DOI: 10.5061/dryad.pk0p2nh23
title: Chloroplast genome of the critically endangered ginger Zingiber odoriferum Blume from Java, Indonesia: Characterization, comparison, and conservation insights

description: 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).
 Despite high genome-wide conservation, intergenic spacers exhibit 5–12%
 divergence, aiding species delineation. However, the limited cp diversity
 across Zingiber underscores the need for nuclear genomic integration to
 resolve cryptic diversity and enhance conservation strategies. This study
 advances genomic resources for Z. odoriferum, highlights cp genome
 evolutionary constraints, and provides actionable markers for biodiversity
 monitoring. It emphasizes the urgency of multi-omics approaches to
 safeguard this species and its threatened tropical habitat.
description: # 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 #### File:
 Zingodor_cpGenome_fasta.fasta **Description:** This FASTA file contains
 the complete chloroplast genome sequence of Zingiber odoriferum (family
 Zingiberaceae). The genome was de novo assembled from Illumina paired-end
 sequencing data. The assembled plastome has a typical quadripartite
 structure composed of a large single-copy (LSC) region, a small
 single-copy (SSC) region, and a pair of inverted repeats (IRs). The
 sequence is circular and provided as a single continuous entry in standard
 FASTA format with nucleotide bases (A, T, C, G). ## Access information
 Other publicly accessible locations of the data: Both the nucleotide
 sequence data and the associated SRA data have been submitted to NCBI and
 are currently awaiting release.