A contrast between conserved chloroplast genomes and highly dynamic mitochondrial genomes in S. plebeia is highlighted, driven by repeat-mediated recombination and RNA editing, providing new insights into organelle genome evolution in Lamiaceae.
Abstract
Introduction Salvia plebeia is a medicinal plant in Lamiaceae, but its organelle genome architecture and evolutionary dynamics remain insufficiently understood, particularly for the mitochondrial genome. Methods We assembled and analyzed the mitochondrial and chloroplast genomes of S. plebeia using PacBio HiFi long-read sequencing. Genome assembly, annotation, and correction were performed using PMAT2, Minimap2, NextPolish, and GeSeq. Repetitive elements were identified using SSR, tandem repeat, and dispersed repeat analyses. Repeat-mediated recombination was validated using long-read mapping and PCR. Comparative chloroplast genomics and phylogenetic analyses were conducted using mVISTA, MUMmer4, and IQ-TREE2. RNA-editing sites were predicted using PREPACT, and codon usage bias was analyzed using CodonW. Results The mitogenome is a 444,036 bp circular molecule encoding 58 genes, while the chloroplast genome is 151,062 bp with a typical quadripartite structure. A total of 135 SSRs, 331 dispersed repeats, and 25 mitochondrial plastid DNA transfer (MTPT) regions were identified. Six repeat pairs were experimentally supported to mediate homologous recombination, indicating alternative mitochondrial conformations. RNA-editing analysis identified 587 C-to-U sites. Phylogenetic analyses placed S. plebeia within the Salvia lineage, and plastomes showed high conservation, whereas the mitogenome exhibited extensive structural rearrangements. Discussion These findings highlight a contrast between conserved chloroplast genomes and highly dynamic mitochondrial genomes in S. plebeia, driven by repeat-mediated recombination and RNA editing, providing new insights into organelle genome evolution in Lamiaceae.
Comparative analysis of non-synonymous-to-synonymous substitution rate (Ka/Ks) ratios across divergent species revealed that the mitochondrial genome of P. arundinacea underwent stabilizing evolutionary dynamics, characterized by predominant purifying selection with several lineage-specific variations in selective pressure.
Ze Teng, Chun-Yu Tian, Yan-Ting Yang et al.· Frontiers in Plant Science· 0 citations
BACKGROUND
Krascheninnikovia arborescens is a drought-tolerant subshrub of the Amaranthaceae family that is endemic to China and plays an important role in desert ecosystems. However, little is known about the structure and evolutionary dynamics of its organellar genomes. In this study, we assembled and characterized the mitochondrial and chloroplast genomes of K. arborescens using long-read sequencing data.
RESULTS
The mitochondrial genome was assembled as a master circular genome representation of 387,891 bp and contains 62 annotated genes, whereas the chloroplast genome exhibits a typical quadripartite structure of 152,039 bp with 90 genes. The mitochondrial genome harbors abundant repetitive sequences and multiple plastid-derived insertions, indicating a dynamic structural organization. In contrast, gene content remains highly conserved, and all core protein-coding genes show signatures of purifying selection, particularly those involved in ATP synthesis and respiratory metabolism. Predicted RNA editing sites differ substantially between the two organelles, suggesting distinct post-transcriptional modification patterns. Phylogenetic analyses based on shared organellar genes consistently place K. arborescens within Amaranthaceae and support its evolutionary relationships within Caryophyllales. These results reveal a combination of structural dynamism and functional conservation in the organellar genomes of K. arborescens.
CONCLUSION
This study provides a foundation for future comparative and evolutionary studies of Amaranthaceae and expands genomic resources for this family.
Pennisetum sinese, a perennial grass central to “Juncao Technology,” holds considerable promise for non-grain biomass production and ecological restoration. Despite its agronomic value, the cytoplasmic genetic architecture of this species, particularly its mitochondrial genome, remains uncharacterized. Here, we present the first complete mitochondrial genome of the P. sinese assembled via hybrid long- and short-read sequencing. The genome adopts a multi-branched conformation spanning 405,186 bp with a GC content of 43.98%, and encodes 32 unique protein-coding genes, 20 tRNA genes, and three rRNA genes. We detected significant codon usage bias, abundant tandem repeats, and dispersed repeats. In addition, 24 chloroplast-derived homologous fragments totaling 13,053 bp were identified. Phylogenetic analysis confirms the placement of the P. sinese within the Poaceae clade, whereas synteny analysis reveals extensive structural rearrangements in its mitochondrial genome compared with closely related species. Furthermore, we predicted 454 C−to−U RNA editing sites. These findings establish a foundational genetic resource for P. sinese cytoplasmic inheritance and laying a foundation for future investigations into the molecular mechanisms underlying its high biomass yield and stress tolerance, informing future germplasm innovation.
Xiaobing Hu, Dan Zhu, Xin Ning et al.· Frontiers in Plant Science· 0 citations
This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome, providing new insights into the evolutionary and dispersal pathways of Rosa species within the unique habitats of northwest China.
Gang Lu, Mengmeng Yu, Fazu Xu et al.· PeerJ· 0 citations
Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.
Wen-Xuan Liu, Jia-Wei Wu, Hao-Nan Zheng et al.· International Journal of Mol...· 0 citations
OBJECTIVE
Crateva unilocularis is a widely consumed woody vegetable in the family Capparaceae. This study aimed to generate and comprehensively characterize the first complete mitochondrial genome of C. unilocularis using PacBio HiFi long-read sequencing, elucidating its structural organization and gene content. We also report the complete chloroplast genome for this accession. Together, these organelle genome resources provide a foundation for downstream studies on phylogeny, genome architecture, and adaptive evolution in C. unilocularis and related taxa.
DATA DESCRIPTION
The chloroplast genome length of C. unilocularis is 156,525 bp, harboring 78 unique protein-coding genes (PCGs), 28 transfer RNAs (tRNAs), and four ribosomal RNAs (rRNAs). In addition, the assembly graph supports three circular mitochondrial molecules with a combined length of 566,203 bp, and junction-spanning HiFi reads validate the assembled configurations. Annotation identified 59 genes in total, including 37 PCGs, 19 tRNAs, and three rRNAs. The assembled and annotated organelle genomes represent key reference sequences for C. unilocularis within Capparaceae and will facilitate future comparative and functional genomic analyses.
