The first complete mitochondrial genome of Curcuma amarissima (Zingiberaceae): insights into multi-branch structure, codon usage, and phylogenetic evolution

Abstract

Background: As a key genus in Zingiberaceae, Curcuma is widely studied for its taxonomic diversity, the presence of bioactive curcuminoids and volatile oils, and its extensive applications in traditional medicine and economic products such as spices and cosmetics. Although chloroplast genomes have been assembled and published for over 20 Curcuma species, mitochondrial genomic data remain limited.

Results: We successfully sequenced, assembled, and annotated the mitogenome of Curcuma amarissima (C. amarissima) using both Illumina short reads and Nanopore long reads, achieving the first complete mitogenome characterization in the Zingiberaceae family. The C. amarissima mitogenome features a unique multi-branched structure, spanning 6,505,655 bp and consisting of 39 distinct segments. It contains a total of 43 protein-coding genes, 63 tRNA genes, and 4 rRNA genes, with a GC content of 44.04%. Codon usage analysis indicated a weak bias, with neutrality plot analysis suggesting natural selection as a key factor shaping mitochondrial codon usage in C. amarissima. The mitogenome provides valuable insights into genome size, coding genes, structural features, RNA editing, repetitive sequences, and sequence migration, enhancing our understanding of the evolution and molecular biology of multi-branched mitochondria in Zingiberaceae. The high frequency of repeat sequences may contribute to the structural stability of the mitochondria. Comparing chloroplast genome, phylogenetic analysis based on the mitochondrial genome establishes a foundation for further exploration of evolutionary relationships within Zingiberaceae.

Conclusions: In short, the mitochondrial genome characterized here advances our understanding of multi-branched mitogenome organization in Zingiberaceae and offers useful genomic resources that may support future breeding, germplasm conservation, and phylogenetic studies, though further research is necessary.

Keywords: Curcuma amarissima; Comparative genomics; Mitogenome; Phylogeny.

Fig. 1

The assembly result of the mitochondrial genome of C. amarissima

Fig. 2

The statistics of codon in C. amarissima mitogenome. A The relative synonymous codon usage (RSCU). Codon families displayed on the x-axis. RSCU values represent the frequency of a specific codon relative to the expected frequency of that codon under uniform synonymous codon usage. B GC content of different positions from PCGs. C ENC-plot against GC3 of mitochondrial genome of C. amarissima. D Number of RNA editing sites predicted by individual PCGs

Fig. 3

The distribution of repetitive sequences and homologous in C. amarissima mitogenome. A Distribution of repetitive sequences. The outermost circle represents the mitochondrial genome; the inner circle is SSR, tandem repeat (red), and dispersed repeat (turquoise). B Homologous analysis based on different organelles shows the arc representing mitogenome DNA

Fig. 4

Variation in mitochondrial genes and the evolutionary characteristics of C. amarissima. A Ka/Ks ratio calculated for the PCGs. B nucleotide diversity of the PCGs. C Collinear analysis of C. amarissima and other Commelinanae species. The red arcs indicate inverted regions, while the gray arcs indicate better homologous regions

Fig. 5

Molecular phylogenetic analysis was conducted using sequences from both mitochondrial and chloroplast genomes. A A phylogenetic tree based on conserved mitochondrial proteins was analyzed using ML and BI. ML support values and BI posterior probabilities are shown at the nodes. B A similar tree was constructed from conserved chloroplast proteins using the same methods