Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl

Abstract

Background: Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated.

Result: The F. suspensa mitochondrial genome was obtained in the length of 535,692 bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea.

Conclusion: In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.

Keywords: Bioinformatics analysis; Forsythia suspensa (Thunb.) Vahl; Mitochondrial genome; Phylogenetic evolution.

Fig. 1

F. suspensa mitochondrial genome map

Fig. 2

RNA editing sites in the F. suspensa mitochondrial genome

Fig. 3

Analysis of relative synonymous codon usage (RSCU) in the F. suspensa mitochondrial genome Note: The following blocks represent all codons encoding each amino acid, and the height of the upper column represents the sum of RSCU values of all codons

Fig. 4

Distribution map of repeat sequences in the F. suspensa mitochondrial genome Note: The outermost circle represents simple repeat sequences, followed by tandem repeat sequences, and the innermost line represents scattered repeat sequences

Fig. 5

Schematic representation of the homologous fragments from the F. suspensa chloroplast and mitochondrial genomes

Fig. 6

Boxplots of the Ka/Ks ratio of F. suspensa and four other plant species

Fig. 7

Line plots of Pi values of F. suspensa and four other plant species Note: The abscissa represents the gene name, and the ordinate represents the Pi value

Fig. 8

Collinear dot plot analysis of the F. suspensa mitochondrial genome Note: In each box, the abscissa represents the assembled sequence, the ordinate indicates other sequences, the red line indicates the forward alignment, and the blue line indicates the reverse complementary alignment

Fig. 9

Synteny analysis of the F. suspensa mitochondrial genome

Fig. 10

Phylogenetic analysis of the mitochondrial genomes of 22 plant species Note: A: Phylogenetic tree constructed using the maximum-likelihood method; B: Phylogenetic tree constructed using the Bayesian method