Mitochondrial genome assembly and annotation of Oryza longistaminata

Abstract

Oryza longistaminata serves as a critical germplasm resource for rice breeding; however, its mitochondrial genome structure and evolutionary characteristics remain largely unexplored. Here, we report the first complete mitochondrial genome of O. longistaminata assembled using PacBio HiFi long-read sequencing data. Employing a hybrid assembly strategy combining Hifiasm and RagTag scaffolding, we successfully obtained a single, self-closed circular mitochondrial genome of 611,640 bp. Genome annotation revealed 42 protein-coding genes (CDSs), 26 tRNA genes, and 3 rRNA genes, with multiple duplicated genes identified, including cox1, cox3, and trnM. Codon usage bias analysis indicated a strong preference for AGA/AGG (Arg), GCU (Ala), and UUG (Leu). The ENc-GC3s plot demonstrated that natural selection, rather than mutational pressure alone, is the dominant driving force shaping codon usage preferences. Additionally, a total of 147 simple sequence repeats (SSRs) and 683 high-confidence RNA editing sites (probability ≥ 90%) were predicted, with the editing sites predominantly concentrated in the respiratory chain core genes ccmC and ccmB. Comparative synteny analysis revealed significant structural rearrangements and fragmentation of specific genes (nad1 and rps2) compared with O. sativa and O. glaberrima. Furthermore, we detected 22,248 bp (3.64%) of chloroplast-derived transfer fragments (MTPT) in the mitogenome, encompassing 32 chloroplast-derived genes (19 CDSs and 13 tRNAs). Our findings provide crucial genomic insights into the structural features, evolutionary mechanisms, and inter-organellar gene transfer of the O. longistaminata mitochondrial genome, laying a foundation for mitochondrial breeding and phylogenetic studies in rice.