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

Mitochondria, the energy-producing organelles in every plant cell, carry their own small genomes, separate from the DNA in the nucleus and the chloroplast. In animals, these genomes are compact and predictable, but in plants they are famously unruly: enormous in size, structurally fluid, and prone to recombination that can reshape them from one generation to the next. That instability is precisely why plant mitochondrial genomes fascinate evolutionary biologists, and why they matter commercially, since they carry genes involved in fertility and other agronomically critical traits. Yet for all the attention paid to konjac chloroplasts and nuclear markers, the mitochondrial genomes of A. muelleri and A. krausei had never been sequenced and characterized, leaving a conspicuous gap in the genetic resources available to breeders and biologists working with the genus.

The team, led by corresponding authors Lifang Li and Lei Yu of the Yunnan Key Laboratory of Konjac Biology at Kunming University, sequenced the genomes, assembled them, and annotated their full complement of genes, then placed the two species in comparative and phylogenetic context against close relatives in the arum family. The scale of the assembled molecules alone is striking. The mitochondrial genome of A. muelleri measures 592,591 base pairs, while that of A. krausei reaches 593,535 base pairs, both arranged as circular molecules. To put those numbers in perspective, the entire human mitochondrial genome fits into fewer than 17,000 base pairs; the konjac mitochondrial genomes are roughly thirty-five times larger, a vivid illustration of how extravagantly plant mitochondrial DNA can expand over evolutionary time.

Size, however, is only the headline figure. The GC content, the proportion of the genome composed of the bases guanine and cytosine, came out at 45.90 percent for A. muelleri and 46.05 percent for A. krausei, values that sit within the range typical of flowering plant mitochondria and hint at broadly similar compositional pressures across the two species. More revealing is the gene inventory. A. muelleri carries 59 genes and A. krausei carries 62, with 55 genes shared between them. That core of 55 conserved genes represents the essential functional machinery of the mitochondrion, including the components of the respiratory chain and the ribosomal and transfer RNAs needed to build its proteins, while the differences between the two species illustrate how gene content can drift even between closely related plants.

Beneath the gene counts, the researchers dug into the fine texture of the two genomes, and it is here that the study becomes a treasure map for future work. They identified 28 high-frequency codons, codons used more often than expected, in both species, a signature of the shared translational preferences of the two mitochondrial systems. They also catalogued repetitive elements, the raw material of mitochondrial genome rearrangement: 91 dispersed repeats in A. muelleri against 125 in A. krausei, and 141 versus 148 simple sequence repeats, short tandemly repeated motifs that serve as convenient molecular markers for population studies and cultivar identification. Perhaps most intriguingly, the two species differ dramatically in one particular respect: the team found 43 RNA editing sites in A. muelleri but 220 in A. krausei, a fivefold difference that suggests the two species manage the post-transcriptional correction of their mitochondrial transcripts in notably different ways.

RNA editing is one of the stranger quirks of plant mitochondria. After a gene is transcribed from DNA into RNA, specific letters in the transcript are chemically altered, often converting a C to a U, so that the final protein differs from what the gene sequence alone would predict. Many of these edits are essential, restoring start codons or fixing amino acids that would otherwise render a protein nonfunctional. The stark contrast between 43 editing sites in one species and 220 in its close relative raises questions the study leaves open for future investigation: whether the difference reflects genuinely divergent editing machineries, different analytical sensitivities, or evolutionary turnover in the editing landscape itself. Either way, the catalogued sites provide a concrete dataset for anyone probing how konjac mitochondria maintain the integrity of their proteins.

To understand how these genomes fit into the broader evolutionary picture, the researchers compared the coding sequences of mitochondrial genomes from eight species across the Araceae family, identifying 33 shared sequences that could be aligned across the group. They then applied a classic evolutionary yardstick, the ratio of non-synonymous to synonymous substitution rates, known as Ka/Ks. Non-synonymous substitutions change the amino acid sequence of a protein, while synonymous ones do not; when the ratio of the former to the latter falls below 1, it signals that natural selection is actively weeding out protein-altering changes, preserving function. For most of the shared protein-coding genes, the Ka/Ks ratios were indeed below 1, indicating that these genes have been under purifying selection and that their protein functions have remained remarkably conserved across the family’s evolution. In other words, even as the mitochondrial genomes ballooned in size and shuffled their structures, the proteins they encode have stayed stubbornly faithful to their ancient roles.

The phylogenetic analysis, built on this comparative data, delivered a clear verdict on relationships within the genus: A. muelleri is closely related to both A. krausei and A. albus. That placement matters for more than taxonomy. Konjac breeders seeking to improve glucomannan yield, disease resistance, or tuber traits rely on knowing which species are genetically compatible and which traits can be moved between them. A well-resolved tree anchored in organellar genome data gives breeders and conservationists alike a firmer framework for choosing parents in crossing programs and for prioritizing which wild relatives to preserve as genetic resources.

The practical significance of the work extends beyond the laboratory. Amorphophallus tubers are rich in glucomannan, the soluble dietary fiber that gives konjac foods their characteristic texture and that is increasingly studied for its effects on satiety, blood sugar, and cholesterol. Yunnan Province, where the research team is based, is a center of konjac cultivation and of the wild diversity of the genus, and the study’s funding, which includes support from the Yunnan Provincial Science and Technology Department and the National Natural Science Foundation of China, reflects the region’s investment in konjac biology. Complete mitochondrial genomes add a new class of molecular markers, from the simple sequence repeats to the species-specific gene complements, that can be used to authenticate cultivars, trace germplasm, and monitor genetic diversity in breeding programs, all of which help protect a crop whose supply chains depend on a relatively narrow genetic base.

For the wider scientific community, the study is a reminder of how much fundamental biology remains hidden inside familiar crops. Two species grown and processed for centuries have only now had one of their three genomes read in full, and the reading has already surfaced surprises: genomes approaching six hundred thousand base pairs, a fivefold difference in RNA editing between close relatives, and dozens of repeats poised to drive future rearrangements. The newly assembled mitochondrial blueprints of A. muelleri and A. krausei now stand as a foundation for research into the molecular diversity, genetic evolution, and cultivation of the konjac plants, and they set the stage for the next round of questions, from the mechanisms behind their RNA editing disparity to the structural dynamics that shape the largest genomes in their cells. For a genus that quietly underpins a global food and health industry, that is a significant step out of the genomic dark.

Subject of Research: Complete mitochondrial genome assembly and comparative analysis of two Amorphophallus species

Article Title: Characterization and comparative analysis of the complete mitochondrial genomes of two Amorphophallus species (Araceae)

Article References: Shi, H., Yang, M., Qi, Y., Gao, P., Zhao, Y., Guo, J., Huang, F., Liu, J., Zhao, J., Li, L., & Yu, L. (2026). Characterization and comparative analysis of the complete mitochondrial genomes of two Amorphophallus species (Araceae). BMC Genomics. https://doi.org/10.1186/s12864-026-13344-z

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13344-z

Keywords: Amorphophallus, mitochondrial genome, konjac, Araceae, genomics, RNA editing, purifying selection, phylogenetics, simple sequence repeats, glucomannan, genome assembly, plant evolution