Zinian Wu

Introduction: 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. Methods: 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. Results and discussion: 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.

In the present research, the mitogenome of V. philippica-a perennial herbaceous plant with medicinal, ornamental, and edible value-was sequenced, assembled, and annotated using Illumina and Nanopore sequencing technologies. The complete mitogenome is 446,926 bp in length with a GC content of 44.31%, containing 38 protein‑coding genes (including all core subunits), 23 tRNA genes, and 3 rRNA genes. The genome features 143 dispersed repeats and 96 SSRs, and exhibits a strong codon usage bias toward A/T‑ending codons. A total of 400 potential RNA‑editing sites were predicted, predominantly in ccmB and nad4, with leucine showing the highest substitution frequency. We also identified 22,495 bp of chloroplast‑derived DNA, mainly comprising tRNA genes, underscoring the evolutionary conservation of tRNAs. Phylogenetic analysis firmly places V. philippica within Violaceae, closely related to Salicaceae and Passifloraceae. This comprehensive characterization provides crucial insights into the genetic architecture, evolutionary dynamics, and phylogenetic relationships of the V. philippica mitogenome, offering a valuable resource for future genetic studies, conservation strategies, and broader investigations into plant mitogenome evolution. We sequenced, assembled, and annotated the mitochondrial genome of Viola philippica, a medicinal herb used for treating infections and inflammation. V. philippica has a circular mitogenome with a total length of 446,926 bp, a GC content of 44.31%, and contains 38 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A total of 143 dispersed repeat sequences and 96 simple-sequence repeats (SSRs) were identified in the genome, with tetranucleotide repeats accounting for the highest proportion (38.55%). Codon preference analysis showed that V. philippica prefers codons ending in A/T, accounting for 86.66% of high-frequency codons. Four hundred RNA-editing sites were predicted, mainly distributed in ccmB and nad4 genes, with leucine showing the highest conversion frequency after editing (43.75%). In addition, the mitogenome contained a 22,495 bp sequence homologous to the chloroplast genome, mainly comprising tRNA genes. Phylogenetic analysis showed that V. philippica belongs to the family Violaceae and has a close relationship with Salicaceae and Passifloraceae. This study presents the first complete V. philippica mitogenome, providing insights into its genetic evolution and a scientific basis for elucidating the species' phylogenetic relationships and genetic diversity. It expands our understanding of Violaceae genomic evolution and supports the conservation and utilization of this medicinal plant's germplasm resources.

Introduction: Festuca pratensis is a perennial herb of Festuca in Poaceae. It has become an important forage and ecological restoration grass species due to its strong stress resistance and high nutritional value. Limited by the complexity of the forage grasses genome, the number of mitochondrial genome assembly in this genus is limited, which seriously restricts the research process of early mitochondrial genome evolution and key gene mining. Methods: We assembled and annotated the first high-quality mitochondrial genome of Festuca pratensis using third-generation and second-generation sequencing technology. The genome structure, sequence characteristics, evolutionary selection pressure and genetic relationship of Festuca pratensis mitochondrial genome were analyzed. Results and discussion: The mitochondrial genome has a multichromosomal structure with a total length of 449,613 bp. A total of 51 genes were detected, including 14 core genes, 15 tRNA genes, 19 variable genes and 3 rRNA genes. Three types of repetitive sequences were detected, including 121 simple repetitive sequences, 12 tandem repetitive sequences and 112 scattered repetitive sequences. A total of 9,810 codons encoding 33 PCGs were detected, and the probability of codon preference and avoidance was 50% and 47%, respectively. A total of 454 effective RNA editing sites were detected, distributed on 30 PCGs with all base change types C-U. 84 inter-genome transfer fragments were identified, and four complete transfer DNA fragments were rps12 , trnS-UGA , trnM-CAU and trnN-GUU , respectively. The rps3 gene showed positive selection (Ka/Ks > 1) in 36 (90%) of 40 species, indicating that it may be a functional gene adapted to rapid evolution. The Pi values of 33 genes ranged from 0 to 0.16277. Phylogenetic analysis divided 43 species into 6 categories. Combined with the results of collinearity, it was found that Festuca pratensis had the closest genetic relationship with Lolium perenne . In this study, the first high-quality mitochondrial genome of Festuca pratensis was assembled, which provided key high-quality reference data for subsequent organelle genome evolution, stress-resistant functional gene mining and germplasm resource identification of related species.

As an important perennial herb in the Iridaceae family, Iris lactea shows strong resistance to saline-alkali, drought, and cold stress, possessing significant ecological, medicinal, and economic value. In this study, we assembled the complete mitochondrial genome of I. lactea using whole-genome sequencing data. The assembled genome was 449,819 bp in length (GenBank Accession: PX667947) with a GC content of 46.97%. We found 113 simple sequence repeats, with tetranucleotide motifs being the most common (56, or 49.56%). The genome contains 600 dispersed repeats, consisting of 288 palindromic and 312 forward sequences. This mitogenome contains 36 protein-coding genes with a combined length of 32,343 bp. Analysis of codon usage revealed a strong preference for arginine, leucine, and serine, whereas methionine and tryptophan were infrequently used. We identified 556 RNA-editing sites, all exhibiting cytosine-to-uracil transitions. Analysis of the sequences inserted into the mitochondrial genome revealed that these chloroplast-derived fragments integrated into non-coding IGS regions and rRNA genes. The successful assembly and analysis of the Iris lactea mitogenome significantly enrich the genomic resources of the genus Iris, providing a solid foundation for future research on phylogenetic evolution, germplasm conservation, and genetic improvement of this genus.

Background: Astragalus (Fabaceae), the largest genus of flowering plants with its phytogeographic center in Southwest Asia, is ecologically and medicinally vital, as high-quality forage and a source of traditional medicine. However, its ambiguous morphological traits hinder taxonomic clarity, prompting increased reliance on molecular phylogenetic approaches to resolve relationships. Result: In the research, we assembled and annotated mitochondrial genomes of three Astragalus species, integrating them with two published mitochondrial genomes for comparative analysis. Newly sequenced genomes (269,019–364,431 bp) encoded 55–59 genes (31–34 protein-coding, 22–25 tRNAs, 3 rRNAs). Comparative analysis identified four genes ( cox2 , rps4 , atp8 , rps12 ) with high nucleotide variability, establishing them as reliable molecular markers for Astragalus phylogenetics, critical for future taxonomic and evolutionary studies. Mitochondrial plastid sequences were widespread across all five species, with petG and trnW-CCA conserved as chloroplast-derived fragments. Phylogenetic trees based on concatenated mitochondrial genes revealed Astragalus species shared close affinities with A. cicer and A.laxmanii , refining subgeneric classification frameworks. Conclusion: Our study confirms mitochondrial genomes as powerful tools for resolving relationships in morphologically cryptic genera. The novel genomic resources, including repeats and RNA editing sites, and validated markers, lay a foundation for future research into Astragalus biogeography, adaptive evolution, and medicinal resource development—thereby, enhancing the genus’ ecological and economic value.

FT-interacting proteins (FTIPs) function in signal transduction and metabolite transport, which are important to plant growth, development, and reproduction. Their bioinformatic characteristics and functions in Medicago ruthenica, a forage crop used for ecological restoration, remain unknown. We identified 19 MrFTIPs from the M. ruthenica genome, and they were unevenly distributed across seven chromosomes. Most of them are alkaline, labile and hydrophilic, with a structure comprising irregular coils, α-helices and extended chains. Phylogenetic analysis revealed five evolutionary clades with MrFTIPs. In total, two pairs of segmental duplication events were found, indicating a major pattern for MrFTIP expansion. Overall, 16, 11, and 22 gene pairs were identified from M. truncatula, Arabidopsis thaliana, and Glycine max, respectively. The promoter regions of MrFTIPs were enriched with abiotic stress responses and light or hormone signaling. Tissue-specific analysis revealed that 7 MrFTIPs were highly expressed in leaves, 9 MrFTIPs were highly expressed in petals, and 6 MrFTIPs were highly expressed in stigma and anthers. MrFTIP17 continues to be upregulated among tissues under salt stress, and MrFTIP8 continues to be upregulated among tissues under salt–alkali stress. Collectively, our study systematically characterized the genomic features, evolutionary patterns and cis-regulatory characteristics of the MrFTIP gene family in M. ruthenica, and identified MrFTIP8 and MrFTIP17 as candidate genes associated with salt stress responses in this species, thus providing insights into and potential targets for the molecular and conventional breeding of M. ruthenica.

Leymus chinensis , also known as alkali grass, is a perennial rhizomatous herbaceous plant with a significant ecological and economic value. However, its industrial development is hindered by low seed germination rates. Therefore, how to break the seed dormancy and improve the germination rate of L. chinensis seeds has become a hot topic nowadays. In this study, the increase of gibberellin (GA) content is one of the main factors promoting the seed germination of L. chinensis . Furthermore, to further explore the molecular mechanisms underlying seed germination regulation, RNA sequencing (RNA-seq) analysis of seeds at different developmental stages was carried out to explore the potential regulatory factors of seed hulls affecting the seed germination of L. chinensis . A total of 21,564, 21,010, and 31,795 differentially expressed genes (DEGs) were identified in “H_CK_0 vs . DH_CK_0”, “H_CK_2 vs . DH_CK_2”, and “H_CK_7 vs . DH_CK_7”, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were significantly enriched in plant hormone signal transduction, starch and sucrose metabolism, and mitogen-activated protein kinase (MAPK) signaling pathways. Within these pathways, we identified several candidate genes potentially involved in seed hull-mediated germination regulation, including those encoding α-amylase (AMY1), β-amylase (BAM1), α-xylosidase (XYL1), β-glucosidase (BGLU10/45), auxin-responsive protein (IAA18), and transcription factors (WRKY, AP2/ERF, ABI2, bZIP, and NAC). These results provide valuable genetic resources for studying the molecular mechanism of L. chinensis seed germination.