Search Results (173)

Background: Isotomidae is one of the most common Collembola families, comprising 1484 species belonging to four subfamilies: Isotominae, Proisotominae, Anurophorinae, and Pachyotominae, while the subfamilial classification remains contentious, largely due to limited molecular phylogenetic evidence. Methods: We sequenced and assembled the mitochondrial genomes (mitogenomes) of three species (Parisotoma sp., Folsomia sp. 1, and Folsomia sp. 2. Combining these with 10 mitogenomes available from GenBank, we reconstructed the phylogeny of Isotomidae based on a dataset of 13 species representing all four subfamilies. Results: These new mitogenomes, with lengths of 15,741 bp, 16,295 bp, and 16,765 bp, respectively, exhibit the typical metazoan gene set (13 PCGs, 22 tRNAs, 2 rRNAs) and show high structural conservation with other Collembola. However, phylogenetic analyses based on concatenated protein-coding genes revealed significant incongruence with traditional classification. While Isotomidae was recovered as monophyletic, both Isotominae and Anurophorinae were recovered as paraphyletic. Specifically, Parisotoma sp. formed a distinct lineage closer to the derived subfamilies than to the core Isotominae, and the representative of Pachyotominae (Paranurophorus simplex) was recovered nested within Anurophorinae, suggesting potential subfamilial misclassification or paraphyly. Furthermore, Proisotoma minuta was identified as an independent sister lineage to the Anurophorinae + Pachyotominae clade. Conclusions: Our findings suggest that the current subfamily boundaries are not natural and that key diagnostic traits, such as furcal structure, likely reflect symplesiomorphies or various forms of homoplasy-including convergent evolution, parallelism, and evolutionary reversals—rather than unique synapomorphies defining monophyletic groups. This study provides essential genomic resources and highlights the need for an integrative taxonomic revision of Isotomidae that incorporates both molecular and morphological data, with particular emphasis on redefining subfamilies boundaries and reassessing diagnostic morphological traits. Full article

Rye (Secale cereale L.) is a small-grain cereal traditionally cultivated under low-input conditions, where locally adapted populations have contributed substantially to the maintenance of genetic diversity. Despite this importance, Greek rye germplasm has received limited attention at the molecular level. In the present study, 33 rye accessions, including gene bank landraces, locally cultivated populations and one commercial variety, were analyzed using inter-simple sequence repeat (ISSR), start codon-targeted (SCoT), and exon-based amplified polymorphism (EBAP) markers. All three marker systems generated high proportions of polymorphic loci and comparable estimates of expected heterozygosity, indicating considerable genetic variability within the studied material. Multivariate analyses revealed moderate population structuring and consistently identified a small number of genetically divergent accessions, most notably T-492, K-163, and K-166. No clear clustering according to geographical origin was detected, as in most cases of landraces or local populations. Taken together, the results provide a detailed molecular overview of Greek rye germplasm—which has never been performed before for Greek rye genetic material—and offer a useful basis for conservation priorities and future pre-breeding efforts. Full article

Sphaerodactylidae play a crucial role in ecosystems, possessing significant ecological, scientific, and conservation value. They contribute to pest control and the maintenance of ecological balance, and also provide abundant materials for research in evolutionary biology and biodiversity. To refine the phylogenetic position of Teratoscincus scincus within the Sphaerodactylidae using mitogenomic data, this study sequenced the complete mitochondrial genome of T. scincus using the Illumina NovaSeq Xplus platform, and subsequently performed assembly, annotation, and analysis. The phylogenetic relationships of T. scincus within the Sphaerodactylidae were analyzed using 13 protein-coding genes (PCGs) from the mitochondrial genome via Bayesian inference (BI) and maximum likelihood (ML) methods. The complete mitochondrial genome of T. scincus is 16,943 bp in length and consists of 13 PCGs, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The base composition shows a distinct AT preference, with the highest A + T content (56.3%) found in the PCGs region. A phylogenetic tree was constructed based on the amino acid sequences of 13 PCGs from the mitochondrial genomes of nine Sphaerodactylidae species retrieved from GenBank and the newly sequenced T. scincus generated in this study. The results confirm that T. scincus belongs to the genus Teratoscincus within the family Sphaerodactylidae. Phylogenetic analysis reveals that T. scincus and Teratoscincus keyserlingii cluster into a monophyletic group, suggesting a close phylogenetic relationship. Additionally, the phylogenetic tree provides new molecular evidence for understanding the formation mechanism of Sphaerodactylidae diversity. This study not only enriches the mitochondrial genome database of Sphaerodactylidae but also lays an important foundation for subsequent research on the adaptive evolution and conservation biology of T. scincus. Full article

Influenza A viruses exhibit broad host tropism, infecting multiple species including humans, avian species, and swine. Swine influenza virus (SIV), while primarily circulating in porcine populations, demonstrates zoonotic potential with sporadic human infections. In this investigation, we identified two H1N1 subtype swine influenza A virus strains designated A/swine/China/SD6591/2019(H1N1) (abbreviated SD6591) and A/swine/China/SD6592/2019(H1N1) (abbreviated SD6592) in Shandong Province, China. The GenBank accession numbers of the SD6591 viral gene segments are PV464931-PV464938, and the GenBank accession numbers corresponding to each of the eight SD6592 viral gene segments are PV464939-PV464946. Phylogenetic and recombination analyses suggest potential evolutionary differences between the isolates. SD6591 displayed a unique triple-reassortant genotype: comparative nucleotide homology assessments demonstrated that the PB2, PB1, NP, NA, HA, and NEP genes shared the highest similarity with classical swine-origin H1N1 viruses. In contrast, SD6592 maintained genomic conservation with previously characterized H1N1 swine strains, although neither of these two isolates exhibited significant intrasegmental recombination events. Through comprehensive sequence analysis of these H1N1 SIVs, this study provides preliminary insights into their evolutionary history and underscores the persistent risk of cross-species transmission at the human–swine interface. These findings establish an essential foundation for enhancing national SIV surveillance programs and informing evidence-based prevention strategies against emerging influenza threats. Full article

The mitochondrial genome of Decametra tigrina (A.H. Clark, 1907) was fully sequenced and characterized. This circular, double-stranded genome spans 15,794 bp and encompasses 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. The arrangement of genes remains conserved, matching those of Cenometra bella and the MW405444 (submitted to GenBank as Oligometra serripinna). The base composition consists of 24.6% A, 47.6% T, 16.2% G, and 11.6% C. Most PCGs use ‘ATG’ as the initiation codon, with NADH4L and NADH5 initiating with ‘GTG’. Each PCG terminates with a complete stop codon (‘TAA’ or ‘TAG’). Twelve tRNA genes, three NADH genes, and two rRNA genes are located on the L strand, while the remaining genes reside on the H strand. Phylogenetic analysis utilizing all 13 PCGs demonstrated that D. tigrina forms a clade with MW405444 (submitted to GenBank as O. serripinna, reassessed here as D. tigrina) and Florometra sp. (MN883538). Decametra tigrina forms a sister group with C. bella; together, they cluster with Stephanometra indica (Mariametridae) and Zygometra comata (Zygometridae) in the ML tree. Full article

Contemporary seed gene bank management emphasizes the importance of understanding seed storage behaviour to maximize the preservation of genetic material. In this context, the patterns of naturally occurring ageing-related changes in physiological and biochemical markers were evaluated by comparing the performance of freshly regenerated seed samples (control) to samples kept under cold storage (CS) for 37 years (original, CS1 samples) and five years (CS2 samples). A significant decline in seed viability and physiological quality—initial seedling development—was directly associated with the duration of cold storage, leading to a marked reduction in seedling vigour index (SVI) performance. Key biochemical markers influencing early seedling growth and vigour included total protein, the glutelins protein fraction, fructose, sucrose, both insoluble-bound and soluble-free phenolics—including phenolic acids, and β-carotene. The CS2 samples, which experienced severe water deficit during the post-zygotic phase, exhibited increased sucrose, insoluble-bound p-coumaric acid (p-CouA), insoluble-bound ferulic acid (FA), and α-tocopherol contents. Conversely, glutelins and glucose contents decreased, while genotype-specific variations were observed in albumins, globulins, fructose, maltose, insoluble-bound caffeic acid, and soluble-free p-CouA, as well as in β+γ- and δ-tocopherol contents. Given the consistent pattern of natural ageing-related changes, β-carotene, lutein+zeaxanthin, insoluble-bound FA, and particularly soluble-free FA emerge as relevant biomarkers for improved monitoring of ageing processes under ex situ conservation. Full article

The species Caesalpinia spinosa, is a native forest tree of the Andes, which has multiple and valuable uses. In this study, a total of 39 guarango accessions from INIAP´s Gene Bank collection, were evaluated to determine their morphological and ecogeographical diversity. Seventeen quantitative and seven qualitative descriptors were used to characterize morphologically seeds and trees. Multivariate analyses revealed four morphological groups mainly differentiated by seed germination, viability rates, total tree height, and seed and leaflet dimensions, whereas descriptors such as seed color, shape and hilum position, presence of spines, and stem color were not discriminant. On the other hand, ecogeographical characterization, based on 21 bioclimatic, edaphic, and geophysical variables, identified six groups distributed latitudinally along the Ecuadorian Andes. A lack of significant correlation between morphological and ecogeographical variation (Mantel test) was found, suggesting that phenotypic expression is shaped by independent genetic and environmental drivers. This research is the first comprehensive morphological and ecogeographical characterization of the species in Ecuador. This new information will strengthen in situ and ex situ conservation efforts as well as promote the sustainable use of the species in the near future. Full article

Sturgeons, once resilient enough to outlive dinosaurs, are now critically endangered. All 26 species of Acipenseriformes face extinction due to anthropogenic causes. Despite their ecological and economic significance, sturgeon research lacks essential tools such as larval cell lines; the Cellosaurus database lists only one larval cell line (AOXlar7y from Atlantic sturgeon). Larval stages are key to understand fish development, representing a transitional phase between embryonic and adult life that is highly sensitive to temperature shifts, oxygen depletion and pollution. Larval cell lines therefore provide potential in vitro models for studying development and stress responses in endangered species. This study focused on establishing and initially characterizing five novel larval cell lines from siblings of the Siberian sturgeon (Acipenser baerii). The lines proved viable for long-term culture, bio-banking and transfer, displaying different morphologies ranging from epithelial-like to fibroblast-like. Functional assays showed variable mitochondrial activity and extracellular acidification rates. A preliminary targeted gene expression analysis revealed similarity to whole larvae within early passages and in vitro adaptations for certain genes (gapdh, vim, col1a1, pcna). These sibling-derived cell lines hold potential as in vitro tools to deeper explore the biology of Siberian sturgeon larvae and support conservation-focused research. Full article

The Mediterranean Germplasm Gene Bank (MGG) of the CNR-IBBR in Bari (Italy) is the oldest gene bank of the Mediterranean area. Thanks to Vavilov, this area is considered an important gene centre. The first safeguarding activities of the MGG began in 1969 and continue today following traditional and innovative approaches. The strategy followed by the MGG for safeguarding plant genetic resources of Mediterranean origin and of agricultural interest is described in detail together with the activities and methods used. Some examples of rare agrobiodiversity discovered in the area are reported and described. The MGG seed collection (as ex situ conservation) contains about 59,000 accessions from 34 families, 208 genera and 872 species. Over 13,000 samples have been directly collected over time by exploration teams, while others have been acquired from 314 donor institutions through a seed exchange. MGG studies in the Mediterranean region show a severe genetic erosion of about 75%. The approach adopted by the CNR-IBBR research group to combat this phenomenon can be broken down into two main areas. Firstly, new collecting missions could secure still available valuable material as old landraces cultivated in the fields and gardens of less anthropized areas; the considerable experience and knowledge acquired over the span of five decades, accumulated through this endeavour, undoubtedly plays a pivotal role. Moreover, the integration of conservation methods, ex situ and on farm, for cultivated material, and predominantly in situ for wild species, is necessary for the sustainable development and use of Mediterranean plant genetics resources. In pursuit of this objective, the international standing of the MGG and its extensive network of collaborations represent a foundational element. Full article

Diarrhea in young ruminants is a global issue and causes significant economic losses worldwide. In addition to common pathogens like rotavirus, coronavirus, and astrovirus, new viruses can be identified through unbiased next-generation sequencing (NGS) techniques. Here, we report the initial identification of a hunnivirus from a one-month-old goat with diarrhea using shotgun metagenomic NGS. A complete hunnivirus genome was recovered. Phylogenetic tree analysis revealed that this goat hunnivirus was more closely related to cattle hunnivirus than to small ruminant hunnivirus strains, suggesting a prior cross-species transmission event. The genome was used to design primers/probes for the conserved 3D^pol RdRP gene for real-time RT-PCR to screen banked ruminant fecal samples. Screening of 144 ruminant fecal samples showed that 9 of 38 goat, 22 of 96 cattle, and 0 of 8 sheep samples were positive for hunnivirus. Sequencing of the 3D^po region was performed on selected positive samples and revealed two lineages of hunnivirus circulating in North America. Our study highlights the importance of further investigation and monitoring of fecal samples using unbiased metagenomic tools to identify potential pathogens or co-infections in ruminants. Full article

Through binding to complementary mRNAs, microRNAs (miRNAs) mediate gene silencing. The stability and half-life of microRNAs are controlled by two isoforms of the RNA-binding protein Roquin. This study aimed at identifying the role of Roquin to miRNA-dependent regulation of the transcriptome in the post-ischemic heart. Both Roquin isoforms are highly conserved between rats and humans and constitutively expressed in cardiomyocytes. In both cell species, hypoxia induces a down-regulation of Roquin-1 and Roquin-2. An integrative miRNA-and-mRNA analysis (MMIA) identified miR-23b-5p as a potential interaction partner of Roquins. The open data bank TargetScan8.0 suggests that the transcription factor ZBTB20 is a potential target of miR-23b-5p. The level of expression of ZBTB20 correlated with the functional recovery of rat hearts after myocardial infarction. Moreover, the down-regulation of Roquin-2 in AC16 cells by siRNA under normoxic conditions was associated with an up-regulation of miR-23b-5p and a down-regulation of ZBTB20. Furthermore, in the case of hypoxia-dependent down-regulation of Roquin, the subsequent down-regulation of ZBTB20 was reversed with the help of an antagomir against miR-23b-5p. In conclusion, hypoxia-induced down-regulation of the two Roquin isoforms was associated with an increased stability of miR-23b-5p, a Roquin-2-dependent miRNA, which subsequently led to silencing of the transcription factor ZBTB20. Full article

In an era of global warming, sustainable agriculture, which emphasises the conservation of biodiversity and the rational use of natural resources, is growing in importance. One of the key elements is to increase the genetic diversity of crops through the use of crop wild relatives (CWRs) and local varieties, which provide a source of genes for resistance to biotic and abiotic stresses. Modern agricultural systems are characterised by low biodiversity, which increases the susceptibility of plants to diseases and pests. Growing mixtures of varieties, both intra- and interspecific, is a practical strategy to increase plant resistance, stabilise yields and reduce pathogen pressure. This manuscript has a review character and synthesises the current literature on the use of CWRs, local varieties, and variety mixtures in sustainable agriculture. The main research question of the study is to what extent plant genetic resources, including CWRs and local varieties, as well as the cultivation of variety mixtures, can promote plant resistance, stabilise yields and contribute to sustainable agriculture under climate change. The objectives of the study are to assess the role of genetic resources and variety mixtures in maintaining biodiversity and yield stability, and to analyse the potential of CWRs and local varieties in enhancing plant resistance. Additionally, the study investigates the impact of variety mixtures in reducing disease and pest development, and identifies barriers to the use of genetic resources in breeding along with strategies to overcome them. The study takes an interdisciplinary approach including literature and gene bank data analysis (in situ and ex situ), field trials of cultivar mixtures under different environmental conditions, genetic and molecular analysis of CWRs, the use of modern genome editing techniques (CRISPR/Cas9) and assessment of ecological mechanisms of mixed crops such as barrier effect, and induced resistance and complementarity. In addition, the study considers collaboration with participatory and evolutionary breeding programmes (EPBs/PPBs) to adapt local varieties to specific environmental conditions. The results of the study indicate that the integration of plant genetic resources with the practice of cultivating variety mixtures creates a synergistic model that enhances plant resilience and stabilises yields. This approach also promotes agroecosystem conservation, contributing to sustainable agriculture under climate change. Full article

The AGC kinases constitute a large and ancient gene superfamily with origins that coincided with the appearance of multicellularity. Three AGC kinase families—protein kinase A (PKA), protein kinase G (PKG), and protein kinase C (PKC)—mediate the actions of neuropeptide hormones, biogenic amines, and other ligands on various physiological processes in metazoans. Metazoans express two PKG types. Jawed vertebrates express three PKA catalytic (C) subunits, four regulatory (R) subunits, and twelve PKCs, organized into conventional, novel delta-like, novel epsilon-like, atypical, and protein kinase N (PKN) subfamilies. By contrast, invertebrate PKA and PKC sequences are not well characterized. Consequently, limited database resources can result in misidentification or mischaracterization of proteins and can lead to misinterpretation of experimental data. A broad phylogenetic and sequence analysis of CrusTome transcriptome and GenBank databases was used to characterize 640 PKA-C sequences, 1122 PKA-R sequences, and 1844 PKC sequences distributed among the Annelida, Arthropoda, Chordata, Cnidaria, Nematoda, Mollusca, Echinodermata, Porifera, Platyhelminthes, and Tardigrada. Phylogenetic analysis and multiple sequence alignments revealed conservation of certain PKA-C, PKA-R and PKC isoforms across metazoans, as well as diversification of additional taxon-specific isoforms. Decapods expressed four PKA-C isoforms, designated PKA-C₁, -C_D1, -C_GLY1, and -C_GLY2; five PKA-R isoforms, designated PKA-RI₁, -RI_D1, -RII_GLY, and -RII_D1; and five PKC isoforms, designated PKN_D1-3, conventional cPKC_D1, novel nPKC_D1δ and nPKC_D1ε, and atypical aPKC_D1. PKA-C_GLY1, -C_GLY2, and -RII_GLY had glycine-rich N-terminal sequences that were unique to crustaceans. These data suggest lineage-specific diversification that retained the core catalytic function of each kinase, while regions outside of the kinase domain may provide specialized regulatory mechanisms and/or spatiotemporal subcellular localization in invertebrate tissues. Full article

Distant hybridization is key to trait innovation and speciation, with Cyprinidae hybrid phylogeny helping to clarify diversification mechanisms. Yet, a major gap persists in Cyprinidae studies: the stabilization mechanisms of interspecific distant hybrid lineages. To address this, we systematically analyzed the molecular phylogeny of seven Cyprinidae distant hybrid lineages and their parental species, using an integrative genetic framework encompassing four mitochondrial genes (Cytb, COI, 16S rRNA, D-loop) and five nuclear genes (EGR2b, IRBP2, RAG1, RAG2, RH2). Homologous sequences of 41 representative Cyprinidae species (85 samples) were retrieved from GenBank to supplement the dataset. Phylogenies were reconstructed from concatenated sequences, complemented by haplotype networks. Intra-/interspecific divergence was quantified using two mitochondrial genes (COI, Cytb) and two nuclear (RAG1, RH2). The results showed that these hybrid lineages exhibited variation patterns analogous to other Cyprinidae species. Both ML and BI trees reconstructed exhibited congruent topologies with high support (bootstrap/BPP > 80%), resolving genus/species-level relationships. While most hybrids clustered intermediately between their parental species, they typically displayed maternal affinity. A notable exception was the 2nNCRC (a homodiploid hybrid from Cyprinus carpio ♀ × Megalobrama amblycephala ♂), which displayed convergent evolution toward Carassius auratus. COI-based K2P genetic distance analysis revealed 2nNCRC had a much closer relationship with C. auratus (0.0119) than with its parents (0.1249 to C. carpio, 0.1552 to M. amblycephala). These nine genes elucidate the genetic relationships between Cyprinid hybrid lineages and progenitors, serving as pivotal molecular markers for parentage tracing and genetic dissection of distant hybridization mechanisms. The integrated mitochondrial–nuclear marker system in this study advances understanding of cytonuclear coadaptation and the stabilization of interspecific distant hybrid lineages in Cyprinidae. Specifically, it provides a precise tool for parentage tracing, Cyprinid germplasm conservation, and targeted regulation of hybrid breeding—laying a foundation for exploring hybrid speciation and developing elite aquaculture germplasms. Full article

Between 1% and 2% of the world’s population is sensitised to mites. Aetiological diagnosis is key to the management of allergic patients. However, methods based solely on morphological criteria are ambiguous in many cases. Polymerase chain reaction of ribosomal genes represents a valuable complementary approach. The 5 most representative species (Dermatophagoides pteronyssinus, Dermatophagoides farinae, Tyrophagus putrescentiae, Blomia tropicalis and Lepidoglyphus destructor) were selected as sources of allergens. They were first identified morphologically and the 18S rRNA gene sequences were obtained from the GenBank database. Alignment of the nucleotide sequences of the 18S rRNA ribosomal gene enabled the identification of the conserved and divergent regions in all of them. The alignment allowed the design of a pair of oligonucleotides in conserved regions of the gene, to amplify the sequence of interest in each of the species. We performed genomic DNA extraction, quantification and purity. PCR, using oligonucleotides designed to amplify the 18S sequence fragment of interest, showed the exact size for each species. Amplification, efficiency curves and melting points resulting from the amplification of the 18S amplicon of the five species were obtained. The oligonucleotides designed for real-time PCR studies, allow species identification by amplifying the specific fragment of each species using real-time PCR. Full article