Chloroplast genome of the critically endangered ginger Zingiber odoriferum Blume from Java, Indonesia: Characterization, comparison, and conservation insights

Zingiber odoriferum (Zingiberaceae), a critically endangered ginger species endemic to Java, Indonesia, is ecologically vital yet genomically understudied. We present the first complete chloroplast (cp) genome (163,538 bp), revealing a quadripartite structure with a large single-copy region (88,033 bp), a small single-copy region (15,885 bp), and a pair of inverted repeat regions (29,810 bp each), with a total GC content of 36.04%. The genome encodes 133 genes, including protein-coding genes, tRNA genes, rRNA genes, and pseudogenized ycf1 – a conserved Zingiberaceae feature. Leucine (10.33%) and cysteine (1.14%) are the most and least abundant amino acids, respectively. Codon usage favors A/T-rich codons (e.g., AGA [Arg], TTA [Leu]), while C/G-ending codons (e.g., AGC [Ser]) are underutilized. Hypervariable loci in non-coding regions and repeats are identified as molecular markers. Phylogenetic analysis places Z. odoriferum sister to Z. teres and Z. smilesianum (100% bootstrap support)...., , # Chloroplast genome of the critically endangered ginger Zingiber odoriferum Blume from Java, Indonesia: Characterization, comparison, and conservation insights

Dataset DOI: [10.5061/dryad.pk0p2nh23](10.5061/dryad.pk0p2nh23)

## Description of the data and file structure

Data source: Fresh leaf samples of Zingiber odoriferum were collected from Bogor Botanic Gardens, Indonesia. Total genomic DNA was extracted using the CTAB method and sequenced on an Illumina platform. The chloroplast genome was assembled de novo to generate a FASTA file of Zingiber odoriferum.

Data description: This dataset contains the FASTA file of the complete chloroplast genome sequence

The total length of the chloroplast genome is 163,538 bp with a typical quadripartite structure: a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeats (IRa and IRb). A total of 133 unique genes were annotated, including protein-coding genes, tRNAs, and rRNAs.

### Files and variables

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印度尼西亚爪哇岛特有、处于极危状态的姜科（Zingiberaceae）香姜（Zingiber odoriferum）在生态系统中具有重要价值，但目前其基因组学相关研究仍较为匮乏。本研究首次报道了该物种的完整叶绿体（cp）基因组，全长163538 bp，其结构为典型的四分体结构：包含一个大单拷贝区（88033 bp）、一个小单拷贝区（15885 bp）以及一对反向重复区（每个长度为29810 bp），总GC含量为36.04%。该基因组共编码133个基因，包括蛋白编码基因、转运RNA（tRNA）基因、核糖体RNA（rRNA）基因，以及假基因化的ycf1——这是姜科的一个保守特征。亮氨酸（10.33%）和半胱氨酸（1.14%）分别为丰度最高和最低的氨基酸。密码子使用偏好A/T富集型密码子（如AGA[精氨酸（Arg）]、TTA[亮氨酸（Leu）]），而以C/G结尾的密码子（如AGC[丝氨酸（Ser）]）则使用不足。非编码区与重复序列中的高变位点可作为分子标记。系统发育分析显示，香姜与Z. teres及Z. smilesianum互为姐妹群（自举支持率100%）。
# 来自印度尼西亚爪哇岛的极危姜科物种香姜（Zingiber odoriferum Blume）的叶绿体基因组：特征解析、比较分析与保护启示

数据集DOI：[10.5061/dryad.pk0p2nh23](10.5061/dryad.pk0p2nh23)

## 数据与文件结构说明

数据来源：研究样本采自印度尼西亚茂物植物园的香姜新鲜叶片。采用CTAB（十六烷基三甲基溴化铵）法提取总基因组DNA，并在Illumina测序平台完成测序。通过从头组装得到香姜叶绿体基因组的FASTA格式文件。

数据说明：本数据集包含完整叶绿体基因组序列的FASTA格式文件。

该叶绿体基因组全长163538 bp，具有典型的四分体结构：大单拷贝（LSC）区、小单拷贝（SSC）区以及两个反向重复区（IRa和IRb）。共注释得到133个独特基因，包括蛋白编码基因、转运RNA（tRNA）以及核糖体RNA（rRNA）。

### 文件与变量

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