Assembly and comparative analysis of the complete mitochondrial genome of the endangered plant Fraxinus mandshurica

Assembly and comparative analysis of the complete mitochondrial genome of Viola philippica (Malpighiales, Violaceae)

Assembly, annotation, and comparative analysis of the first complete mitochondrial genome of Pennisetum sinese

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.

Characteristics, comparative genomics, and phylogenetic analysis of the chloroplast genome of Rosaplatyacantha

Background Rosa platyacantha is a rose species endemic to the high-altitude regions of Xinjiang in China. To date, no complete chloroplast genome has been reported for this species, limiting our understanding of its genomic characteristics and phylogenetic relationships within the genus Rosa. Methods This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome. Comparative genomics and phylogeny analyses were then conducted using this data alongside chloroplast genome data from other Rosa species. Results The chloroplast genome of R. platyacantha spans 157,133 bp, and it annotates 132 genes and has a total guanine cytosine (GC) content of 37.21%. Fifty-one simple sequence repeat (SSR) loci were identified, predominantly adenine/thymine (A/T)-type mononucleotide repeats. Codon usage preference analysis revealed a marked bias towards synonymous codons ending in adenine/uracil (A/U). Compared to closely related species, R. platyacantha exhibited higher nucleotide diversity (Pi) in non-coding regions and the large single copy (LSC) and small single copy (SSC) region. Potential adaptive hot spots were identified at ycf3-trnS -GCU (Pi = 0.29005), trnC-GCA, trnT-UGU, and trnV-UAC. Rose genus chloroplast genomes are generally conserved, with most species exhibiting identical inverted repeat regions a and b (IRa and IRb) lengths. However, only R. acicularis shows a 62 bp difference, and the associated fragment length of the duplicated gene ycf1 varies between species from 1,108 to 1,117 bp. Phylogeny analysis revealed that R. platyacantha did not cluster with the sympatric R. fedtschenkoana. This finding confirms their distant evolutionary relationship at the genome level, providing new insights into the evolutionary and dispersal pathways of Rosa species within the unique habitats of northwest China.

Comparative analysis of the complete mitochondrial and chloroplast genomes of Krascheninnikovia arborescens reveals its evolutionary features in Amaranthaceae.

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.

The first complete chloroplast genome of Calamus erectus (Arecaceae): Phylogenetic placement and divergence time estimation

The complete plastome of C. erectus is characterized, providing the first complete cp genome resource for C. erectus, and offering a foundation for further phylogenomic and conservation studies within Arecaceae.

Chromosome-level genome assembly and annotation of the endemic and endangered karst medicinal plant Corydalis saxicola

Corydalis saxicola , an endangered herbaceous plant belonging to the Papaveraceae family and used traditionally as folk medicine, is exclusively endemic to karst habitats. However, the lack of a reference genome limits the implementation of molecular techniques in its breeding, pharmacology and domestication. Here, we present a high-quality chromosome-level genome assembly of C. saxicola based on PacBio HiFi and Hi-C data. The assembled genome size is 240.94 Mb with a contig N50 of 29.21 Mb and BUSCO completeness of 97.71%. Approximately 93.26% of the assembled sequences could be anchored to eight pseudo-chromosomes. A total of 74.29 Mb repeat sequences were identified, which account for 32.33% of the genome. In addition, 24,203 protein-coding genes were identified with a BUSCO completeness of 97.89%. This high-quality genome assembly will serve as a valuable resource for understanding the ecology, genetics, and evolution of C. Saxicola and will help towards its cultivation.