-psaI could differentiate A. villosum, A. villosum var. xanthioides and A. longiligulare from their closely related speciesbut could not distinguish these three species from each other
Summary
Amomum villosum Lour., which belongs to the monophyletic Zingiberaceae family, is a valuable medicinal plant in China with a history of more than 1300 years [1]. Cp genome sequences are known for their highly conserved gene order and content. Cp genomes have been shown to be an efficient tool to reveal phylogenetic relationships [20], identify the related species as a super-barcode [13,14], and develop cp genetic engineering [22]. For the whole plant community, the total number of plants that have determined cp genome sequences is still insufficient. Up to now, approximately 3300 cp genome sequences of plants have been recorded in NCBI, and this proportion is still small. Differences in their essential characteristics and repeat sequences were revealed. Intraspecific and interspecific comparative analyses among the Amomum genus were conducted to discover highly divergent regions for species authentication. A phylogenetic tree was constructed to identify Amomum species and reveal their phylogenetic positions
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