Thrips are widely distributed insects with economic importance, but their evolutionary dynamics of the mitochondrial genome remain poorly understood. This study presented a computational mitogenomic analysis of six Thrips species obtained from a public repository. An analysis was performed to investigate patterns of genomic architecture and evolutionary variations. Mitochondrial genomes were analyzed using bioinformatic approaches, including annotation, syntenic comparison, gene content analysis, and SSR identification. Codon usage bias was measured using RSCU and CAI metrics, while skewness in nucleotide composition was studied using AT and GC skew analyses. Results suggest that there is generally a conservation of mitochondrial genome organization among the different species, but only limited rearrangements occur, and these are mainly associated with tRNA and non-coding sequences. The presence or absence of genes in Thrips was verified by re-annotation with MITOS2, followed by confirmation in the feature table in GenBank. SSR analysis showed few notable interspecific variability, where T. palmi and T. hawaiiensis seemed to have higher motif diversity and density, sort of. Codon usage patterns looked like they had a strong bias towards A/T-ending codons, and the CAI values suggested different levels of codon usage adaptation across species, using reference sets that were built from the mitochondrial protein-coding genes themselves. Also, we consistently observed positive AT-skew and negative GC-skew across all genomes, with more pronounced asymmetry in T. palmi and T. hawaiiensis. Overall, this work points to both conserved traits and lineage-specific features in Thrips mitochondrial genomes, giving some clues about their evolutionary dynamics while also broadening our understanding of insect mitochondrial genome evolution.

Biodiversity is undergoing an unprecedented global decline, and genetic diversity plays a fundamental role in ensuring species persistence. Miconia ulei, an endemic species from the eastern Atlantic Forest in Santa Catarina, southern Brazil, is rare and has few known populations. We investigated genetic diversity and population structure using microsatellite markers and assessed its conservation status following IUCN guidelines and by incorporating genetic parameters in the evaluation. Five extant populations were sampled across the species' known distribution, and twelve species-specific microsatellite markers were developed. Populations exhibited low to moderate levels of genetic diversity. Genetic differentiation among populations was generally low, although one population showed a distinct genetic structure. No isolation by distance was detected, suggesting that factors other than geographic distance may influence patterns of gene flow. Evidence of historical reductions in population size was detected in most populations. Together, these findings indicate that M. ulei has limited genetic variation and small, fragmented populations, increasing its vulnerability to future genetic loss. Our results support the need for conservation actions, including the formal inclusion of M. ulei in official Red Lists and the maintenance of habitat connectivity to promote long-term population persistence. As the first population genetic assessment of M. ulei, this study provides an important baseline for conservation planning and highlights the need for conservation genetic studies of other rare Atlantic Forest species.

Understanding how positive selection shapes molecular evolution at the protein level remains a major challenge, particularly in non-model species. Here, we integrated phylogenetic evidence from candidate genes evolving under lineage-specific positive selection with comparative structural and biophysical analyses to investigate patterns of molecular divergence in the Cereus fernambucensis-C. insularis clade, which occupies contrasting island and continental environments. Based on a previous branch-site analysis, five orthogroups were selected for downstream analyses. Orthologous protein structures were predicted and compared, variability hotspots were identified, pockets proximity were evaluated, and the stability effects of lineage-specific substitutions were estimated. Across orthogroups, global folds were largely conserved, whereas molecular divergence was primarily associated with localized structural variation in flexible loops and surface-exposed regions. Variability hotspots were significantly enriched near predicted cavities in several orthogroups, indicating that molecular diversification was concentrated in structurally permissive regions frequently associated with putative interaction surfaces. Stability analyses of reconstructed branch-specific substitutions revealed heterogeneous energetic effects, ranging from stabilizing to strongly destabilizing changes, while global protein architecture remained largely conserved. Together, these results suggest that evolutionary divergence in Cereus lineages is primarily associated with localized modifications of surface-accessible regions rather than large-scale structural innovation. More broadly, our findings demonstrate how integrating molecular evolutionary analyses with structural bioinformatics provides a robust framework for interpreting candidate adaptive genes in non-model organisms, while highlighting both the potential and limitations of structure-informed evolutionary inference.

Thiamine pyrophosphate (TPP) riboswitches are the only riboswitch class identified in eukaryotes. They therefore provide a unique model for reconstructing the evolution of RNA-based gene regulation across life's domains. We investigated the molecular evolution, structural diversification, and genomic-context reassignment of the TPP riboswitch across archaea, bacteria, cyanobacteria, fungi, algae, and land plants using phylogenetic reconstruction, covariance-model-guided sequence analysis, comparative secondary-structure analysis, genomic-context annotation, and covariation-based inference. Our analyses establish an early prokaryotic origin of the TPP riboswitch as a 5'- UTR-associated regulatory element. Archaea retain the most compact ancestral scaffold. The transition to bacteria is characterized by extensive compensatory evolution. Bacteria preserve the canonical fold but exhibit the strongest covariation. Within bacteria, cyanobacteria exhibit a reduced architecture while retaining a conserved ligand-binding core, indicating an early reform event. Methylogaea oryzae branches within the cyanobacterial clade, identifying horizontal acquisition of a thiC-TPP riboswitch cassette. The transition into the green lineage is marked by the repositioning of the riboswitch from the ancestral 5'-UTR to the 3'-UTR. This architecture is found in the charophyte Closterium, indicating that the plant-type 3'-UTR state predates land plants. Fungi retain mainly 5'-UTR organization but also contain a distinct 3'-UTR NMT1/thi5-associated clade, defining a second eukaryotic regulatory configuration derived through horizontal transfer from early green lineages. These results suggest a continuous evolutionary trajectory of the TPP riboswitch from an ancestral prokaryotic 5'-UTR regulator to the green-lineage repositioning of the 3'-UTR, to fungal functional reassignment, and the secondary emergence of an alternative 3'-UTR state.

The giant freshwater prawn (Macrobrachium rosenbergii) is an economically important aquaculture species in Southeast Asia. Despite its significance, complete mitochondrial genome data from Malaysian populations remain scarce, limiting insights into genetic variation and phylogenetic relationships. This study aimed to sequence and characterized the complete mitochondrial genome of M. rosenbergii from Perak, Malaysia, and to assess its phylogenetic position relative to other regional populations. Genomic DNA was extracted and sequenced using next-generation sequencing. The mitochondrial genome was assembled, annotated, and its nucleotide composition and gene arrangement were analyzed. Phylogenetic analysis was performed using Maximum Likelihood method based on the 13 mitochondrial protein-coding genes of representative Palaemonidae species. The circular mitochondrial genome of M. rosenbergii was 15,332 bp in length, comprised by 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. Most genes were encoded on the heavy strand, with several located on the light strand, consistent with other crustaceans. The nucleotide composition exhibited an A + T bias. Phylogenetic analysis placed the Perak specimen in a strongly supported M. rosenbergii clade, confirming its identity and monophyly. Minor sequence divergence from previously reported mitogenomes was observed; however, given that this study is based on a single individual, these differences should be interpreted cautiously and do not allow inference of population-level differentiation. This mitogenome represents a valuable genetic resource for M. rosenbergii, supporting applications in aquaculture breeding programs, population genetics, and functional genomics. It also provides a reference for transcriptomic studies, enabling mitochondrial gene expression profiling and functional annotation.

Reindeer and caribou (Rangifer tarandus) occupy a vast northern range spanning Eurasia and North America, where understanding population structure is essential for conservation and management. However, comparative analyses across this circumpolar distribution are hindered by systematic allele-size offsets introduced by differences in genotyping platforms, laboratory protocols, and allele-calling procedures. Here, we applied a locus-specific mode-shift harmonisation procedure to integrate legacy microsatellite datasets from Alaska, Canada, and Russia. The final harmonised dataset included 1544 individuals from 42 populations genotyped at nine shared microsatellite loci. The procedure used dataset- and locus-specific modal allele differences to reduce systematic allele-size offsets while preserving within-dataset allele-frequency structure and heterozygosity status. To evaluate robustness, we compared diversity statistics before and after harmonisation, tested alternative reference alignments, and performed sensitivity analyses excluding populations with small sample sizes and loci with large modal allele shifts. We also assessed a pooled small-sample dataset in which sparsely represented populations were grouped within biologically meaningful regional or ecological units. Diversity estimates remained unchanged after harmonisation, as expected for constant locus-specific allele-size shifts, and broad interregional structure was retained across reference alignments and sensitivity filters. After harmonisation, PCA, DAPC, Nei-distance analysis, pairwise FST, and exploratory ADMIXTURE analyses consistently supported broad differentiation among Russian, Canadian, and Alaskan populations, with Alaskan populations occupying an intermediate position between Canadian and Russian groups. These results are consistent with historical connectivity across the Beringian region. Our study shows that reference-based mode-shift harmonisation can provide a practical framework for improving the comparability of heterogeneous microsatellite datasets when shared reference samples are unavailable, while remaining complementary to direct cross-laboratory calibration approaches.

Aster indicus L. is a medicinally important species with therapeutic value from its entire plant. However, genomic research, particularly concerning the mitochondrial genome, remains sparse. This study sequenced the mitochondrial genome of A. indicus, revealing a length of 224,973 bp with an A/T content of 54.5%. The mitogenome encodes 54 protein-coding genes, 21 tRNAs, and 3 rRNAs. Identification of genomic features included 20 simple sequence repeats, 143 dispersed repeats, 15 tandem repeats, and 10 segments derived from chloroplast DNA. Analysis of codon usage indicated a preference for A/U-terminating codons. Comparative synteny analysis with 11 species in Asteraceae showed a 94.77% sequence identity with Aster batangensis Bureau & Franch., accompanied by extensive genomic rearrangements. Most protein-coding genes exhibited evidence of purifying selection, with the exception of nad1. Phylogenetically, A. indicus is closest to A. batangensis; as expected, the genus Aster is genetically closer to the genus Erigeron, in agreement with their placement in tribe Astereae, but distant from Arctium and Carthamus, that belongs to tribe Cardueae. This study delineates the structural characteristics and sequence features of the A. indicus mitochondrial genome and enriches the genetic resources of the genus Aster and Asteraceae family, and establishing a foundational basis for future functional, evolutionary, and pharmacological investigations of this therapeutically significant species.

B chromosomes are supernumerary, dispensable chromosomes present in many eukaryotic genomes and are often considered as genomic parasites. However, their distribution and phenotypic effects in natural populations remain incompletely understood, particularly at local scales. Here, we surveyed 14 natural populations of the plant Prospero autumnale (L.) Speta (Asparagaceae) in southern Iberia and detected B chromosomes in only four of them. We quantified vegetative and reproductive traits and found that, at the population level, B-carrying populations exhibited significantly higher reproductive output, including increased seed number and fertility, than populations lacking Bs. However, we did not find significant differences between individuals with and without B chromosomes in populations that carry Bs. In contrast, no consistent differences emerged for vegetative traits. These findings suggest that B chromosomes tend to persist in populations with greater reproductive performance, consistent with their maintenance in benign environments where hosts can better tolerate their parasitic effects. Overall, our study sheds light on the ecological factors influencing B chromosome distribution and highlights the association between genomic parasites and host reproductive success.

To improve our understanding of the taxonomy and evolutionary relationships of Naticidae within the framework of Littorinimorpha, the complete mitochondrial genome of the Eunaticina papilla, was sequenced and analyzed using next generation sequencing (GenBank accession no. OR575181.1). The mitogenome is 16,415 bp in length and is comprised by the typical set of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs), with a pronounced AT bias. Most tRNAs exhibit the typical cloverleaf secondary structure, whereas trnS2 and trnI lack the dihydrouridine (DHU) arm. Comparative analysis with ancestral gastropod gene order revealed extensive gene rearrangements in E. papilla, involving three gene clusters and encompassing 15 tRNA genes and 8 PCGs. Among these, inversion events were identified as the predominant rearrangement pattern, often accompanied by translocations. Phylogenetic analyses strongly support the monophyly of Littorinimorpha. E. papilla is placed in a well supported Naticidae clade and forms a sister group relationship with species of Polinices and Mammilla. Overall, this study uncovers inversion-driven mitochondrial gene rearrangements as a major evolutionary force in Littorinimorpha, expanding genomic resources for Naticidae and refining phylogenetic relationships within this diverse clade.

The genus Zehneria (Cucurbitaceae) presents significant taxonomic challenges due to morphological similarities among species and a lack of resolution in molecular studies. In this study, we sequenced and assembled the chloroplast genomes of seven African Zehneria species collected from Kenya, complementing a previously published accession (Zehneria sp. MZ427944.1), to establish a comprehensive plastome-based framework for the genus. The plastomes ranged from 157,150 to 157,365 bp and exhibited a conserved quadripartite structure, with 130-132 annotated genes, including 86-87 protein-coding genes, 36-37 tRNAs, and 8 rRNAs. Structural variation, particularly in non-coding regions and inverted repeat boundaries, was observed, with eight hypervariable loci providing potential targets for molecular marker development. Simple sequence repeat (SSR) analysis revealed a predominance of A/T mononucleotides across species. Codon usage analysis revealed a strong AT-bias across all species, with codons ending in A or U accounting for 72.2% of synonymous codon preferences. Selective pressure analysis identified eight protein-coding genes with Ka/Ks ratios exceeding 1.0, including psaJ and rps8, proposed as candidate molecular barcodes pending further validation. Phylogenomic analysis of 79 protein-coding genes strongly supported the monophyly of Zehneria (ML bootstrap = 96-100%; PP = 1.0), with one node showing slightly reduced support (BS = 96%), and enhanced resolution of interspecific relationships compared to prior studies using fewer loci. This work offers novel insights into genomic diversity and evolutionary history of sampled Zehneria species, providing a critical molecular resource for future taxonomic and phylogenetic studies within Cucurbitaceae. Broader taxon sampling, particularly from Asian lineages, will be necessary to fully resolve interspecific relationships across the genus.

The order Scorpiones represents a lineage of arachnids that has exhibited considerable evolutionary success, encompassing over 1700 recognized species. However, the mitogenomes within this group have received limited attention. To increase the taxonomic sampling of species available for studies based on mitogenomes, we reconstructed the complete mitogenome of Androctonus crassicauda Olivier, 1807 (Scorpiones, Buthidae). The specimen was obtained from insect markets in Nanjing, Jiangsu, China. The mitogenome is a circular molecule with a length of 14,834 bp. The proportion of adenine and thymine (A + T) was 67.3%. The Ka/Ks ratios for all protein-coding genes (PCGs) were determined to be less than 1, implying that purifying selection likely plays a dominant role in shaping the evolutionary patterns of these genes. The frequency of codons ending in A/U was significantly higher than that of codons ending in C/G, reflecting the strong AT bias of the third codon position. Phylogenetic analyses based on PCGs corroborated previously recognized taxonomic relationships in family Buthidae. These findings enhance our understanding of the evolution of Buthidae mitogenomes.

Glycogen serves as the principal energy source for gonadal development in marine bivalves, such as oysters. Glycogen phosphorylase is the rate-limiting enzyme of glycogenolysis by catalyzing the first step of glycogen breakdown. In this study, two different glycogen phosphorylase genes were identified in the Kumamoto oyster (Crassostrea sikamea) genome, including the previously reported GPH and an unknown PYG. C. sikamea GPH and PYG share high mRNA and protein sequence identities, but they have distinct gene structures and show significant sequence variations in their adenine loops. Interestingly, contrary to the ubiquitous expression of GPH in various adult tissues and development stages, PYG is specifically expressed in oyster male gonads. Transcriptome and quantitative real-time PCR (qRT-PCR) analyses reveal differential expression levels of other glycogen metabolism enzymes between female and male gonads, including glycogen phosphorylase (GPH), glycogen debranching enzyme (AGL), glycogen synthase (GYS), and glycogen branching enzyme (GBE). Yeast one-hybrid assays suggest the sex-determining gene DMRT1 could directly bind to oyster PYG promoters. Further investigations demonstrate GPH and PYG are two conserved glycogen phosphorylases in bivalve genomes. The bivalve PYG seems to originate from the retroposition of GPH, making it the first retrogene identified in molluscs, to the best of our knowledge. In conclusion, these results characterized the second and testis-specific glycogen phosphorylase in the oyster.

Ceratonia siliqua is a nutritionally and economically important Mediterranean tree species whose natural stands in Morocco are increasingly threatened by habitat degradation and genetic erosion. However, the spatial organisation of genetic diversity across its natural range in Morocco remains insufficiently resolved. To support conservation and germplasm management initiatives, interpopulation genetic differentiation among Moroccan carobs populations was assessed using a pooled DNA sample and SSR markers analysed through three genotyping workflows: high-resolution melting (HRM), conventional PCR, and capillary electrophoresis. Genetic relationships among populations were evaluated using Neighbour-Joining (NJ) analysis, principal component analysis (PCA), and K-means clustering. Among the evaluated approaches, HRM provided the highest discriminatory resolution and generated the most informative polymorphism profiles across loci. All analytical frameworks consistently revealed substantial interpopulation differentiation and broad geographic grouping patterns. Southern populations formed genetically cohesive groups, whereas northern and central populations displayed more complex patterns of genetic similarity. K-means clustering supported the presence of four major population groups, while PCA identified a subset of highly discriminative SSR loci contributing to regional differentiation. Overall, the results reveal a genetically diverse and spatially differentiated Moroccan carob germplasm and demonstrate that SSR-HRM is a robust and cost-effective approach for population-level genetic screening. These findings provide useful genetic resources for future conservation, germplasm management, and breeding programmes in Moroccan carob.

Transposable elements drive plant genome size variation and structural diversification, but their recent dynamics remain poorly characterized in medicinal plants. We analyzed 95 medicinal plant genomes to evaluate repeatome divergence, recent transposable element composition and long terminal repeat retrotransposon dynamics. Genome-wide transposable element proportion varied substantially among species and was strongly positively associated with genome size, indicating that repeat accumulation is a major axis of genome-size divergence. Recent transposable element fractions, operationally defined by sequence identity ≥ 85%, were dominated by long terminal repeat retrotransposons in most genomes. Higher recent transposable element fractions were negatively associated with Shannon diversity and Pielou's evenness, suggesting compositional concentration rather than balanced expansion across major classes. Phylogenetically informed Bayesian models revealed class-specific differences in the magnitude and uncertainty of estimated recent transposable element proportions across taxonomic orders. Insertion-time analyses showed heterogeneous recent accumulation patterns, whereas phylogenetic reconstruction of intact long terminal repeat retrotransposons with paired long terminal repeat identity ≥ 95% revealed contrasting lineage composition between Copia and Gypsy. Copia elements were concentrated mainly in two dominant lineages, whereas Gypsy elements were distributed across a broader set of lineages. An exploratory 2-kb gene-centered analysis of predicted biosynthetic gene clusters showed that 62.5% of 31,162 unique genes had at least one proximal long terminal repeat retrotransposon annotation, usually together with other transposable element classes. These results indicate that medicinal plant repeatome evolution is associated with genome-wide transposable element burden, recent compositional concentration and lineage-level long terminal repeat retrotransposon dynamics.

Sex-ratio distorters (SRDs) are heritable elements that bias offspring sex-ratios to enhance their transmission. In the terrestrial isopod Armadillidium vulgare, feminization of genetic males can occur through vertical transmission of the sex-ratio distorter known as the f-element, as well as through infection by Wolbachia, a maternally inherited bacterial endosymbiont that can alter host reproduction. We investigated whether associations between sex-ratio distorters and mitochondrial haplotypes in U.S. populations differ from those reported in European populations. To address this, we sampled A. vulgare from 12 U.S. states and screened individuals for Wolbachia infection, the presence of the f-element, and mitochondrial COI haplotypes. We found that Wolbachia exhibits a heterogeneous distribution across populations and haplotypes, in contrast to the stronger associations observed in European populations. The f-element occurred at lower overall frequencies but showed a strong association with mitochondrial haplotype VI. These results indicate that patterns associated with SRDs differ from those observed in Europe and are consistent with multiple introductions and population mixing shaping these distributions in U.S. populations.