Analysis of the complete mitochondrial genome of Panax quinquefolius reveals shifts from cis-splicing to trans-splicing of intron cox2i373.

[Display omitted] • The complete mitochondrial genome of Panax quinquefolius has been successfully assembled. • Compared to the previous version, our new version has improved the quality of tRNA gene annotation. • Recombination via short repetitive sequences causes cleavage of the mitochondrial intron cox2i373 in Panax genus. • Horizontal gene transfer from chloroplast to mitochondrial is frequent in Panax species. Panax quinquefolius is a perennial plant with medicinal values. In this study, we assembled the complete mitochondrial genome (mitogenome) of P. quinquefoliu s using PMAT assembler. The total length of P. quinquefoliu s mitogenome is 573,154 bp. We annotated a total of 34 protein-coding genes (PCGs), 35 tRNA genes, and 6 rRNA genes in this mitogenome. The analysis of repetitive elements shows that there are 153 SSRs, 24 tandem repeats and 242 pairs of dispersed repeats this mitogenome. Also, we found 24 homologous sequences with a total length of 64,070 bp among its mitogenome and plastome, accounting for 41.05 % of the plastome, and 11.18 % of the mitogenome, showing a remarkable frequent sequence dialogue between plastome and mitogenomes. Besides, a total of 583 C to U RNA editing sites on 34 PCGs of high confidence were predicted by using Deepred-mt. We also inferred the phylogenetic relationships of P. quinquefolius and other angiosperms based on mitochondrial PCGs. Finally, we observed a shift from cis - to trans -splicing in P. quinquefolius for two mitochondrial introns, namely cox2i373 and nad1i728 , and a pair of 48 bp short repetitive sequences may be associated with the breaking and rearrangement of the cox2i373 intron. The fragmentation of the cox2i373 intron was further confirmed by our PCR amplification experiments. In summary, our report on the P. quinquefolius mitogenome provides a new perspective on the intron evolution of the mitogenome. [ABSTRACT FROM AUTHOR]