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).
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.