Characterization of Rheum palmatum mitochondrial genome and comparative analysis among Caryophyllales species

Abstract

Objective: This work aimed to report the first complete mitochondrial genome (mitogenome) of Rheum palmatum, summarize the features of Caryophyllales mitogenomes, and to reveal the potential of utilizing the mitogenomes of R. palmatum and other Caryophyllales species for inferring phylogenetic relationships and species identification. Methods: Both Illumina short reads and PacBio HiFi reads were utilized to obtain a complete mitogenome of R. palmatum. A variety of bioinformatics tools were employed to characterize the R. palmatum mitogenome, compare the reported mitogenomes in Caryophyllales and conduct phylogenetic analysis. Results: The mitogenome of R. palmatum was assembled into a single master circle of 302,993 bp, encoding 35 known protein-coding genes, 18 transfer RNA genes, and three ribosome RNA genes. A total of 249 long repeats and 49 simple sequence repeats were identified in this mitogenome. The sizes of mitogenomes in Caryophyllales varied from 253 kb to 11.3 Mb. Among them, 23 mitogenomes were circular molecules, one was linear, and one consisted of relaxed circles, linear molecules, and supercoiled DNA. Out of the total mitogenomes, 11 were single-chromosome structure, whereas the remaining 14 were multi-chromosomal organizations. The phylogenetic analysis is consistent with both the Engler system (1964) and the Angiosperm Phylogeny Group III system. Conclusions: We obtained the first mitogenome of R. palmatum, which consists of a master circle. Mitogenomes in Caryophyllales have variable genome sizes and structures even within the same species. Circular molecules are still the dominant pattern in Caryophyllales. Single-chromosome mitogenomes account for nearly a half of all the mitogenomes in Caryophyllales, in contrast to previous studies. It is feasible to utilize mitochondrial genomes for inferring phylogenetic relationships and conducting species identification.