Comparative analysis of the mitochondrial and chloroplast genomes of Purple nutsedge (Cyperus rotundus), a noxious weed

Abstract Background Cyperus rotundus L. is a notorious weed that harms agricultural ecosystems worldwide. Although the chloroplast genome (cpgenome) of C. rotundus has been studied, there have been no reports on the mitochondrial genome (mitogenome) of C. rotundus. Results The mitogenome and the cpgenome of C. rotundus XFZ01 have four circular DNA moleculesand one circular DNA molecule, respectively. Their total lengths were 1,491,358 bp and 186,119 bp, respectively. The mitogenome contained 75 genes, including 40 protein-coding genes (PCGs), 9 rRNA genes, and 26 tRNA genes. The cpgenome contained 121 genes, including 69 PCGs, 8 rRNA genes, and 44 tRNA genes. Analysis of repetitive sequences identified 350 and 88 SSRs, 144 and 123 tandem repeats, 686 and 1,210 interspersed repeats in the mitogenome and cpgenome, respectively. Homologous fragment analysisindicated that 11 homologous fragments migrated from the cpgenome to the mitogenome. Codon preference analysis showed that both the mitogenome and cpgenome had weak codon preferences. Furthermore, cpgenome PCGs had 23 RNA editing sites compared to 13 in mitogenome PCGs. Phylogenetic analysis verified that C. rotundus had the closest genetic relationship with C. esculentus. Finally, Ka/Ks research showed that most mitogenomic PCGs, except for the nad6 gene, undergo negative selection. Conclusions In this study, we assembled and annotated the mitogenome of the noxious weed C. rotundus and conducted a differential analysis using its cpgenome. These results lay a theoretical foundation for understanding the genetic variation, phylogeny, and population control of C. rotundus.