The plant mitochondrial genome exhibits high complexity and structural diversity, which pose major challenges to its accurate assembly and in-depth interpretation. In recent years, the rapid advancement of sequencing technologies has driven the development of multiple assembly tools tailored for plant mitochondrial genomes. This review systematically summarizes recent progress in plant mitochondrial genome assembly, focusing on several representative computational tools, including GetOrganelle, GSAT, HIMT, PMAT, TIPPo, and PMAT2, and discusses their algorithmic principles, major advantages, and potential limitations. Furthermore, we highlight the methodological transition of mitochondrial genomics from traditional static sequence reconstruction to dynamic structural modeling. Finally, we outline future perspectives in data integration, standardization, and community benchmarking, which will collectively contribute to establishing a unified analytical framework for interpreting the complexity of plant mitochondrial genomes.

To understand ester compound biosynthesis in kiwifruit, two Actinidia species with distinct characteristics were compared. The firmness of Donghong (Actinidia chinensis) and Ganlv-1 (Actinidia eriantha) fruits gradually decreased as the fruit ripened after harvest, whereas the total soluble solids increased continuously, reaching a peak on the 8th day. The Ganlv-1 fruit ester content was significantly lower than in the Donghong fruits at the optimal eating stage, and the alcohol acyltransferase (AAT) activity in the Ganlv-1 fruits was significantly lower than in the Donghong fruits. The gene expression levels of AAT1 and AAT17 in the Donghong fruits were significantly higher than in the Ganlv-1 fruits, with a particularly remarkable difference observed for AAT1, which exhibited a 36-fold higher expression in the Donghong fruits when compared with the fully ripened Ganlv-1 fruits. A transient overexpression of the AAT1 gene in the kiwifruit led to a significant increase in ester content. Interestingly, a natural variation was observed in the promoter sequence of AAT1 between the Donghong and Ganlv-1 cultivars. Furthermore, separate analyses of the respective promoter activities revealed significantly higher activity levels in the Donghong fruits than in the Ganlv-1 fruits. In conclusion, a natural variation in the AAT1 promoter is primarily responsible for the disparity in AAT1 gene expression between the Donghong and Ganlv-1 fruits, resulting in a divergent accumulation of ester aroma compounds during the postharvest ripening stages.

Previous genetic mapping helped detect a ~7.52 Mb putative genomic region for the pollen fertility trait on peach Chromosome 06 (Chr.06), which was too long for candidate gene characterization. In this study, using the whole-genome re-sequencing data of 201 peach accessions, we performed a genome-wide association study to identify key genes related to peach pollen fertility trait. The significant association peak was detected at Chr.06: 2,116,368 bp, which was in accordance with the previous genetic mapping results, but displayed largely improved precision, allowing for the identification of nine candidate genes. Among these candidates, gene PpABCG26, encoding an ATP-binding cassette G (ABCG) transporter and harboring the most significantly associated SNP (Single Nucleotide Polymorphism) marker in its coding region, was hypothesized to control peach pollen fertility/sterility based on the results of gene function comparison, gene relative expression, and nucleotide sequence analysis. The obtained results will help us to understand the genetic basis of peach pollen fertility trait, and to discover applicable markers for pre-selection in peach.