Aug 2026· Frontiers in Plant Science· 0 citations· 81 references
TL;DR
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.
Abstract
As a perennial herb of Poaceae,
Phalaris arundinacea
plays key roles in grazing, production, and soil and water conservation because of its well-developed rhizomes and seed dispersal. We assembled and annotated the first mitogenome of
P. arundinacea
to support evolutionary and taxonomic research.
We assembled and annotated the first complete mitochondrial genome of
P. arundinacea
by integrating Illumina short reads with Nanopore long reads via a hybrid assembly strategy. The genome architecture was comprehensively characterized, encompassing codon usage bias, repetitive sequence organization, and inter-organellar genetic exchange with the chloroplast genome.
Assembly of the
P. arundinacea
mitogenome revealed two circular structures with a combined length of 526,717 bp. The genome comprised a set of 37 protein-coding genes (PCGs), 27 tRNAs, and 8 rRNAs, with the rRNA genes exhibiting full assembly (100% coverage). The mitochondrial genome contained 154 forward and 164 palindromic repeats, along with 25 tandem repeats and 124 simple sequence repeats (SSRs). Notably, 102 SSRs were distributed on contig1, predominantly in tetrameric form. Furthermore, 376 RNA editing sites were predicted. A total of 104 fragments were integrated into the mitochondrial genome from the chloroplast, amounting to 55,866 bp of transferred sequence. Finally, phylogenetic analysis of 28 plant mitogenomes placed
P. arundinacea
closest to species within the genus
Poa
(
P. chaixii
and
P. pratensis
). 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. Our findings support the close phylogenetic relationship between P. arundinacea and species of the genus Poa and provide a reference mitochondrial genome resource for future comparative studies within Phalaris that incorporate broader taxon sampling. These results support deeper phylogenetic investigations of
P. arundinacea
and facilitate future work on its germplasm characterization and applied use.
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.
Xun Gong, Keming Zhu, E. Fleming et al.· Frontiers in Plant Science· 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.
BACKGROUND
Angraecum sesquipedale (DC.) Danser (commonly called Darwin's orchid) is an ornamental horticultural wild plant with ecological, economic, and evolutionary research value. While its chloroplast and nuclear genome sequence have been reported, the mitochondrial genome research remains absent. To analyze the genetic variation foundation of Darwin's orchid at the genomic level, this study utilizes genomic data of 45.38 Gigabase Illumina and 36.79 Gigabase PacBio HiFi sequencing in CNCB (PRJCA030186), to decipher the mitochondrial genome structure, composition, and sequence variation patterns of this plant.
RESULTS
Herein, the A. sesquipedale mitochondrial genome length was 711,372 bp, composing of 14 circular DNAs and including 38 protein-coding, 30 tRNA, three ribosomal RNA genes, and two pseudo-genes. Its sub-mitochondrial genome length ranges among Circle 1 and Circle 14 were from 23,873 bp to 105,231 bp, and the GC content ranges from 39.22% to 44.41%, respectively. In total, 216 SSR, 103 tandem, and 1019 dispersed repeats are discriminated. RNA editing site prediction revealed 709 RNA editing events. Codon usage analysis indicated a preference for A/T (U) codon ending. Intergenomic DNA transfer was identified in all of the 14 chromosomes, with chloroplast DNA transfer fragments accounting for 11.03% of the mitochondrial genome. Comparative analysis showed that GC content is conserved, but their structure, size, and gene content of mitochondrial genome chromosomes vary significantly. Phylogenetic analysis showed that Hygrochilus parishii clustered with A. sesquipedale, indicating that the two were closely related. The relationship is agreement with the evolutionary history and taxonomic status of Darwin's Orchid. Compared to the A. sesquipedale mitochondrial genomes and other reported Orchidaceae plants, the mitochondrial genome of Darwin's Orchid has lost three ribosomal protein-coding genes and sdh3.
CONCLUSION
The mitochondrial genome characteristics and phylogenetic evolution relationship of Darwin's orchid were analyzed, providing a reference basis for enhancing germplasm identification, resource diversity development, utilization, and new variety breeding research.
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
