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Evolution analysis of P. vulgaris. (A) The plants in the diagram belong to of Lamiales. Different families are represented by different colors, with P. vulgaris represented in red. (B) Red-curved regions indicate where inversions occur, gray regions indicate regions of good homology, and white regions indicate species-unique sequences.
Source publication
Prunella vulgaris (Lamiaceae) is widely distributed in Eurasia. Former studies have demonstrated that P. vulgaris has a wide range of pharmacological effects. Nevertheless, no complete P. vulgaris mitochondrial genome has been reported, which limits further understanding of the biology of P. vulgaris. Here, we assembled the first complete mitochond...
Citations
... This conserved topological feature may be associated with its relatively low frequency of homologous recombination, thereby maintaining the stability of the genomic structure. In previous studies, the mitochondrial genomes of some Lamiaceae species have been shown to possess complex multimeric structures, as observed in Prunella vulgaris, Salvia officinalis, and Scutellaria tsinyunensis [33][34][35] . The mtDNA of phylogenetically closely related species exhibits remarkable conformational diversity, a characteristic that fully demonstrates the high degree of adaptability and structural complexity displayed by Lamiaceae mtDNA during evolutionary processes 34 . ...
... This indicates that the frequency of editing sites for genes associated with cytochrome c biogenesis and NADH dehydrogenase is higher in the mtDNA of L. japonicus. Based on previous studies, we have observed that RNA editing events in the mitochondrial mtDNA of many Lamiaceae species exhibit a strong bias towards genes associated with cytochrome c biogenesis and NADH dehydrogenase 33,37,38,51 . This editing preference likely reflects the Lamiaceae family's critical dependence on energy metabolism and redox homeostasis, which is closely linked to their biological characteristics such as high essential oil content, rapid growth rates, and environmental adaptability [52][53][54] . ...
Leonurus japonicus Houtt. (L. japonicus), as an important plant resource with both ornamental and medicinal value, has now spread worldwide and is widely studied. Currently, its chromosomal genome and chloroplast genome (cpDNA) have been reported, but the mitochondrial genome (mtDNA) has not yet been explored. In this study, we extracted DNA from fresh leaves of L. japonicus and performed sequencing and assembly of its mtDNA using both second-generation and third-generation sequencing technologies. The complete mtDNA of L. japonicus is 382,905 bp in length, with a GC content of 45.13%. This genome includes 15 tRNA genes, 32 protein-coding genes (PCGs), and 4 rRNA genes. In this mtDNA genome, we predicted a total of 480 RNA editing sites among the 32 PCGs. Subsequently, we conducted analyses on repetitive sequences, organelle genome sequence migration, and Relative Synonymous Codon Usage (RSCU). There are 28 homologous sequence fragments between the mtDNA and cpDNA of L. japonicus, which are related to the migration of 10 mtDNA genes. The RSCU analysis predicted 28 high-frequency codons, most of which prefer to end with A/U. Selection pressure analysis indicated that the Ka/Ks ratio for the majority of PCGs is less than 1, suggesting they are highly conserved during evolutionary processes. Phylogenetic results from 24 species indicate that the genera Leonurus and Scutellaria within the Lamiaceae family have the closest relationships. In summary, we have successfully assembled the complete mtDNA of L. japonicus by integrating second-generation and third-generation sequencing data for the first time. Subsequent multi-faceted analyses have allowed us to gain deeper insights into the numerous features of this genome, providing important reference data for the molecular genetics, dynamic evolution, and species identification of this plant. This work promotes the conservation and development of this important resource of medicinal and edible plants.
... The number and type of repeat sequences identified in the T. mongolicus mitogenome are similar to those reported for S. miltiorrhiza. Notably, however, unlike the mitogenome of P. vulgaris, which contains tandem repeats [71], those of T. mongolicus and S. miltiorrhiza lack these features. The differences in these repeat sequences are consistent with their mitochondrial genome size, which may be related to the amplification and deletion of elements [72]. ...
... This result is more consistent with the phylogenetic relationship of chloroplasts of T. mongolicus [1]. In addition, the phylogenetic relationships of S. tsinyunensis, S. franchetiana, S. barbata, P. heyneanus, A. reptans, V. trifolia, and P. chinense, etc., are in better agreement with the results of previous phylogenetic studies on the mitochondrial genomes of L. angustifolia [57] and P. vulgaris [71], suggesting that these phylogenetic relationships have a high degree of reliability. Currently, the mitochondrial genome of T. mongolicus has not been reported; therefore, this study further explores the phylogenetic relationships of T. mongolicus from the perspective of the mitochondrial genome, providing new insights into the evolutionary studies of this taxon. ...
Thymus mongolicus (Lamiaceae) is a plant commonly found throughout China, in which it is widely used in chemical products for daily use, traditional medicinal preparations, ecological management, and cooking. In this study, we have assembled and annotated for the first time the entire mitochondrial genome (mitogenome) of T. mongolicus. The mitochondrial genome of T. mongolicus is composed in a monocyclic structure, with an overall size of 450,543 base pairs (bp) and a GC composition of 45.63%. It contains 32 unique protein-encoding genes. The repetitive sequences of the T. mongolicus mitogenome include 165 forward repetitive sequences and 200 palindromic repetitive sequences, in addition to 88 simple sequence repeats, of which tetramers accounted for the highest proportion (40.91%). An analysis of the mitogenome codons revealed that synonymous codons generally end with A/U. With the exception of nad4L, which uses ACG/ATG as an initiation codon, all other genes begin with the ATG start codon. Codon analysis of the mitogenome also showed that leucine (909) are the most abundant amino acid, while tryptophan (134) are the least prevalent. In total, 374 RNA editing sites were detected. Moreover, 180 homologous segments totaling 105,901 bp were found when the mitochondrial and chloroplast genomes of T. mongolicus were compared. Phylogenetic analysis further indicated that T. mongolicus is most closely related to Prunella vulgaris in the Lamiaceae family. Our findings offer important genetic insights for further research on this Lamiaceae species. To the best of our knowledge, this study is the first description of the entire mitogenome of T. mongolicus.
... Mutations at the second codon position accounted for the highest number of 259 sites or 60.2%, followed by the first codon position (151 or 35.1%). Most of the RNA editing events resulted in transitions to leucine (189 times), with serine to leucine accounting for the highest number (98), followed by proline to leucine (85), and five synonymous mutations. The presence of a higher number of RNA editing sites causing mutations into leucine in the mitogenome of V. diffusa also corroborates the findings of Sheng and Wang et al. [16,74]. ...
... The annotation of these genes revealed the presence of nine complete genes, including one protein-coding gene (ycf15) and eight tRNA (trnD-GUC, trnH-GUG, trnI-GAU, trnN-GUU, trnM-CAU, trnP-UGG, trnS-GGA, trnW-CCA ) in the mitogenome. The discovery of ycf15, a highly conserved protein-coding gene in the plastome, suggests that gene migration from the plastome to the mitogenome has occurred, similar to the observation in other higher plants [84][85][86]. Additionally, eight translocated tRNAs in the plastome may have become pseudogenes [87,88]. ...
Background
Viola diffusa is used in the formulation of various Traditional Chinese Medicines (TCMs), including antiviral, antimicrobial, antitussive, and anti-inflammatory drugs, due to its richness in flavonoids and triterpenoids. The biosynthesis of these compounds is largely mediated by cytochrome P450 enzymes, which are primarily located in the membranes of mitochondria and the endoplasmic reticulum.
Results
This study presents the complete assembly of the mitogenome and plastome of Viola diffusa. The circular mitogenome spans 474,721 bp with a GC content of 44.17% and encodes 36 unique protein-coding genes, 21 tRNA, and 3 rRNA. Except for the RSCU values of 1 observed for the start codon (AUG) and tryptophan (UGG), the mitochondrial protein-coding genes exhibited a codon usage bias, with most estimates deviating from 1, similar to patterns observed in closely related species. Analysis of repetitive sequences in the mitogenome demonstrated potential homologous recombination mediated by these repeats. Sequence transfer analysis revealed 24 homologous sequences shared between the mitogenome and plastome, including nine full-length genes. Collinearity was observed among Viola diffusa species within the other members of Malpighiales order, indicated by the presence of homologous fragments. The length and arrangement of collinear blocks varied, and the mitogenome exhibited a high frequency of gene rearrangement.
Conclusions
We present the first complete assembly of the mitogenome and plastome of Viola diffusa, highlighting its implications for pharmacological, evolutionary, and taxonomic studies. Our research underscores the multifaceted importance of comprehensive mitogenome analysis.
... The GC content was evolutionarily conserved, with values ranging from 45.71 to 45.78%, and was higher than that of Sunflower (45.22%), Angelica dahurica (45.06%), and Prunella vulgaris (43.92%); these are high levels among higher plants [45][46][47]. The protein-coding region occupies only approximately 2.5-3.5% of the full length, and the noncoding region occupies approximately 90%. ...
Background
The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the “Queen of the Tea Family”, most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.
Results
In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836 bp (C. nitidissima) to 1,098,121 bp (C. tianeensis) with GC content of 45.71–45.78% and contained 48–58 genes, including 28–37 protein-coding genes, 17–20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.
Conclusions
In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.
... Compared to cpDNA, plant mtDNA is generally larger and more complex, with not only single circular DNA, polycyclic DNA [38], and linear DNA [39], but also possibly DNA with a complex structure [40,41]. Species such as Camellia sinensis [42], Coptis deltoidei [43], Fallopia multiflora [44], and Prunella vulgaris [45] possess two circular DNA in their mtDNA, whereas buckwheat possesses 10 [46] and Amorphophallus albus possesses 19 [47]. This study also confirmed that the mtDNA of C. stoloniferus possesses two circular DNA, whereas C. esculentus with a closer genetic relationship, possesses only one [14] and C. breviculmis with a further genetic relationship, may exhibit four different conformations [15]. ...
Background
Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes.
Results
We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection.
Conclusion
We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.
Perilla frutescens (L.) Britton, a member of the Lamiaceae family, stands out as a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in Îś-linolenic acid, holding substantial economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. The assembled P. frutescens mitochondrial genome spanned 299,551 bp and exhibited a typical circular structure, involving a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes. Additionally, 18 introns were observed in 8 protein-coding genes. Notably, the codons of the P. frutescens mitochondrial genome displayed a notable A/T bias. The analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Moreover, RNA editing sites preferentially produced leucine at amino acid editing sites. Furthermore, 70 sequence fragments (12,680 bp) having been transferred from the chloroplast to the mitochondrial genome were identified, accounting for 4.23% of the entire mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia miltiorrhiza and Platostoma chinense . Meanwhile, inter-species Ka/Ks results suggested that Ka/Ks < 1 for 28 PCGs, indicating that these genes were evolving under purifying selection. Overall, this study enriches the mitochondrial genome data for P. frutescens and forges a theoretical foundation for future molecular breeding research.
Perilla frutescens (L.) Britton, a member of the Lamiaceae family, is a versatile plant highly valued for its unique aroma and medicinal properties. Additionally, P. frutescens seeds are rich in α-linolenic acid, holding significant economic importance. While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete Mitochondrial genome sequence has yet to be reported. In this investigation, we conducted the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens using a combination of Illumina and PacBio data. The resulting assembled P. frutescens Mitochondrial genome spans 299,551 bp and exhibits a typical circular structure, with a GC content of 45.23%. Within the genome, a total of 59 unique genes were identified, encompassing 37 protein-coding genes, 20 tRNA genes, and 2 rRNA genes, with 18 introns present in 8 protein-coding genes. Notably, the codons of the P. frutescens Mitochondrial genome display a notable A/T bias. Our analysis also revealed 293 dispersed repeat sequences, 77 simple sequence repeats (SSRs), and 6 tandem repeat sequences. Additionally, RNA editing sites exhibited a preference for the formation of leucine at amino acid editing sites. Furthermore, we identified 70 sequence fragments (12,680 bp) that have been transferred from the chloroplast to the Mitochondrial genome, accounting for 4.23% of the entire Mitochondrial genome. Phylogenetic analysis indicated that among Lamiaceae plants, P. frutescens is most closely related to Salvia miltiorrhiza and Platostoma chinense. Inter-species Ka/Ks results suggested that Ka/Ks <1 for 28 PCGs, indicating that these genes will continue to evolve under purifying selection pressure. The findings of this study will contribute to the enrichment of Mitochondrial genome data for P. frutescens and provide a theoretical foundation for future molecular breeding research on P. frutescens.
