Assembly and structural analysis of the mitochondrial genome of six Cucumis species

Abstract

Plant mitochondrial genomes exhibit remarkable structural plasticity and evolutionary complexity; however, their diversity and evolutionary mechanisms remain poorly understood in many crop lineages. In this study, we systematically characterized the mitochondrial genome structures of Cucumis species to provide new insights into mitochondrial genome evolution and structural variation within the Cucurbitaceae family. High-quality long-read sequencing data were generated and integrated with PacBio HiFi sequencing to achieve accurate de novo assembly of Cucumis mitochondrial genomes. The assembled mitogenomes exhibited highly dynamic architectures, displaying non-canonical multipartite structures composed of multiple independent circular and linear molecules. Comprehensive annotation identified conserved protein-coding genes, transfer RNA (tRNA) genes, and ribosomal RNA (rRNA) genes, accompanied by pronounced codon usage preferences. Repeat sequence analyses revealed that long-distance dispersed repeats (LDRs) play a crucial role in mediating homologous recombination and driving mitochondrial genome structural rearrangements. Furthermore, multiple mitochondrial plastid DNA transfer events (MTPTs) were identified, highlighting frequent genetic exchanges between organellar genomes in Cucumis. Phylogenetic analyses revealed lineage-specific evolutionary patterns within Cucumis, accompanied by signatures of accelerated mitochondrial genome evolution. RNA editing analysis identified numerous editing sites, with respiratory-related genes, including nad4, ccmB, mttB, and nad2, exhibiting relatively high editing frequencies. Most RNA editing events occurred at the second nucleotide position of codons, suggesting their potential contribution to maintaining mitochondrial protein stability and respiratory function. Collectively, this study provides comprehensive insights into mitochondrial genome architecture, structural evolution, and functional regulation in Cucumis, offering valuable genomic resources and a theoretical foundation for understanding organelle genome evolution and adaptation in Cucurbitaceae.