Mitochondrial Genomic Characterization and Phylogenetic Analysis of Wild Rapeseed <i>Rorippa indica</i>

Rorippa indica is a wild oilseed crop of Brassicaceae with good environmental adaptability and strong stress resistance. This plant has become an important wild relative species for rapeseed (Brassica napus L.) and is used to improve its agronomic traits, with important development and utilization value. However, the research of R. indica genetics is still lacking. And no mitochondrial genome (mitogenome) in the genus Rorippa has been expounded. To analyze the structural characteristics of the R. indica mitogenome, second-generation and third-generation sequencing techniques were made to assemble its mitogenome. The results showed that its mitogenome is composed of a single master circle DNA molecule, with 59 genes (33 protein-coding, 23 tRNA, and 3 ribosomal RNA genes) annotated. The length of the circular genome is 219,775 bp, with a GC content of 45.24%. The mitochondrial genome contains 55 SSRs, 17 tandem repeats, and 252 scattered repeat sequences, with scattered repeat sequences accounting for 77.78%. The top two codons with the highest expression levels are TTT and AUU. Moreover, 377 RNA editing sites were forecasted in the R. indica mitogenome. And 22 collinear gene fragments were discriminated in the R. indica chloroplast and mitogenomes, with a total 13,153 bp length, accounting for 4.08% of the mitogenome sequence. The longest gene migration fragment is 2186 bp, and the shortest fragment is 42 bp. Furthermore, 12 genes undergo complete migration between the two genomes, and 10 genes undergo partial migration. Systematic evolutionary analysis shows that R. indica and Brassica napus are grouped, indicating a close genetic relationship between the two. Herein, the R. indica mitogenome was sequenced and annotated, and it was compared with other Brassicaceae mitogenomes. A genomic data foundation was supplied for elucidating the R. indica origin and evolution.