Background Okra (Abelmoschus esculentus L. Moench) is an economically important crop and is known for its slimy juice, which has significant scientific research value. The A. esculentus chloroplast genome has been reported; however, the sequence of its mitochondrial genome is still lacking. Results We sequenced the plastid and mitochondrial genomes of okra based on Illumina short reads and Nanopore long reads and conducted a comparative study between the two organelle genomes. The plastid genome of okra is highly structurally conserved, but the mitochondrial genome of okra has been confirmed to have abundant subgenomic configurations. The assembly results showed that okra’s mitochondrial genome existed mainly in the form of two independent molecules, which could be divided into four independent molecules through two pairs of long repeats. In addition, we found that four pairs of short repeats could mediate the integration of the two independent molecules into one complete molecule at a low frequency. Subsequently, we also found extensive sequence transfer between the two organelles of okra, where three plastid-derived genes (psaA, rps7 and psbJ) remained intact in the mitochondrial genome. Furthermore, psbJ, psbF, psbE and psbL were integrated into the mitochondrial genome as a conserved gene cluster and underwent pseudogenization as nonfunctional genes. Only psbJ retained a relatively complete sequence, but its expression was not detected in the transcriptome data, and we speculate that it is still nonfunctional. Finally, we characterized the RNA editing events of protein-coding genes located in the organelle genomes of okra. Conclusions In the current study, our results not only provide high-quality organelle genomes for okra but also advance our understanding of the gene dialogue between organelle genomes and provide information to breed okra cultivars efficiently.

Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is not only a Chinese herbal medicine but also a functional food widely planted in China. Its fruits are used to treat many diseases or can be processed into food products. This study aims to find key metabolic components, distinguish the differences between geographical regions and find more medicinal and edible values of C. speciosa fruits. We used ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) and widely targeted metabolomics analysis to reveal key and differential metabolites. We identified 974 metabolites and screened 548 differential metabolites from 8 regions. We selected significantly high-content differential metabolites to visualize a regional biomarker map. Comparative analysis showed Yunnan had the highest content of total flavonoids, the highest amounts of compounds related to disease resistance and drug targets and the most significant difference from the other regions according to the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database, a unique platform for studying the systematic pharmacology of Chinese herbal medicine and capturing the relationship between drugs, targets and diseases. We used oral bioavailability (OB) ≥ 30% and drug likeness (DL) ≥ 0.18 as the selection criteria and found 101 key active metabolites, which suggests that C. speciosa fruits were rich in healthy metabolites. These results provide valuable information for the development of C. speciosa.