Dataset Information

The complete chloroplast genome sequence of three medicinal species; Curcuma longa, Curcuma wenyujin, and Curcuma phaeocaulis (Zingiberaceae).

ABSTRACT: Curcuma longa, C. wenyujin and C. phaeocaulis are important herbal medicine which of rhizomatous herbaceous perennial plant of the family Zingiberaceae. This study generated a complete chloroplast genome sequence of three medicinal species were characterized by de novo assembly with whole genome sequencing data. The length of complete chloroplast genome were 162,180 bp (C. longa), 162,266 bp (C. wenyujin), and 162,133 bp (C. phaeocaulis), respectively, with four structures that were included in large single copy region (87,001 bp, 87,042 bp, and 87,013 bp), small single copy region (15,681 bp, 15,710 bp, and 15,622 bp), and duplicated inverted regions (29,749 bp, 29,757 bp and 29,749 bp of each). Based on phylogenetic trees, C. longa, C. wenyujin, and C. phaeocaulis were grouped by high bootstrap value with Curcuma species. This result approved that C. longa, C. wenyujin and C. phaeocaulis were comprised in Alpinia and Wurfbainia. Therefore, this chloroplast genome data firstly generated valuable genetic resource in discrimination of herbal materials, phylogeny and development DNA marker.

SUBMITTER: Kim MK

PROVIDER: S-EPMC8043548 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of three medicinal species; Curcuma longa, Curcuma wenyujin, and Curcuma phaeocaulis (Zingiberaceae).

Kim Min-Kyeoung MK Lee Woo Kyu WK Choi Yoo Rae YR Kim Jonghwan J Kang Ilhyun I Kang Juhye J

Mitochondrial DNA. Part B, Resources 20210408 4

Curcuma longa, C. wenyujin and C. phaeocaulis are important herbal medicine which of rhizomatous herbaceous perennial plant of the family Zingiberaceae. This study generated a complete chloroplast genome sequence of three medicinal species were characterized by de novo assembly with whole genome sequencing data. The length of complete chloroplast genome were 162,180 bp (C. longa), 162,266 bp (C. wenyujin), and 162,133 bp (C. phaeocaulis), respectively, with fou ...[more]

PMID: 33889750

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Project description:Alpinia katsumadai (A. katsumadai), Alpinia oxyphylla (A. oxyphylla) and Alpinia pumila (A. pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and phylogenetic analysis. Here, we sequenced three complete chloroplast genomes of A. katsumadai, A. oxyphylla sampled from Guangdong and A. pumila, and analyzed the published chloroplast genomes of Alpinia zerumbet (A. zerumbet) and A. oxyphylla sampled from Hainan to retrieve useful chloroplast molecular resources for Alpinia. The five Alpinia chloroplast genomes possessed typical quadripartite structures comprising of a large single copy (LSC, 87,248-87,667 bp), a small single copy (SSC, 15,306-18,295 bp) and a pair of inverted repeats (IR, 26,917-29,707 bp). They had similar gene contents, gene orders and GC contents, but were slightly different in the numbers of small sequence repeats (SSRs) and long repeats. Interestingly, fifteen highly divergent regions (rpl36, ycf1, rps15, rpl22, infA, psbT-psbN, accD-psaI, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, rps11-rpl36, infA-rps8, psbC-psbZ, and rpl32-ccsA), which could be suitable for species identification and phylogenetic studies, were detected in the Alpinia chloroplast genomes. Comparative analyses among the five chloroplast genomes indicated that 1891 mutational events, including 304 single nucleotide polymorphisms (SNPs) and 118 insertion/deletions (indels) between A. pumila and A. katsumadai, 367 SNPs and 122 indels between A. pumila and A. oxyphylla sampled from Guangdong, 331 SNPs and 115 indels between A. pumila and A. zerumbet, 371 SNPs and 120 indels between A. pumila and A. oxyphylla sampled from Hainan, and 20 SNPs and 23 indels between the two accessions of A. oxyphylla, were accurately located. Additionally, phylogenetic relationships based on SNP matrix among 28 whole chloroplast genomes showed that Alpinia was a sister branch to Amomum in the family Zingiberaceae, and that the five Alpinia accessions were divided into three groups, one including A. pumila, another including A. zerumbet and A. katsumadai, and the other including two accessions of A. oxyphylla. In conclusion, the complete chloroplast genomes of the three medicinal Alpinia species in this study provided valuable genomic resources for further phylogeny and species identification in the family Zingiberaceae.

Dataset Information

The complete chloroplast genome sequence of three medicinal species; Curcuma longa, Curcuma wenyujin, and Curcuma phaeocaulis (Zingiberaceae).

Publications

The complete chloroplast genome sequence of three medicinal species; <i>Curcuma longa, Curcuma wenyujin,</i> and <i>Curcuma phaeocaulis</i> (Zingiberaceae).

Similar Datasets

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