A population-scale chloroplast genome dataset for the endangered orchids Cypripedium taibaiense and C. flavum.

The Complete Chloroplast Genome of Ficus gasparriniana var. laceratifolia Reveals Discordance Between Morphology-Based Classification and Plastid Phylogeny

Background/Objectives: Ficus gasparriniana var. laceratifolia (H. Lév. & Vaniot) Corner is treated as a variety of F. gasparriniana and placed in Ficus subg. Ficus on morphological grounds, but complete plastome evidence for its plastid phylogenetic placement has been lacking. We assembled and analyzed its chloroplast genome to evaluate this morphology-based placement using plastid genomic evidence and to expand genomic resources for the genus. Methods: The plastome was assembled from paired-end reads using GetOrganelle and subsequently annotated. We characterized its genome architecture, simple sequence repeats (SSRs), codon-usage bias, inverted repeat (IR) junctions, and nucleotide diversity after standardizing sequence start positions and small single-copy (SSC) region orientation. Plastid phylogenetic relationships were inferred from four single-IR datasets: whole-plastome, coding, non-coding, and partitioned. Results: The 160,476-bp plastome exhibited the typical quadripartite structure and contained 110 unique genes. Its repeat composition and preference for A/U-ending codons were consistent with an AT-rich plastome, and 61 SSRs and five candidate variable regions represented potential marker resources for future Ficus studies. In all four phylogenetic datasets, F. gasparriniana var. laceratifolia was consistently grouped with F. pumila with maximum ultrafast bootstrap support (UFBoot = 100), conflicting with its morphology-based classification. Approximately unbiased (AU) tests rejected the sampled morphology-based constraint in every dataset, indicating that this morphology–plastid discordance was robust to dataset choice. Conclusions: This plastome provides a valuable genomic resource and reveals robust discordance between morphology-based classification and plastid phylogenetic placement. These findings provide a foundation for future nuclear-genomic and population-level tests of the alternative evolutionary scenarios underlying this discordance.

Complete Mitochondrial Genome of Eurostus validus (Hemiptera: Tessaratomidae): Genomic Features and Comparative Analysis

The genus Eurostus is distributed across East and Southeast Asia, inhabiting forest and agricultural ecosystems and participating in plant-insect interactions. However, the absence of a complete mitochondrial genome has limited understanding of its evolution and phylogeny. Here, we report the first complete mitogenome of Eurostus validus. The circular genome is 15,948 bp and contains the typical 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and a control region. Comparative analyses with other tessaratomid mitogenomes revealed strong AT bias, consistent strand asymmetry, and conserved patterns of amino acid and codon usage. Among Pentatomoidea, atp8 showed the highest nucleotide diversity, whereas cox1 was the most conserved. ENC-plot and neutrality analyses indicated that both mutation pressure and natural selection shape codon usage bias, with natural selection playing a dominant role. Phylogenetic analyses based on the PCG12RNA dataset using Bayesian inference and maximum likelihood strongly supported family monophyly. The topology recovered Dinidoridae and Tessaratomidae as sister groups, with well-resolved relationships within Tessaratomidae. These results provide a valuable genomic resource and improve understanding of Pentatomoidea evolution.

Mitochondrial Genome Assemblies of Four “Bee-Assassin” (Hemiptera: Reduviidae: Apiomerus) Recovered Using Shallow Whole-Genome sequencing

Apiomerus (“bee-assassin” assassin bugs) is a Neotropical genus of Reduviidae with ecological importance as a group of predatory insects and notable morphological diversity, yet mitochondrial genomic resources have remained unavailable for the genus. We generated low-coverage whole-genome sequencing data from four vouchered specimens collected in Colombia and reconstructed mitochondrial genomes for Apiomerus sp., A. ochropterus , A. luctuosus , and A. nitidicollis . Quality-filtered reads were assembled using an organelle-specific GetOrganelle workflow, and the resulting assembly graphs and candidate sequences were evaluated against initial SPAdes/BLASTN-based reconstructions. GetOrganelle recovered complete circular mitochondrial genomes for Apiomerus sp., A. ochropterus , and A. nitidicollis , whereas A. luctuosus was represented by a single gap-free, non-circularized mitochondrial scaffold in which the control region was not completely recovered. The selected assemblies ranged from 14,943 to 19,405 bp and were strongly AT-rich. Annotation and manual curation recovered the complete complement of 13 protein-coding genes, 22 tRNA genes, and two rRNA genes in all four taxa. Comparative analysis showed complete conservation of mitochondrial gene content, gene order, and transcriptional orientation, with no evidence of gene rearrangements among the sampled species. Phylogenetic analysis based on concatenated mitochondrial protein-coding genes recovered the four Apiomerus taxa as a monophyletic group, with A. ochropterus and Apiomerus sp. forming a sister pair, A. nitidicollis sister to that clade, and A. luctuosus occupying the basal position among the sampled taxa. These assemblies constitute the first mitochondrial genomic resources for Apiomerus and expand the representation of Apiomerini for comparative mitogenomic, taxonomic, and phylogenetic studies.

Retrieving complete plastid genomes from historical xylaria: a hybridization capture approach for Fraxinus phylogenetics and wood authentication

Plastid genome evolution and phylogenomics with broad taxon sampling: insights into intrafamilial classification of Hamamelidaceae

Hamamelidaceae, within the order Saxifragales, comprises 27 genera and approximately 120 species. The family has a pantropical and temperate distribution across the Americas, Asia, Africa, and Australia. Previous molecular investigations, constrained by limited taxon sampling and inadequate genetic markers, supported a five-subfamily classification system. However, these studies predominantly focused on Asian taxa, resulting in poor resolution of the evolutionary relationships among American, African, and Australian genera. To address these sampling gaps, we employed near-complete generic sampling (26 of 27 genera) to investigate plastome architecture, structural variation, and phylogenetic relationships. We newly sequenced and assembled 15 plastid genomes representing geographically and taxonomically underrepresented genera and analyzed them alongside 59 publicly available plastomes retrieved from GenBank. Plastid genomes exhibited conserved quadripartite architecture with sizes ranging from 158, 076 bp to 160, 814 bp, minimal structural variation, consistent GC content (37.7-38.2%), and identical gene order. Inverted repeat (IR) regions had limited size variation (26, 211-26, 429 bp). Simple sequence repeat (SSR) distribution (2, 219 loci) showed no clear correlation with the genus-level phylogenetic relationships. We identified ten hypervariable regions, including coding sequences ( accD, ycf1, clpP, ndhF , and rpl22 ) and intergenic spacers ( rpl33-rps18 , the trnG-UCC intron, trnH-GUG-psbA, accD-psaI , and petA-psbJ ), as promising candidate regions for future applications in species delimitation and phylogenetic studies. Phylogenetic analyses revealed largely congruent topologies across datasets and methods, providing improved resolution and strong support for most subfamilial and tribal relationships compared with previous studies. This study highlights the utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae. The genome architecture reflects the high conservation of plastid genomes, while the identified mutation hotspots represent potential resources for future taxonomic and phylogenetic studies. Our results support the existing subfamily classification while improving geographical coverage and generic representation, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.

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

Fraxinus mandshurica, a deciduous tree species in the Oleaceae family, is valued for its high-quality timber, medicinal properties, and ecological functions. It is classified as a second-class national protected wild plant in China. However, the complete sequence information of its mitochondrial genome has yet to be reported, and systematic studies on its genetic background and phylogenetic evolution remain limited. The mitochondrial genome of F. mandshurica was assembled into a linear structure, measuring 645,536 bp and 44.40% GC content. Annotation of the mitochondrial genome yielded 77 genes, including 44 protein-coding genes, 30 tRNAs, and 3 rRNAs. A total of 585 dispersed repeats, 184 simple repeats, and 21 tandem repeats were detected, and 476 RNA editing sites with C-to-U type changes were predicted. Codon usage analysis revealed a bias toward codons terminating with A/T. Furthermore, homology analysis revealed 36 chloroplast-derived fragments, spanning 55,673 bp and accounting for 8.62% of the mitochondrial genome. Collinearity analysis exposed considerable genomic rearrangements between F. mandshurica and its close relatives, reflecting structural divergence across evolution. Positive selection was observed for 14 genes, in which Ka/Ks ratios exceeded 1 in at least one pairwise comparison. Analysis of nucleotide polymorphisms showed differences in every gene, where nad4 displayed the greatest variation. Phylogenetic analyses suggested that F. mandshurica and F. excelsior are closely related. This study presents an integrated analysis of the F. mandshurica mitochondrial genome, revealing its unique structural and evolutionary characteristics. Moreover, this mitochondrial genome was compared with seven published Oleaceae mitochondrial genomes to investigate genome dynamics across the family. Our findings enrich the mitochondrial genome resources for Oleaceae species and highlight the potential of mitochondrial genes to elucidate plant evolutionary history.