The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications

Simple Summary Mitochondria are semiautonomous organelles in eukaryotic cells, which play a critical role in cellular energy production. The plant mitochondrial genomes harbor large degrees of variation and complexity in structures. Crassulaceae is the largest family in the order Saxifragales. However, no entire mitogenome data have been available for species of Crassulaceae up to now. In the present study, we sequenced the first mitogenome of Crassulaceae (presented by Sedum plumbizincicola). Through comprehensive analyses, we found Saxifragales mitogenomes have undergone rapid structural evolution, with low synonymous substitution rates. Moreover, RNA editing, gene transfer, secondary structures of mitochondrial RNAs, and phylogenetic implications were also analyzed by using mitochondrial data. The present work may provide new insights into the mitogenome evolution of Saxifragales. As the largest family within the order Saxifragales, Crassulaceae contains about 34 genera with 1400 species. Mitochondria play a critical role in cellular energy production. Since the first land plant mitogenome was reported in Arabidopsis, more than 400 mitogenomic sequences have been deposited in a public database. However, no entire mitogenome data have been available for species of Crassulaceae to date. To better understand the evolutionary history of the organelles of Crassulaceae, we sequenced and performed comprehensive analyses on the mitogenome of Sedum plumbizincicola. The master mitogenomic circle is 212,159 bp in length, including 31 protein-coding genes (PCGs), 14 tRNA genes, and 3 rRNA genes. We further identified totally 508 RNA editing sites in PCGs, and demonstrated that the second codon positions of mitochondrial genes are most prone to RNA editing events. Notably, by neutrality plot analyses, we observed that the mitochondrial RNA editing events have large effects on the driving forces of plant evolution. Additionally, 4 MTPTs and 686 NUMTs were detected in the mitochondrial and nuclear genomes of S. plumbizincicola, respectively. Additionally, we conducted further analyses on gene transfer, secondary structures of mitochondrial RNAs, and phylogenetic implications. Therefore, the findings presented here will be helpful for future investigations on plant mitogenomes.

Automated summary

In this study, we sequenced the first mitogenome of Crassulaceae (presented by Sedum plumbizincicola) and comprehensively analyzed its structural evolution and RNA editing features. This research is important for further understanding the evolutionary history of plant mitogenomes.