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

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.

Assembly and comparative analysis of the complete mitochondrial genome of Bupleurum chinense DC.

BACKGROUND: Bupleurum chinense(B. chinense) is a plant that is widely distributed globally and has strong pharmacological effects. Though the chloroplast(cp) genome of B. chinense has been studied, no reports regarding the mitochondrial(mt) genome of B. chinense have been published yet. RESULTS: The mt genome of B.chinense was assembled and functionally annotated. The circular mt genome of B. chinense was 435,023 bp in length, and 78 genes, including 39 protein-coding genes, 35 tRNA genes, and 4 rRNA genes, were annotated. Repeat sequences were analyzed and sites at which RNA editing would occur were predicted. Gene migration was observed to occur between the mt and cp genomes of B. chinense via the detection of homologous gene fragments. In addition, the sizes of plant mt genomes and their GC content were analyzed and compared. The sizes of mt genomes of plants varied greatly, but their GC content was conserved to a greater extent during evolution. Ka/Ks analysis was based on code substitutions, and the results showed that most of the coding genes were negatively selected. This indicates that mt genes were conserved during evolution. CONCLUSION: In this study, we assembled and annotated the mt genome of the medicinal plant B. chinense. Our findings provide extensive information regarding the mt genome of B. chinense, and help lay the foundation for future studies on the genetic variations, phylogeny, and breeding of B. chinense via an analysis of the mt genome.

[Clustering analysis of karyotype resemblance-near coefficient for 6 Bupleurum species].

OBJECTIVE: To explore the genetic evolutionary distance between plants by using karyotype parameters identification of medicinal plants. METHOD: The cluster analysis of karyotype resemblance-near coefficient and evolutionary distance was used for 6 Bupleurum species. RESULT: The results showed that there were the biggest karyotype resemblance-near coefficient (0.9920) and the smallest evolutionary distance (D(e) = 0.0080) between B. scorzonerifolium and B. chinense, indicating the closest relationship, and the minimum karyotype resemblance-near coefficient (0.4794) and the maximum evolutionary distance (D(e) = 0.7352) between B. smityii and B. falcatum, indicating the most distant relationship. CONCLUSION: Karyotype was an important parameter for identification of medicinal plants because karyotype was stabilized for species. The genetic distance between in 6 species of Bupleurum species was obtained by karyotype clustering analysis of karyotype resemblance-near coefficient. There was the bigger evolutionary distance between the species which had different chromosome number.