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
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.
Solanaceae is an important crop plant family and its plastomes have been extensively studied to understand evolution and breeding. Capsicum (chili peppers) includes five domesticated species and worldwide are important economic resources. Lycianthes is the third most species rich genus within the family. Capsicum and Lycianthes are closely related genera and form the Capsiceae. While plastomes are available in public databases for some species of Capsicum, no plastomes for Lycianthes have been published. We anticipate that the plastomes of Lycianthes and Capsicum will be similar. In addition, point sequence variation will generate robust phylogenetic hypotheses. We newly sequenced, assembled and annotated the plastomes of six species of Lycianthes to investigate their genomic characteristics. Also, we carried out comparative and phylogenetic analysis within Capsiceae. Lycianthes presented the typical circular quadripartite structure and organization. Plastomes range from 156,108 to 156,721 bp. All contained 133 genes, divided into 84 Coding DNA Sequence, four pseudogenes, 37 tRNAs and eight rRNAs. Plastomes of Capsiceae were highly conserved, were similar in size and showed the same structure and organization. Comparative analyses revealed that 17 genes made the Capsicum plastome longer than the plastome of Lycianthes. However, the variable regions did not match with the length of the genes. Based on plastome sequences, phylogeny recovered the monophyly of Capsiceae. Also, Capsicum and Lycianthes formed monophyletic genera and had a sister group relationship with each other. The plastome of Lycianthes and Capsicum were similar. Phylogenomics supported the monophyly of both genera and a sister group relationship.
Housekeeping genes (HKGs) and tissue-specific genes (TSGs) play essential roles in constitutive cellular maintenance and tissue specialization. However, their transcriptome-wide characterization remains largely unexplored in makhana (Euryale ferox Salisb.), an economically and nutritionally important aquatic crop. In this study, a comprehensive transcriptomic analysis identified 652 HKGs and 5,378 TSGs across diverse tissues and developmental stages of Euryale ferox Salisb. Functional enrichment analyses revealed that HKGs were predominantly associated with conserved cellular processes, including ATP metabolism, ribosome function, oxidative phosphorylation, RNA processing, and proteostasis, whereas TSGs were enriched in developmental regulation, signaling pathways, secondary metabolism, and stress-responsive functions. Protein-protein interaction network analysis further showed that HKG-associated proteins occupied highly interconnected central positions, while TSG-associated proteins formed more specialized peripheral networks. Comparative analyses indicated that many traditional internal reference genes lacked stable constitutive expression across the analyzed biological conditions. To address this limitation, an RSI-based prioritization framework combined with biological functional curation enabled the computational identification of robust candidate reference genes for transcript normalization. Taken together, this study provides the first comprehensive systems-level characterization of HKGs and TSGs in Euryale ferox Salisb. and establishes a valuable computational resource for transcript normalization, functional genomics, and future experimental validation.
Pectate lyases (PELs) are important enzymes involved in the regulation of plant cell wall structure and composition and play essential roles in plant growth and development. However, the characteristics and potential functions of the PEL gene family in soybean remain largely unclear. In this study, a total of 38 GmPEL genes were identified from the soybean genome through genome-wide analysis and classified into five evolutionary groups. Evolutionary analyses indicated that segmental duplication was the major driving force underlying the expansion of the GmPEL family, which has undergone strong purifying selection during evolution. Cis-acting element and expression profile analyses suggested that GmPEL genes are widely involved in plant growth, development and stress responses. Notably, members of Group II exhibited relatively high expression levels in floral tissues and showed significant downregulation in the flower buds of cytoplasmic male sterility (CMS) lines, while their expression levels were responsive to high-temperature (HT) stress during flowering. Subcellular localization analysis further demonstrated that GmPEL3, GmPEL12, GmPEL23, and GmPEL34 are localized to the endoplasmic reticulum. These results suggest that Group II genes may participate in flower development, fertility regulation and HT stress responses in soybean. Overall, this study provides a comprehensive characterization of the soybean PEL gene family and offers candidate genes for further investigation of reproductive development and stress tolerance in soybean.
Flavonoid 3-hydroxylase (F3H) is a key enzyme in the flavonoid biosynthetic pathway; however, its functional roles in maize responses to abiotic stress remain poorly understood. In this study, 14 maize F3H proteins (ZmF3Hs) were identified and characterized through bioinformatics analyses, expression profiling, and functional validation. The ZmF3H genes exhibited structural and physicochemical diversity and were unevenly distributed across seven maize chromosomes. Phylogenetic and synteny analyses classified the ZmF3Hs into four subfamilies and revealed strong evolutionary conservation with homologs from rice, wheat, and sorghum. Conserved motif and promoter analyses suggested functional divergence and multilayered regulatory control. Subcellular localization prediction indicated that ZmF3H6 is localized in the cytoplasm, which was further confirmed by transient expression assays in Nicotiana benthamiana. Expression profiling demonstrated that ZmF3Hs are responsive to multiple abiotic stresses, including cold, heat, and waterlogging. Functional analysis using virus-induced gene silencing revealed that suppression of ZmF3H6 significantly reduced flavonol accumulation and antioxidant enzyme activities while increasing malondialdehyde (MDA) levels under both normal and stress conditions. These findings provide new insights into the biological functions of ZmF3Hs and identify ZmF3H6 as a key regulator of flavonoid biosynthesis and abiotic stress tolerance, offering a promising target for improving stress resilience and flavonoid-mediated defense mechanisms in maize.
Longfin snake eel, Pisodonophis cancrivorus (Anguilliformes: Ophichthidae), is a typical snake eel widely distributed across brackish and marine waters of the Indo-Pacific oceans. As sensitivity to environmental change, it has become a potential bio-indicator for assessing habitat health in tropical coastal ecosystems, and plays a significant ecological role in nutrient cycling and benthic community dynamics. However, to our knowledge, no related genomic studies of P. cancrivorus have been reported until now. In this study, the preliminary genome information of P. cancrivorus was derived by using a whole-genome survey method. The genome size was estimated at 2.01 Gb, with the heterozygosity, repetitive sequence ratio and GC content of 1.35
The Baikal seal (Pusa sibirica) and Saimaa ringed seal (Pusa hispida saimensis) are phocid species inhabiting freshwater regions. Unlike their marine relatives, these freshwater Pusa seals face distinct environmental challenges, particularly osmoregulation, making marine-to-freshwater habitat transitions an excellent model for investigating the molecular basis of adaptive evolution. In this study, we performed comprehensive comparative genomic analyses across 14 pinniped species to elucidate the molecular mechanisms underlying habitat transitions. Phylogenomic analysis placed the grey seal as a sister clade to the common ancestor of Baikal seal and Saimaa ringed seal, and Pusa and Halichoerus as a sister clade of the harbor seal. We identified lineage-specific adaptive changes in genes involved in osmoregulation, wound healing, and circadian rhythm-including ACE2, ALMS1, F12, SERPING1, and PER3-that are critical for freshwater Pusa seals to thrive in environments with reduced salinity and distinct ecological pressures. Additionally, we discovered InDel variants in conserved non-coding elements (CNEs) that may influence the expression of osmoregulatory genes, offering new insights into the regulatory mechanisms underpinning freshwater adaptation. Collectively, this study provides a foundational framework for understanding the molecular basis of freshwater adaptation in pinnipeds, and the candidate genes and regulatory elements identified here may serve as valuable targets for future research into osmoregulation and wound healing across vertebrates, including humans.
The diversity of Theretra Hübner, 1819, a genus from the mid-hill regions of Himachal Pradesh has not been documented in past. This study presents the first comprehensive survey of Theretra species from various localities within this region. The total of five species has been recorded from this area viz., Theretra nessus, T. alecto, T. clotho, T. oldenlandiae, and T. lycetus. The detailed morphological descriptions and illustrations of male genitalia for each species are provided, with emphasis on genitalic structures supporting accurate species identification. Diagnostic features at the genus level are also elaborated. To authenticate the morphological identification, molecular analysis using mitochondrial cytochrome oxidase I (COI) gene sequences has been carried out. The results reveal significant interspecific variation in genital morphology among the five species studied, highlighting the taxonomic relevance of genitalic characters in genus Theretra.
The partial sequence of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been analyzed in representatives of the genera Oreoleuciscus, Tribolodon, and Rhynchocypris, using Phoxinus phoxinus as an outgroup. The genus Rhynchocypris includes only freshwater fish (which is typical for cyprinids), while representatives of the genera Tribolodon and Oreoleuciscus have colonized the sea and water bodies of the arid zone (including brackish ones), respectively. The data we obtained suggest that during the colonization of these waters and the formation of these two genera, evolution accelerated, but subsequently, at the stage of adaptive radiation of all three genera, their evolutionary rates no longer differed.
Potentilla sensu lato, a taxonomically complex genus within the Rosaceae, comprises approximately 300 taxa worldwide. Thirteen taxa, each restricted to limited localities, are currently recognized as endemic to the Mongolian flora. Therefore, the conservation of Potentilla faces significant challenges due to habitat loss caused by climate change and overharvesting. In this study, we explore the phylogenetic relationships and local evolutionary patterns of five endemic Potentilla species in Mongolia based on their complete chloroplast genomes. We utilized high-throughput sequencing of complete chloroplast genomes and conducted comparative analyses. The complete chloroplast genomes ranged from 156,273 to 156,395 bp long and exhibited a typical quadripartite structure. Genome annotation revealed 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Two intergenic regions (ndhF–rpl32 and rpl32–trnL) in the SSC region showed markedly high diversity among chloroplast genomes. Analysis of selection signatures identified two genes (rpoC1 and ycf1) under positive selection. These genes may play important roles in the adaptation of these species to specific geographical environments. Phylogenetic analysis placed all five newly sequenced species within the Argentea clade, and divergence time estimation indicated that diversification within this clade occurred from the late Miocene to the Pleistocene. This study provides valuable genomic resources for endemic Potentilla species in Mongolia, offers insights into their evolutionary history, and lays a foundation for future phylogenetic research and molecular marker development. Furthermore, this study fills a geographic gap in chloroplast genomes sampling of Potentilla in Central Asia.
Worldwide, the pig industry suffers financial losses due to the extremely contagious disease caused by the classical swine fever virus (CSFV). However, comprehensive and global genotyping information for CSFV remains scarce. A total of 1,053 full length E2 sequences of CSFV from the NCBI database were used in this study. According to phylogenetic analysis, the strains were grouped into dominant genetic subgroups. The positive selection pressures on the CSFV E2 envelope protein genes were also evaluated and a site-by-site examination of the dN/dS ratio was conducted to pinpoint certain codons that diversify under positive selection. Phylogenomic analyses using maximum likelihood (ML) and Bayesian inference (BI) confirmed that the 1,053 strains clustered within the previously defined five subgenotypes (1.1, 1.2, 2.1, 2.3 and 3.4). One positively selected site was identified at amino acid residue position 71. Bayesian coalescent analysis estimated an evolutionary rate of 1.364 × 10⁻³ substitutions per site per year (95
Simulium asakoae is a widespread species of black fly in Southeast Asia and a potential vector of parasites of medical and veterinary importance. Despite its broad distribution and diverse habitats, population genetic information remains limited. We investigated the genetic diversity, population structure, and demographic history of S. asakoae in Laos and examined its genetic relationships with populations from other Southeast Asian countries, using mitochondrial cytochrome c oxidase subunit I (COI) sequences. A total of 369 COI sequences (241 generated in the present study and 128 retrieved from GenBank) were analyzed. Of these, 284 sequences (241 from this study and 43 from GenBank) originated from nine locations across five provinces in Laos. Among the Laotian specimens, 51 haplotypes were identified, showing high haplotype diversity (Hd = 0.9063) and moderate nucleotide diversity (π = 0.0080). Intraspecific genetic divergence among Lao populations ranged from 0 to 2.49
The Criollo Argentino horse is a national symbol and a heritage breed that represents both cultural identity and a key component of traditional production systems in Argentina. This study aimed to assess the genetic differentiation of the Criollo Argentino relative to other horse breeds and to infer potential factors shaping its diversity through the genomic analysis of 24 representative animals. Samples were genotyped using a medium-density SNP array containing 65,157 markers, and genetic diversity analyses were conducted across autosomal SNP sets filtered under different criteria. Contemporary effective population size was estimated using both linkage disequilibrium from SNP data (Ne = 155.6) and pedigree analysis (fe = 157.7), showing remarkable consistency between genomic and genealogical approaches. Measures of expected heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium showed that Criollo Argentino horses retain moderate to high levels of genetic variability. Results further revealed that the Criollo Argentino is a genetically well-defined population with high within-individual diversity and clear differentiation from other breeds. In addition, the Criollo Argentino population was compared with eight other horse breeds to evaluate genetic distance and population structure. Estimates of genetic distance, population structure, and fixation index values were consistent with the documented history and development of the breed, while PCA and Bayesian clustering analyses supported a shared origin between the Criollo Argentino and the Peruvian Paso, both derived from Iberian horses introduced to the Americas during colonization. Overall, this work provides genomic evidence that strengthens the historical and biological characterization of the Criollo Argentino and supports informed decision-making for breeding, management, genetic improvement, and conservation programs for the breed.
Transposable elements (TEs) frequently generate incomplete derivative copies during transposition. The relative abundance of these variants is important in shaping the genomic landscape, but how these variants interact and compete within genomes remains poorly understood. To examine potential evolutionary conflicts among TE variants, we compared the replication behaviors of the full-length P element (FP) and one of its internally-deleted derivatives, the KP element, in Drosophila under three experimental conditions. KP elements were introduced into chromosomes at significantly higher frequencies than FP elements from a plasmid vector in both D. melanogaster and D. simulans. When both variants coexisted in D. simulans, KP elements also transposed between chromosomal sites more frequently than FP elements. Furthermore, the presence of KP elements reduced the long-term stability of FP elements in D. melanogaster. Together, these results demonstrate that KP elements possess an intrinsic replicative advantage over FP elements in competitive contexts, providing a mechanistic explanation for the global predominance of KP elements in D. melanogaster. This superiority is probably attributable to nucleotide sequence-specific properties of KP elements, rather than to differences in element size, genomic insertion position, or repression of transposition.
Of the two otariid species endemic to the Galapagos Islands, the Galapagos fur seal (GFS, Arctocephalus galapagoensis) remains the least studied due to its remote distribution restricted to the western islands of the archipelago, a region uniquely influenced by the cold, productive Equatorial Undercurrent (EUC). This study presents the first two complete GFS mitogenomes, assembled from scat samples collected at the Cabo Douglas rookery on Fernandina Island, to contribute to elucidating the evolutionary history of this endangered species. Time-calibrated phylogenies indicate most Arctocephalus species form a monophyletic group. These also show GFS as sister to South American and New Zealand fur seals, diverging 1.91–1.68 MYA (million years ago). This divergence coincides with the early Pleistocene cooling (Gelasian–Calabrian transition), when colder oceans favored otariid dispersal, thus suggesting the time of arrival of fur seals to the Galapagos Islands. The Galapagos region, maintained by the EUC, likely served as a climate refugium enabling fur seal persistence in tropical waters despite later interglacial warming. This study underscores the utility of non-invasive genetic sampling and highlights the role of the Galapagos marine ecosystem as a climate refugia for biodiversity in the face of oceanic warming.
Retrocopies are processed copies of other genes that originate through reverse transcription and are randomly integrated into the genome. Once considered genomic “junk,” emerging evidence shows they contribute to novel gene evolution and may aid adaptation to environmental and lifestyle changes. However, the role of retrocopies in the emergence of virulence in Plasmodium parasites remains largely unexplored. This study systematically characterizes retrocopies across 23 Plasmodium pathogenic genomes to elucidate their evolutionary origins, functional relevance, and potential contributions to the emergence of virulence. Using a stringent computational framework, we identified 724 high-confidence retrocopies exhibiting canonical signatures of retroposition. Retrocopies are frequently intact, under purifying selection, and often display detectable apparent transcription during intraerythrocytic stages, with a subset showing FPKM values from RNA-seq data comparable to or exceeding those of their parental genes, particularly in PPIase, PIR, and actin-related families linked to host interaction and immune evasion. Domain, GO, and KEGG enrichment analyses indicate that retrocopies are preferentially associated with processes such as cytoadhesion, chromatin remodeling, stress response, and cytoskeletal organization, and that retroposition has contributed to the expansion and diversification of pathogenic gene families in a lineage and host-specific manner. Ancestral state reconstruction indicates episodic gains and losses of retrocopies, with notable expansions in primate-infecting lineages. The findings show retrocopies in Plasmodium are widespread, evolutionarily dynamic, and functionally associated with key virulence-associated pathways rather than representing inert genomic byproducts. This study highlights retroposition as an underappreciated mechanism contributing to genomic plasticity in malaria parasites and provides a framework for future functional investigations.
N6-methyladenosine (m6A) is a prevalent modification of eukaryotic mRNAs that plays a crucial role in gene regulation and genome integrity. YT521-B homology (YTH) domain-containing RNA-binding proteins act as essential m6A readers, influencing the fate of m6A-modified RNAs through their involvement in RNA splicing, processing, stability, and translation. In plants, YTH genes regulate plant growth and development by modulating these post-transcriptional processes. Despite the significance of barley (Hordeum vulgare L) as a staple crop, the YTH genes in this species remain largely unexplored. We conducted a detailed analysis of the barley genome and identified 14 YTH genes. Phylogenetic classification categorized these genes into 5 distinct groups. These genes are distributed across seven chromosomes, and their predicted protein products are primarily localized within the nucleus. We observed conserved exon structures and domains among the various groups of HvYTHs. Analysis of the promoter region identified several regulatory elements associated with developmental processes, stress responses, and hormone regulation. Protein-protein interaction predictions suggested associations with m6A methyltransferase components and stress-responsive factors. Additionally, miRNA target analysis identified potential post-transcriptional regulators of HvYTH genes. Expression profiling using RNA-seq data revealed both tissue-specific and stress-responsive patterns. Several HvYTH genes showing differential expression under cold, heat, and heavy metal stress. qRT-PCR validation confirmed the upregulation of HvYTH8 across all stress conditions, while HvYTH5, HvYTH10, and HvYTH12 members exhibited stress-specific upregulation or downregulation. These results underscore the functional divergence of HvYTH genes in mediating abiotic stress tolerance, providing potential targets for improving barley resilience.
