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Background <p><i>Amomum cinnamomeum</i> Škorničk., Luu &amp; H.Ð.Trần was first identified as an endemic species of Vietnam in 2019. It has a cinnamon-like odor. Over the years, the phytochemical and phylogenetic relationships of <i>A. cinnamomeum</i> have been investigated; however, its genomic features remain uncharacterized.</p> Methods and results <p>In this study, we employed the Illumina platform and bioinformatic tools to sequence the complete chloroplast genome of <i>A. cinnamomeum</i>, which is 163,763&#xa0;bp in length and exhibits a circular quadripartite structure. This structure includes a large single-copy region of 88,612&#xa0;bp, a small single-copy region of 15,519&#xa0;bp, and two inverted repeat regions of 29,816&#xa0;bp each. Comparative genomic analysis revealed a conserved pattern in this chloroplast genome as regards its gene content and order, comprising 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, the following three hypervariable regions were identified in this chloroplast genome: <i>atpF</i>-<i>atpI</i>, <i>rpoB</i>-<i>psbM</i>, and <i>ycf1</i>. Additionally, phylogenetic analysis revealed a close relationship among <i>A. cinnamomeum</i>,<i> Amomum maximum</i>, and <i>Amomum longipetiolatum.</i></p> Conclusions <p>This study successfully sequenced and characterized the chloroplast genome of <i>A. cinnamomeum</i>. Its findings provide an initial comparative chloroplast genomic analysis of accepted <i>Amomum</i> species. This analysis will be useful for further research concerning the evolutionary history, development of molecular markers, and population genetics of <i>Amomum</i> and related <i>Zingiberaceae</i> species.</p>

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The complete chloroplast genome of Amomum cinnamomeum (Zingiberaceae)

  • 期刊论文

  • 发表日期：

    2026年5月30日

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  • Nhat Nam Nguyen,
  • Hoang Dang Khoa Do

摘要

Background

Amomum cinnamomeum Škorničk., Luu & H.Ð.Trần was first identified as an endemic species of Vietnam in 2019. It has a cinnamon-like odor. Over the years, the phytochemical and phylogenetic relationships of A. cinnamomeum have been investigated; however, its genomic features remain uncharacterized.

Methods and results

In this study, we employed the Illumina platform and bioinformatic tools to sequence the complete chloroplast genome of A. cinnamomeum, which is 163,763 bp in length and exhibits a circular quadripartite structure. This structure includes a large single-copy region of 88,612 bp, a small single-copy region of 15,519 bp, and two inverted repeat regions of 29,816 bp each. Comparative genomic analysis revealed a conserved pattern in this chloroplast genome as regards its gene content and order, comprising 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, the following three hypervariable regions were identified in this chloroplast genome: atpF-atpI, rpoB-psbM, and ycf1. Additionally, phylogenetic analysis revealed a close relationship among A. cinnamomeum, Amomum maximum, and Amomum longipetiolatum.

Conclusions

This study successfully sequenced and characterized the chloroplast genome of A. cinnamomeum. Its findings provide an initial comparative chloroplast genomic analysis of accepted Amomum species. This analysis will be useful for further research concerning the evolutionary history, development of molecular markers, and population genetics of Amomum and related Zingiberaceae species.