De novo assembly and comparative analysis of the mitochondrial genome of Reynoutria japonica

Jianhui Chen; Hongping Ma; Haili Fan; Fan Lin; Tuanyao Chai; Hong Wang

doi:10.3389/fgene.2023.1289811

De novo assembly and comparative analysis of the mitochondrial genome of Reynoutria japonica

Front Genet. 2023 Nov 23:14:1289811. doi: 10.3389/fgene.2023.1289811. eCollection 2023.

Authors

Jianhui Chen¹, Hongping Ma¹, Haili Fan¹, Fan Lin¹, Tuanyao Chai¹, Hong Wang¹

Affiliation

¹ College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.

Abstract

Reynoutria japonica Houtt. is an important medical plant with a long history of thousands of years in China, however, its mitochondrial genome (mitogenome) has not been reported yet. In this work, we reported and analyzed the R. japonica mitogenome. The main results include: The R. japonica mitogenome was 302,229 bp in length and encoded 48 genes, including 27 protein-coding genes (PCGs), 3 rRNA genes, and 18 tRNA genes. Repeat sequence analysis revealed that there were 54 repeat sequences ranging from 193 bp to 1,983 bp in the R. japonica mitogenome. Relative synonymous codon usage (RSCU) analysis showed that leucine (900, 11.01%) and serine (732, 8.96%) were the two most abundant amino acids, and the codons with RSCU values showed the preference of A or T ending when greater than 1. The RNA editing sites of PCGs in the R. japonica mitogenome were characterized, and 299 RNA editing sites were found. Extensive sequences transfer between mitochondrion and chloroplast were found in R. japonica, where 11 complete plastid-derived tRNA genes stayed intact in the R. japonica mitogenome. Three genes (ccmFC, cox1, and nad1) were seen to play essential roles in the evolution through selection pressure analysis. The phylogenetic analysis showed that Fallopia multiflora was the closest species with R. japonica, in consistency with the results of chloroplast genome. Overall, the current work presents the first mitogenome of R. japonica and could contribute to the phylogenetic analysis of the family Polygonaceae.

Keywords: RNA editing; Reynoutria japonica; codon usage; evolution; mitogenome; repeat sequences.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Science Foundation of China (Grant Nos. 61972374 and 32370403) and the Fundamental Research Funds for the Central Universities (Grant No. E1E40605).