Introduction: Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding.Methods: A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes.Results: The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing.Conclusion: In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.

Trihelix transcription factors (TFs) play crucial roles in plant growth, development, and environmental adaptation. However, there have been no systematic studies on the trihelix gene family in watermelon (Citrullus lanatus). A comprehensive study of trihelix genes in watermelon could provide new insights into its evolution and breeding potential. In this study, we identified 29 watermelon trihelix genes and analyzed their genome-wide information, molecular evolution, and expression patterns. The 29 watermelon trihelix genes were distributed across 12 chromosomes and grouped into five subfamilies. Evolutionary analysis revealed that four watermelon trihelix genes were collinear with six trihelix genes in Arabidopsis thaliana, and 20 watermelon trihelix genes were collinear with 20 trihelix genes in cucumber (Cucumis sativus). Gene duplication event analysis suggested that the expansion of the trihelix gene family mainly occurred through segmental duplications. Gene expression analysis showed distinct expression patterns of trihelix genes in watermelon, with evidence of tissue-specific expression. Furthermore, expression pattern analysis of watermelon trihelix genes in response to stress revealed that the Cla97C10G2055470 gene was associated with the response to salt stress, while the Cla97C06G127520 gene was associated with watermelon resistance to SqVYV disease. In conclusion, the phylogenetic, evolutionary, and expression analyses of the trihelix gene family in watermelon provide a solid foundation for future functional studies.