Assembly and comparative analysis of the complete mitogenome of Rubus chingii var. suavissimus, an exceptional berry plant possessing sweet leaves

Abstract

Rubus chingii var. suavissimus is a special berry plant of Rubus in the Rosaceae family. Its leaves contain high-sweetness, low-calorie, and non-toxic sweet ingredients, known as rubusoside. As a medicine and food biofunctional plant, it is a combination of "tea, sugar, and medicine." In this study, the complete mitogenome of R. chingii var. suavissimus was successfully assembled and annotated based on PacBio HiFi sequencing technology. The mitogenome of R. chingii var. suavissimus was a typical master circle structure, spanning 432,483 bp and containing 34 unique protein-coding genes (PCGs), 20 tRNAs, and 3 rRNAs. The majority of these PCGs was subjected to purifying selection, and only one gene (ccmB) showed sign of positive selection. The mitogenome of R. chingii var. suavissimus contained a large number of repeats, and the homogeneous fragments transferring between plastid genome and mitogenome, with a total of 55 pairs of mitochondrial plastid sequences (MTPTs), and the total size was 56,913 bp. Comparative analysis showed that the non-coding region in the mitogenome of R. chingii var. suavissimus had undergone frequent rearrangements during evolution, but the coding region was still highly conserved. Furthermore, the maximum likelihood and Bayesian inference phylogenetic trees were reconstructed of 10 shared PCGs in 36 plant species. The topological structures of two phylogenetic trees were consistent with the APG IV classification system and had high support rates. In general, this study clarifies the mitogenome of R. chingii var. suavissimus and provides valuable insights into the genetic evolution of the Rosaceae family.

Keywords: Rubus chingii var. suavissimus; master circle structure; mitochondrial genome; phylogenetic analysis; rearrangement.

Figure 1

Assembly and annotation of R. chingii var. suavissimus mitochondrial genome. (A) The preliminary assembly graph of mitochondrial genome. Among them, contigs of different lengths are arranged with numbers, from long to short. Red contigs represent repeated fragments. The connection order of the mitochondrial sequence constituent circle is also presented in numerical order. (B) Mitochondrial genome annotation. Genes with different functions are given different colors. The colored parabolas in the center circle represent dispersed sequence repeats.

Figure 2

Haplotype network analysis of 22 shared protein-coding sequences from 15 Rosaceae mitogenomes. Different species are given different colors.

Figure 3

The Ka/Ks ratio values of 30 common PCGs in eight Rosaceae mitogenomes. Different species are given different colors.

Figure 4

Codon usage bias analysis of mitogenomes from eight Rosaceae species. (A) Statistics of relative synonymous codon usage (RSCU) values for different species. Each bar represents a species, from left to right, namely, A. anserina, F. ananassa, G. urbanum, P. armeniaca, R. chingii, R. chingii var. suavissimus, R. chinensis, and S. chinensis. (B) Statistics on the total number of codons used for amino acids in protein-coding genes from different species.

Figure 5

The different type sequence repeats analysis and RNA editing sites prediction. (A) Identification of SSR loci in eight Rosaceae mitogenomes. (B) Identification of dispersed sequence repeats from eight Rosaceae mitogenomes. (C) Prediction of RNA editing sites in the mitogenome of R. chingii var. suavissimus. (D) The length distribution of dispersed sequence repeats in eight Rosaceae mitogenomes. Mono, mononucleotide repeats; Di, dinucleotide repeats; Tri, trinucleotide repeats; Tetra, tetranucleotide repeats; Penta, pentanucleotide repeats; Hexa, hexanucleotide repeats; F, forward repeats; R, reverse repeats; P, palindromic repeats; C, complementary repeats; TR, tandem repeats.

Figure 6

Homologous sequences analysis. (A) Homologue fragments between the chloroplast and mitochondrial genomes of R. chingii var. suavissimus. The red arc represents the mitochondrial genome. The green arc represents the chloroplast genome. The khaki lines represent the MTPTs. (B) Multicollinearity between R. chingii var. suavissimus and seven related species. Different colored bars represent the mitochondrial genome, the red line areas indicate the reversal occurred, and the gray areas indicate good similarity. Blocks with a length >500 bp are reserved.

Figure 7

The maximum likelihood (ML) phylogenetic tree (A) and Bayesian inference (BI) phylogenetic tree (B) were constructed based on 10 shared PCGs from the mitogenomes of 36 species. The support rates of the evolutionary trees are shown on the branches.