Search Results (543)

Bluetongue (BT) is an arthropod-borne viral disease primarily affecting domestic and wild ruminants. In recent years, several BTV serotypes and genotypes have been detected in Israel almost annually, raising questions about their origin and routes of introduction. Some BTV serotypes closely related to those first identified in Israel, including BTV-3, BTV-8, and BTV-12, were subsequently reported in Europe after a delay of several years. In this study, we sequenced the complete genomes of one representative strain of all newly identified Israeli BTV genotypes/serotypes—BTV-1, -4, -5, -8, and -11—first detected between 2021 and 2023. Additionally, complete sequences of enzootic Israeli BTV (2015) and eleven BTV-3 strains (2019–2023), with two representative strains for every year of isolation, except 2021 (three strains), were analyzed using phylogenetic, BLAST, and pairwise identity approaches. Genetic analyses revealed that recently identified Israeli and European BTV strains share common African ancestors, with some genomic “incursions” from Mayotte Island or the Arabian Peninsula. These incursions appeared more frequently in Israeli than in European strains. Nevertheless, nucleotide sequence differences of at least 2–3% across all genes indicate several years of independent evolution. The observed divergence suggests that no direct transmission of BTV occurred between Israel and Europe during the past decade. Full article

Quinoa (Chenopodium quinoa, 2n = 4x = 36, AABB subgenomes) is a highly nutritious crop with the potential to diversify global diets and alleviate malnutrition. It is also adaptable for production in soils increasingly affected by salinization and water scarcity. Quinoa was domesticated and artificially selected as a crop within the Andes Mountains, the geographically isolated Mediterranean climate zone of coastal Chile, and along the northwestern fringe of the Argentine dry Pampas. In addition, there is now abundant information regarding the wild species that were its immediate ancestors and which should be viewed as its secondary and tertiary breeding gene pools. These same ancestors contributed to independent domestications of the other forms of “quinoa” in ancient Mesoamerica and eastern North America from a common AABB ancestor-species, C. berlandieri, known commonly as pitseed goosefoot (PG). This review explores the biogeography of the diploid and polyploid relatives of the AABB allotetraploid goosefoot complex (ATGC). The seven or more ecotypes of PG, including the South American taxon C. hircinum, or avian goosefoot (AG), contain broad genetic variability, and some can be used directly as crossing partners in making quinoa breeding populations. Of the extant diploid relatives, C. subglabrum (SMG) is most closely related to the original maternal subgenome A of PG, while C. suecicum (SWG) or C. ficifolium (FG) are most closely related to paternal subgenome B. These and the other AA and BB diploids are valuable model organisms for locating and modifying genes of interest and their expression, the ultimate goals being to increase quinoa’s yield potential, improve its nutritional attributes, explore value-adding industrial uses, and enhance quinoa’s already formidable mechanisms to resist environmental stresses. This review is an update on the current state of quinoa breeding, with an emphasis on the value of wild genetic resources for quinoa improvement. It provides a comprehensive review of the scientific literature for scientists interested in adding quinoa to their breeding program. Full article

Gene conversion contributes to gene copy number changes, DNA mutations, and functional innovation and has been widely reported in three domains of life. However, it has hardly been described in Aspergillus, including industrially and commercially important or pathogenic fungi. Here, we revealed multiple sets of homologous genes located in a region of chromosome 1 of A. flavus, and its orthologous counterpart of A. oryzae. Phylogenetic analysis showed evidence of frequent gene (DNA) conversion between ectopic paralogs in each species, accompanied by prominent point mutations and DNA deletion (from several to hundreds of base pairs). At least two independent cases showed that the converted genes in A. oryzae have been repeatedly split into shorter genes by the introduction of stop codons, and then ectopic conversion rendered paralogous genes (regions) to have the same configuration of tandemly located new genes. Inference of nucleotide substitution and ancestral gene content showed that the conversion-affected regions have seen 3.48 times as many substitutions and 4–6 times as many gene losses compared to the non-affected regions. We predicted that a DNA loop between proximal regions, in the common ancestor and inherited by each species, facilitates ectopic gene (DNA) conversion and elevated rates of mutations and losses. Overall, we found that gene conversion proves to be a key factor resulting in genome instability, elevated gene evolutionary rates, and an effective avenue to produce new genes, likely leading to the speciation of two Aspergillus lineages. Full article

Background/Objectives: Understanding the genetic basis of growth and fat deposition is crucial for improving beef productivity in Kalmyk cattle, a breed well adapted to the extreme climatic conditions of Kazakhstan. The present study aimed to determine the effects of single-nucleotide polymorphisms (SNPs) in the CRTC2 and ELOVL6 genes on intramuscular fat content and to evaluate their associations with growth and meat quality traits in 18-month-old Kalmyk heifers raised under different environmental conditions. Methods: A total of 400 clinically healthy Kalmyk heifers (200 from LLP “Qazaq Asyldary” and 200 from LLP “Agrofirma Turikpen”) were examined. All animals originated from closed breeding herds, and only unrelated individuals without common ancestors to the third generation were included. Zootechnical measurements— live weight, withers height, chest depth, chest girth, and body length—were performed twice by a trained specialist. Backfat thickness and musculus longissimus dorsi depth were measured postmortem. Blood samples were collected for genomic DNA extraction using the GeneJET purification kit, and DNA quality was assessed by Nanodrop, Qubit, and agarose gel electrophoresis. Target fragments of CRTC2 and ELOVL6 were amplified (150–200 bp) and sequenced on an ABI 3500 system. SNP identification, allele frequencies, and genotyping were performed by alignment to the Bos taurus ARS-UCD1.2 reference genome. Statistical analyses were conducted in RStudio using linear and mixed models with “farm” as a random effect. Results: Only one informative polymorphism, g.133528A>G in ELOVL6, was detected. Three genotypes (AA, AG, GG) were observed, with the heterozygous AG genotype showing significantly higher live weight, greater body length, and improved linear measurements compared to AA and GG. No significant associations were detected with backfat thickness or muscle depth. The g.133528A>G polymorphism in ELOVL6 positively influences growth traits without increasing fatness, aligning with the naturally lean phenotype of Kalmyk cattle. Conclusions: The AG genotype may serve as a promising marker for selecting faster-growing animals in marker-assisted breeding programs. Full article

Foot-and-mouth disease virus (FMDV) serotype SAT3 is a rarely studied serotype primarily circulating in southern Africa, with African buffalo (Syncerus caffer) serving as its key reservoir. In this study, we performed a comprehensive phylogenetic and phylodynamic analysis of SAT3 based on 81 full-length VP1 gene sequences collected between 1934 and 2018. Maximum likelihood and Bayesian analyses revealed five distinct topotypes, each with clear geographic and host associations. Notably, topotypes I, II and III were observed in both African buffalo and cattle (Bos taurus), while topotype IV appeared restricted to African buffalo. Likelihood mapping indicated moderate to strong phylogenetic signal, and the mean substitution rate was estimated at 3.709 × 10⁻³ substitutions/site/year under a relaxed molecular clock. The time to the most recent common ancestor (TMRCA) was traced back to 1875. Discrete phylogeographic reconstruction identified Zimbabwe as a major center, with multiple supported cross-border transmission routes. Host transition analysis further confirmed strong directional flow from buffalo to cattle (BF = 1631.09, pp = 1.0), highlighting the wildlife–livestock interface as a key driver of SAT3 persistence. Together, these results underscore the evolutionary complexity of SAT3 and the importance of integrating molecular epidemiology, spatial modeling, and host ecology to inform FMD control strategies in endemic regions. Full article

Within the freshwater fish order Cypriniformes, loaches form a monophyletic lineage comprising nine families with more than 1400 species. Secondary sexual dimorphism is widespread among loach families, most notably in the form of enlarged pectoral fins and tubercles or other hard structures on the pectoral fin in adult males. To date, the family Botiidae, phylogenetically sister to all other loach families, was reported to lack such sexually dimorphic structures, leading to the hypothesis that the common ancestor of loaches did not exhibit sexual dimorphism. Here, we report the presence of sexual dimorphism in eight species of Botiidae: Leptobotia bellacauda, L. guilinensis, L. microphthalma, L. taeniops, L. tchangi, Parabotia fasciatus, Sinibotia pulchra, and S. robusta. In all species, adult males possess longer pectoral fins than females. Additionally, males of L. guilinensis and L. tchangi exhibit larger pelvic fins, while males of L. microphthalma have larger anal fins. In L. bellacauda, L. microphthalma, and L. tchangi, portions of the dorsal surface of the pectoral fin bear rows of tubercles. The three genera displaying sexual dimorphism belong to two different subfamilies, demonstrating that sexual dimorphism is widespread across Botiidae and not restricted to a single genus or subfamily. Our results show that sexual dimorphism is present in the most basal family of loaches, suggesting that it represents a synapomorphy of loach fishes. Full article

Background: Cardiomyopathies are a heterogeneous group of heart muscle disorders with diverse genetic origins. Biallelic loss-of-function (LoF) variants in the nebulin-related anchoring protein (NRAP) gene have been linked to dilated cardiomyopathy (DCM) and left ventricular noncompaction cardiomyopathy, though only a few families have been described. NRAP, a member of the Nebulin family, plays a key role in cardiomyocyte development, structural integrity, and muscle function. Methods: We investigated two Italian siblings with DCM born to consanguineous parents from a small village in Campania. Exome sequencing, homozygosity mapping, and comparative analyses with other reported cases were performed. Genealogical research was conducted using civil registry data to reconstruct extended family pedigrees. Results: Both siblings were homozygous for a LoF variant in NRAP (NM_198060.4:c.619del; p.Val207TrpfsTer20). A third brother with tachycardia-induced cardiomyopathy, as well as their living mother, who did not have cardiac abnormalities, were found to be heterozygous. The same homozygous variant was recently identified in another Italian family with DCM coming from North-eastern Italy, whose proband also originated from a nearby village in Campania. These two families exhibited heterogeneity in clinical presentation. Homozygosity analysis revealed a >25 Mb shared region on chromosome 10 encompassing NRAP, supporting a common ancestral origin. While genealogical reconstruction did not allow identification of a shared ancestor, it confirmed consanguinity and enabled the recognition of potential carriers across both families. Conclusions: Our findings strengthen the evidence for NRAP as a disease-causing gene in cardiomyopathies and highlight a likely founder effect in Campania. Incorporating NRAP into genetic testing panels is warranted, especially in populations with high rates of consanguinity or suspected founder variants. Full article

Numerous studies have demonstrated that the Japanese encephalitis virus (JEV) is classified into five genotypes. Historically, JEV GIII and GI were the dominant strains before and after the 1990s, respectively. Recently, the non-dominant genotypes have been implicated in numerous JE outbreaks, posing significant public health challenges. This study conducted a comprehensive phylogenetic analysis of 126 JEVs covering five genotypes from 1938 to 2025 globally. Notably, it is the first study to conduct a time to most recent common ancestor (tMRCA) analysis of JEV GII. The findings indicate the common ancestor of JEV emerged approximately 1081 years ago, followed by the sequential evolution of GV, GIII, GI, GII, and GIV, which are estimated to have originated approximately 237, 184, 138, 130, and 113 years ago, respectively. The overall evolutionary rate of JEV was 3.3 × 10⁻⁴ substitutions/site/year, with genotype specific rates as follows: GI at 7.3 × 10⁻⁴, GII at 8.2 × 10⁻⁴, GIII at 4.4 × 10⁻⁵, GIV at 1.7 × 10⁻³, and GV at 2.2 × 10⁻³. Significant differences were found between the E protein of recent human-derived JEV strains across five genotypes and the vaccine strain. This aligns with evidence of the current JE vaccine’s reduced efficacy against new strains, underscoring the urgent need for broadly protective JE vaccines. Full article

Next-generation sequencing technology was employed to read and assemble the complete plastid genome of the ‘Mejhoul’ date palm cultivar (Phoenix dactylifera L.). The genome consisted of 158,436 base pairs (bp) with a GC content of 37.24%, and it included 95 protein-coding genes, 44 tRNA genes, and eight rRNA genes. The plastome of five ‘Mejhoul’ genotypes from Jordan was compared with three genotypes from the USA, Morocco, and the UAE. It revealed 91 single-nucleotide polymorphisms (SNPs) and 23 insertions–deletions (InDels); the majority of them (62%) were located in intergenic regions, while the remaining variants were located in intragenic regions, including tRNA and rRNA genes. When the plastomes of all eight ‘Mejhoul’ genotypes were aligned, along with major cultivars ‘Barhee’ and ‘Khalas’, 24 SNPs and 23 InDels could be found. This would enable the development of a cultivar-specific fingerprint test for authentication. The phylogenetic tree was constructed using seventeen date palm cultivars. The phylogenetic analysis places ‘Mejhoul’ as a lineage derived within Clade I rather than as an early-diverging cultivar, suggesting it shares a more recent common ancestor with ‘Deglet Noor’ and ‘Barhee’. Full article

Amaranthus L. includes valuable and promising crops of multi-purpose use, having high morphological diversity and complicated taxonomy. Their karyotypes and genomic relationships remain insufficiently studied. For the first time, a comparative repeatome analysis of Amaranthus tricolor L., Amaranthus cruentus L., and Amaranthus hypochondriacus L. was performed based on the high-throughput sequencing data obtained via bioinformatic analyses using the RepeatExplorer2/TAREAN/DANTE_LTR pipelines. Interspecific variations in the abundance of Ty1 Copia and Ty3 Gypsy retroelements, DNA transposons, and ribosomal and satellite DNA (satDNA) were detected. Based on fluorescence in situ hybridization (FISH), chromosome mapping of 45S rDNA, 5S rDNA, and satDNAs AmC9 and AmC70, and unique karyograms of A. tricolor, A. cruentus, Amaranthus paniculatus L., and A. hypochondriacus were constructed. The analysis of the interspecies genome diversity/similarity in DNA repeat contents, sequences of the identified satDNAs, and chromosome distribution patterns of the studied molecular markers indicated that these species might also share a common evolutionary ancestor. However, the genomes of A. cruentus, A. paniculatus, and A. hypochondriacus were more similar compared to A. tricolor, which aligns with the previous phylogenetic data. Our results demonstrate that cytogenomic studies might provide important data on Amaranthus species relationships elucidating taxonomy and evolution of these valuable crops. Full article

Our article presents a holistic analysis aimed at discerning patterns from ancient–modern comparative contexts of malaria. The article’s interdisciplinary and consilient methodology is drawn from a range of disciplines: the humanities and social sciences, medical knowledge (particularly epidemiology and pathology), molecular phylogenetics, demography, archaeology, paleopathology, numismatics, complex systems theory, etc. The article begins with a detailed exploration of a 463 BCE epidemic event that likely marked the, ultimately transformative, debut of P. falciparum evolutionary lineage malaria for ancient Roman civilization. It is important to note that the concept of evolutionary lineage is defined herein as a sequence of organisms, descended from a common ancestor and culminating, for the present at least, in the form existing currently. An interdisciplinary retrospective diagnosis methodology is utilized to establish, with what we believe to be a high degree of probability, a conclusion that effectively marks the beginning point for the ancient side of our comparative example. The deep interdisciplinary/historical methods used to elucidate the ancient side of the disease equation both lead to a clear conclusion and suggest potential modern analogies or even “prophecies.” These are used to highlight the threats emanating from the current spread of zoonotic P. knowlesi malaria in Southeast Asia. The article also utilizes six broader holistic and interdisciplinary factors in its contextual and comparative analysis: (A) political, military and security contexts; (B) the effects of cultural perceptions; (C) the role of climate and climate change; (D) additional anthropogenic environmental factors; (E) perceptions, practices and capabilities of prevailing medical systems and (F) holistic underlying states of the health of affected populations. Full article

Background: The early months of the COVID-19 pandemic were characterized by high transmission rates and mortality, compounded by the emergence of multiple SARS-CoV-2 lineages, including Variants of Concern (VOCs). This study investigates the phylodynamic and spatio-temporal trends of VOCs during the peak of the pandemic in Nigeria. Methods: Whole-genome sequencing (WGS) data from three major VOCs circulating in Nigeria, B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.529 (Omicron), were analyzed using tools such as Nextclade, R Studio v 4.2.3, and BEAST X v 10.5.0. The spatial distribution, evolutionary history, viral ancestral introductions, and geographic dispersal patterns were characterized. Results: Three major lineages following WHO nomenclature were identified: Alpha, Delta, and Omicron. The Delta variant exhibited the widest geographic spread, detected in 14 states, while the Alpha variant was the least distributed, identified in only eight states but present across most epidemiological weeks studied. Evolutionary rates varied slightly, with Alpha exhibiting the slowest rate (2.66 × 10⁻⁴ substitutions/site/year). Viral population analyses showed distinct patterns: Omicron sustained elevated population growth over time, while Delta declined after initial expansion. The earliest Times to Most Recent Common Ancestor (TMRCA) were consistent with the earliest outbreaks of SARS-CoV-2 globally. Geographic transmission analysis indicated a predominant coastal-to-inland spread for all variants, with Omicron showing the most diffuse dispersal, highlighting commercial routes as significant drivers of viral diffusion. Conclusion: The SARS-CoV-2 epidemic in Nigeria was characterized by multiple variant introductions and a dominant coastal-to-inland spread, emphasizing that despite lockdown measures, commercial trade routes played a critical role in viral dissemination. These findings provide insights into pandemic control strategies and future outbreak preparedness. Full article

Sheep play a central role in Kazakhstan’s pastoral economy, yet the maternal genetic composition of its traditional breeds remains poorly characterized. We analyzed partial mitochondrial D-loop sequences (848 bp) from 115 individuals of three fat-tailed coarse-wooled breeds (Edilbay, Kazakh fat-tailed coarse-wooled, and Gissar) to assess genetic diversity, population structure, and phylogenetic relationships. Ninety-eight haplotypes were identified, indicating high haplotype diversity (Hd = 0.996 ± 0.002) and moderate nucleotide diversity (π = 0.02624 ± 0.00048). Haplotypes clustered into haplogroups A (57.4%) and B (42.6%), with Edilbay dominating the star-like cluster of haplogroup A, consistent with recent expansion. AMOVA revealed that most variation (92.03%) occurred within populations, with no significant differentiation among breeds. Phylogenetic analyses placed Edilbay close to the most recent common ancestor of fat-tailed domestic sheep and the wild Ovis species, suggesting retention of an ancestral lineage. These findings highlight Kazakhstan as a genetic crossroads in sheep history and underscore the conservation value of its maternal diversity. Full article

Between 2019 and 2023, 163 cases of subgenotype VII.1.1 Newcastle disease virus infection were registered in backyard poultry in the Russian Federation within the framework of epizootiological monitoring. Subgenotype VII.1.1 Newcastle disease virus was reported in a total of 18 different subjects of the Russian Federation. Most of the Newcastle disease outbreaks caused by the viruses of this subgenotype occurred in the autumn and winter period (60%). Further tests allowed for the determination of complete F and HN gene nucleotide sequences for 40 isolates. The results were used to perform the Bayesian analysis of F gene sequences with BEAST v.1.10.4 software. The obtained nucleotide substitution accumulation rates were practically non-dependent on the selected nucleotide substitution model and varied appreciably depending on the applied molecular clock model (0.0018 and 0.002 site-1year-1). The conducted study established that the formation of the ‘Russian’ NDV isolates of subgenotype VII.1.1 followed several stages. In the early 2000s, ancestral viruses belonging to subgenotype VII-d were detected in the Middle East and Eastern Europe. From these, through intermediate forms identified in Iraq around 2007–2008, a group designated as subgenotype VII-L emerged. This group gave rise to two sister clades: the Iranian subgenotype VII-L and the cluster of isolates from Russia and Poland, whose immediate common ancestor likely existed around 2015–2016, probably in Asia. Full article

Mamba (Dendroaspis species) snakebites are critical medical emergencies across sub-Saharan Africa. Envenomings can result in the rapid onset of complex neurotoxic symptoms, often leading to high rates of mortality without timely intervention with antivenom. The ancestral state of mambas is the green coloured, forest dwelling type, with the tan/grey coloured, savannah dwelling D. polylepis (Black Mamba) representing a derived state both ecologically and morphologically. However, it has not been tested whether these changes are paralleled by changes in venom biochemistry or if there are differential molecular evolutionary patterns. To fill these knowledge gaps, this study evaluated the neurotoxic effects of all Dendroaspis species venoms using the chick biventer cervicis nerve-muscle preparation, assessed the neutralizing efficacy of three antivenoms commercially available in Africa, and reconstructed the molecular evolutionary history of the toxin types to ascertain whether some were unique to particular species. All Dendroaspis venoms demonstrated potent flaccid-paralysis due to postsynaptic neurotoxicity. The only exception was D. angusticeps venom, which conversely exhibited spastic-paralysis due to presynaptic/synaptic neurotoxicity characterised by potentiation of acetylcholine presynaptic release and sustained synaptic activity of this neurotransmitter. Antivenom efficacy varied significantly. All three antivenoms neutralized to some degree the flaccid-paralysis postsynaptic effects for all species, with D. viridis venom being the best neutralized, and this pattern extended to all the antivenoms. However, neutralisation of flaccid-paralysis postsynaptic effects unmasked spastic-paralysis presynaptic/synaptic neurotoxicity within non-angusticeps venoms. Spastic-paralysis presynaptic effects were poorly neutralized for all species by all antivenoms, consistent with prior clinical reports of poor neutralisation of spastic-paralytic effects. Geographic variation in D. polylepis venom was evident for the relative neutralisation of both spastic-paralysis presynaptic/synaptic and flaccid-paralysis postsynaptic/synaptic neurotoxic pathophysiological effects, with differential neutralization capabilities noted between the Kenyan and South African populations studied. Molecular phylogenetic analyses confirmed spastic-paralysis and flaccid- paralysis toxins to be a trait that emerged in the Dendroaspis last common ancestor, with all species sharing all toxin types. Therefore, differences in venoms’ pathophysiological actions between species are due to differential expression of toxin isoforms rather than the evolution of species-specific novel toxins. Our findings highlight the synergistic nature of flaccid-paralysis postsynaptic and spastic-paralysis presynaptic/synaptic toxins, while contributing significant clinical and evolutionary knowledge of Dendroaspis venoms. These data are crucial for the continued development of more effective therapeutic interventions to improve clinical outcomes and for evidence-based design of clinical management strategies for the envenomed patient. Full article