Comparative chloroplast genomics reveals codon usage and phylogeny in 16 Amorphophallus species

A comparative chloroplast-genome study of 16 Amorphophallus species has identified structural differences, shared codon-usage preferences, a potential DNA barcoding window and three major phylogenetic clades. The analysis combines chloroplast genomes newly sequenced for six species with data from 10 previously reported species, providing a broad comparative assessment of the genus. It also examined variation in inverted-repeat regions, nucleotide diversity and base-editing patterns across the sampled genomes.

Amorphophallus is an economically and ornamentally important genus in the arum family, Araceae. Traditional identification is challenging because members of the genus show pronounced morphological plasticity, and the timing of leaf and flower emergence can also be separated. The study therefore used chloroplast-genome comparisons to investigate genome structure, codon usage bias and phylogenetic relationships, including the placement of Amorphophallus among other sampled Araceae.

Researchers sequenced, assembled and annotated chloroplast genomes from A. pendulus, A. glaucophyllus, A. fornicatus, A. macrophyllus, A. titanum and A. hewittii using the PacBio Revio platform. When combined with data from 10 additional species, the dataset covered 16 Amorphophallus taxa. Their chloroplast genomes ranged from 152,492 to 185,810 base pairs and displayed the characteristic quadripartite structure, with the study treating differences in genome size, inverted-repeat regions and gene regions as part of the comparative analysis.

Structural variation was detected in the inverted-repeat regions of several genomes. Expansion of this region occurred in A. macrophyllus and A. glaucophyllus, while contraction was found in A. fornicatus. The comparison also identified the chloroplast gene accD as a highly variable region, with a reported nucleotide diversity value of Pi = 0.1217. These results show that the sampled genomes share a broad structural pattern while differing in specific regions relevant to comparative analysis.

The researchers also assessed codon usage across the 16 chloroplast genomes. Codons showed a bias toward sequences ending in A or U rather than G or C, and the analysis identified natural selection as the predominant driving force behind this pattern. Despite variation among species, six codons were classified as optimal in all 16 Amorphophallus species, indicating a common set of preferred codons within the sampled group. The analysis therefore characterized both shared codon-usage features and differences among individual taxa.

Only C-to-U base-editing events were detected in the chloroplast genomes of the 16 species. In other words, the reported editing pattern was directional within this dataset: cytosine-to-uracil changes were observed, but the analysis did not identify the corresponding U-to-C events. The findings add another layer to the comparison of chloroplast genomes, alongside genome-size variation, inverted-repeat changes and codon-usage bias.

One of the study’s most direct identification results came from its search for an informative DNA barcoding region. The researchers identified the genomic segment spanning 80,401–81,200 base pairs as an optimal barcoding window for the sampled species. Five diagnostic loci within that window could discriminate all 16 Amorphophallus species examined. This finding is specific to the comparative sample used in the study and provides a molecular marker for distinguishing the included taxa.

Phylogenetic reconstruction recovered all sampled Amorphophallus species as a monophyletic group, which the researchers divided into three major clades: Continental Asia I, Continental Asia II and Southeast Asia. The Southeast Asia clade contained A. fornicatus, A. pendulus, A. hewittii and A. titanum. The Continental Asia II clade included A. glaucophyllus, A. macrophyllus, A. konjac, A. krausei, A. albus and A. kachinensis. Continental Asia I comprised A. coaetaneus, A. tonkinensis, A. yunnanensis, A. kiusianus, A. muelleri and one accession that was not identified to species.

Within the wider Araceae sample, Symplocarpus was sister to the remaining sampled members of the family. Amorphophallus was most closely related to Syngonium, Xanthosoma, Zomicarpella and Caladium. Together, the chloroplast analyses provide a comparative account of structural evolution, codon usage and lineage relationships in 16 Amorphophallus species, while the five-locus barcoding window offers a sequence-based means of discriminating the taxa included in the study. The authors identify species identification, germplasm conservation and molecular breeding as areas supported by these findings.

Subject of Research: Comparative chloroplast genomics of structure, codon usage and phylogeny in 16 Amorphophallus species

Article Title: Comparative chloroplast genomics in Amorphophallus: revealing codon usage patterns and phylogenetic clades across 16 species

Article References: Shi, H., Lu, Q., Qi, Y., Yang, M., Zhao, M., Gao, P., Huang, F., Zhao, J., Li, L., & Yu, L. (2026). Comparative chloroplast genomics in Amorphophallus: revealing codon usage patterns and phylogenetic clades across 16 species. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09945-1

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09945-1

Keywords: Amorphophallus, chloroplast genomes, comparative genomics, codon usage bias, plant phylogenetics, DNA barcoding, genome structure, Araceae, base editing, species identification, Comparative, chloroplast