Characterization of the mitochondrial genome of the aquatic vegetable Eleocharis dulcis (Burm. f.) Trin. ex Hensch.: the first representative of genus Eleocharis with evolutionary insights in Cyperaceae

Eleocharis dulcis (Burm. f.) Trin. ex Hensch., commonly known as water chestnut, is an economically important aquatic vegetable crop with high nutritional and medical value, whose underground corms are suitable for both fresh consumption (as a food) and cooking (as a vegetable). Although, the nuclear and chloroplast genome of this plant have been released, its mitochondrial genome (mitogenome) remains unreported. This research gap severely limited our understanding of mitogenomic evolution, structural dynamics, and phylogenetic relationships in Cyperaceae, especially for aquatic vegetable crops. We assembled the complete mitogenome of E. dulcis using a combination of Illumina short-read and PacBio long-read sequencing data. The mitogenome was 2,166,862 bp in length with a GC content of 43.08%. A total of 78 genes were annotated, containing 33 protein-coding genes (PCGs), 35 tRNA, eight rRNA genes and two pseudo-genes. Abundant repetitive sequences were identified, including 532 simple sequence repeats, 23,159 dispersed repeats, and 297 tandem repeats. Comparative analysis across major plant lineages showed that Cyperaceae species exhibited highly conserved GC content (~ 43%) despite significant variations in mitogenome size. RNA editing events were prevalent in PCGs, with most events resulting in amino acid changes that may regulate mitochondrial protein function. Most mitochondrial genes were under strong purifying selection, indicating their conservation during evolution. Synteny analysis revealed high structural rearrangement but low sequence divergence among Cyperaceae mitogenomes. Phylogenetic analysis based on conserved PCGs confirmed that E. dulcis is closely related to Cyperus esculentus within Cyperaceae. This study demonstrates that the genome data reported on public database platforms can be utilized to assemble the organelle genomes of the species, including the mitochondrial and chloroplast genomes, using hybrid assembly software. This is an important mitogenome of an aquatic vegetable and the first mitochondrial genome data reported for the genus Eleocharis. And a data foundation was supplied for further improving this crop.