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The complete chloroplast genome sequence of Amomum villosum Lour.

ABSTRACT: Amomum villosum Lour. (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. villosum was determined using Illumina sequencing platform. The size of whole cp genome was 164,069 bp, containing a small single copy (SSC) region of 15,353 bp and a large single copy (LSC) region of 88,798 bp, which were separated by a pair of inverted repeat (IRs) regions (29,959 bp). The A. villosum cp genome contained 133 genes, including eight ribosomal RNA genes (4 rRNA species), 38 transfer RNA genes (30 tRNA species) and 87 protein-coding genes (79 PCG species). The overall GC content of A. villosum cp genome is 36.05%. To investigate the evolution status of A. villosum, as well as Zingiberales, a phylogenetic tree with A. villosum and other 21 species was constructed based on their complete chloroplast genomes. Phylogenetic analysis revealed that A. villosum was closely related to Amomum krervanh.

SUBMITTER: Ma M

PROVIDER: S-EPMC7748462 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of Amomum villosum Lour.

Ma Mengli M Lu Bingyue B

Mitochondrial DNA. Part B, Resources 20200203 1

Amomum villosum Lour. (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. villosum was determined using Illumina sequencing platform. The size of whole cp genome was 164,069 bp, containing a small single copy (SSC) region of 15,353 bp and a large single copy (LSC) region of 88,798 bp, which were separated by a pair of inverted repeat (IRs) regions (29,959 bp). The A. villosum cp genome contained 133 genes, including eight rib ...[more]

PMID: 33366865

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Project description:BackgroundGenuine Chinese medicine is produced from medicinal plant cultivated in a specific region and is of better quality and efficacy, more consistently qualified and famous than that from the same medicinal plant cultivated in other regions. The cultivating region of genuine medicinal plant is known as the genuine producing area. Yangchun City, which is in Guangdong Province of China, is a genuine producing area for the famous Chinese medicine Amomi Fructus (also called Sharen). Amomi Fructus is the ripe and dry fruit of the Zingiberaceae plant A. villosum Lour.. A. villosum was introduced from the Persian Gulf region and has been cultivated in China for over 1000 years. Until now there are no reports on screening for good germplasm of A. villosum.MethodsThe contents of volatile oil and bornyl acetate of Amomi Fructus from 14 populations were determined with GC method, and the relative contents of the main chemical components in the volatile oils were determined with GC-MS method. Evaluation and variance analysis of the comprehensive quality of the 14 samples were conducted by means of a multi-indicator entropy-weight TOPSIS model (Technique for Order Preference by Similarity to an Ideal Solution) combined with OPLS-DA (Orthogonal Partial Least Squares Discrimination Analysis) and HCA (Hierarchical Clustering Analysis). The ISSR (Inter-Simple Sequence Repeat) molecular marker technique and the UPGMA (unweighted pair-group method with arithmetic means) were employed to analyze the genetic relationship among A. villosum populations.ResultsThe contents of volatile oil and bornyl acetate differed significantly among the different populations, but the main chemical component in the volatile oil was the same in all the samples, which was bornyl acetate. OPLS-DA results showed that 9 indicators were the main factors influencing the quality differences among the 14 populations. The entropy-weight TOPSIS results showed that there were significant differences in the comprehensive qualities of the 12 populations from the genuine producing area. The best quality of fruit was found in the genuine producing area of Chunwan Town; the qualities of 33% of genuine fruits were lower than that of non-genuine fruits. Twenty-three DNA fragments were obtained by ISSR-PCR amplification using four ISSR primers, eleven of which were polymorphic loci, which accounted for 47.8%. The similarity coefficients (GS) of different populations of A. villosum ranged from 0.6087 to 0.9565.ConclusionThere are significant differences among different populations of A. villosum in terms of the kinds of major chemical components and their contents, comprehensive quality and genetic diversity. The germplasm resources of A. villosum are rich in the genuine producing area. It means superior germplasm could be selected in the area. The comprehensive quality of the fruit of A. villosum from the non-genuine producing area is better than some of that from genuine producing area, proving that the non-genuine producing area can also produce Amomi Fructus with excellent quality.

Dataset Information

The complete chloroplast genome sequence of Amomum villosum Lour.

Publications

The complete chloroplast genome sequence of <i>Amomum villosum</i> Lour.

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