Comprehensive plastid phylogenomics reveal the phylogeny of <i>Amomum</i> s.l. (Zingiberaceae) from Peninsular Malaysia

The Zingiberaceae family represents one of the most diverse monocot lineages in tropical Asia; however, the species delimitation of <i>Amomum</i> s.l. remains challenging due to morphological convergence and limited molecular evidence. This study analyzed transcriptomic data from seven <i>Amomum</i> s.l. species in Peninsular Malaysia to evaluate their evolutionary relationships and examine variation across chloroplast genes. RNA sequencing and <i>de novo</i> assembly identified 85 chloroplast protein-coding genes, of which 43 complete genes were retained for subsequent analyses. Comparative assessment revealed conserved genome features, including GC content ranging between 37.4% and 38.0%, alongside lineage-specific divergence in codon usage bias and expression profiles. Heatmap clustering of normalized gene expression patterns indicated distinct transcriptional signatures, particularly in <i>A. elan</i>, suggesting species-specific regulatory divergence. Nucleotide diversity (<i>π</i>) analysis identified hotspots in <i>ndhJ</i>, <i>psbT</i>, <i>psbZ</i>, and <i>rps14</i>, highlighting their potential as molecular markers for improving species delimitation, whereas core genes such as <i>rbcL</i> and <i>psbA</i> remained highly conserved, reducing their effectiveness in distinguishing species-level variation. Phylogenetic reconstruction using Bayesian inference (BI) and maximum likelihood (ML) approaches, based on 43 concatenated chloroplast genes (28,794 bp), supported the paraphyly of <i>Amomum</i> s.l., with Peninsular Malaysian species distributed across multiple clades. <i>Amomum trilobum</i> showed a closer association with <i>Wurfbainia</i> than with <i>Amomum</i>-<i>Alpinia</i>, suggesting the possible transfer of the species to <i>Wurfbainia</i> with further taxonomic evaluation. These findings highlight the important roles of genomic and morphological datasets in understanding the evolutionary relationships in <i>Amomum</i> s.l. and offer new molecular insights into the evolution of Zingiberaceae in Peninsular Malaysia.