Search Results (325)

The common two-banded seabream, Diplodus vulgaris, is a commercially important fish in the Mediterranean and eastern Atlantic, yet its myxosporean parasite diversity remains unknown. To address this gap, we conducted a myxosporean survey in D. vulgaris specimens from eastern Atlantic fishing stocks. Myxospores resembling Kentmoseria were observed in the urinary bladder of three specimens. 18S rDNA analyses, however, identified two isolates as Bipteria lusitanica, with the third also showing the highest similarity to this species. Morphological comparison revealed significant overlap between B. lusitanica and Kentmoseria, particularly in the suture line orientation. Accordingly, we describe a novel species, Kentmoseria sirinensis n. sp., and propose Kentmoseria lusitanica n. comb. The unclear boundaries between Bipteria and Kentmoseria are highlighted, though redefining or suppressing either genus remains premature without sequencing their type species. Moreover, our phylogenetic analyses show these species clustering among Sinuolineidae, rather than Ortholineidae, supporting the dismantling of Ortholineidae and the placement of Kentmoseria within Sinuolineidae. The ancestral placement of Bipteria vetusta suggests that it is taxonomically distinct and not a member of the Sinuolineidae. Finally, the occurrence of two Kentmoseria spp. in D. vulgaris suggests diversification in Diplodus, underscoring the need to study myxosporean diversity in wild stocks to assess aquaculture risks. Full article

Background: The B3-domain transcription factor ABI3 (ABSCISIC ACID INSENSITIVE 3) is a critical regulator of seed maturation, stress adaptation, and hormonal signaling in plants. However, its evolutionary dynamics and functional roles in cotton (Gossypium spp.) remain poorly characterized. Methods: We conducted a comprehensive genome-wide investigation of the ABI3 gene family across 26 plant species, with a focus on 8 Gossypium species. Analyses included phylogenetics, chromosomal localization, synteny assessment, gene duplication patterns, protein domain characterization, promoter cis-regulatory element identification, and tissue-specific/spatiotemporal expression profiling under different organizations of Gossypium hirsutum. Results: Phylogenetic and chromosomal analyses revealed conserved ABI3 evolutionary patterns between monocots and dicots, alongside lineage-specific expansion events within Gossypium spp. Syntenic relationships and duplication analysis in G. hirsutum (upland cotton) indicated retention of ancestral synteny blocks and functional diversification driven predominantly by segmental duplication. Structural characterization confirmed the presence of conserved B3 domains in all G. hirsutum ABI3 homologs. Promoter analysis identified key stress-responsive cis-elements, including ABA-responsive (ABRE), drought-responsive (MYB), and low-temperature-responsive (LTRE) motifs, suggesting a role in abiotic stress regulation. Expression profiling demonstrated significant tissue-specific transcriptional activity across roots, stems, leaves, and fiber developmental stages. Conclusions: This study addresses a significant knowledge gap by elucidating the evolution, structure, and stress-responsive expression profiles of the ABI3 gene family in cotton. It establishes a foundational framework for future functional validation and targeted genetic engineering strategies aimed at developing stress-resilient cotton cultivars with enhanced fiber quality. Full article

Microcystis is a genus of cyanobacteria responsible for harmful algal blooms (HABs) in freshwater ecosystems, posing significant ecological and public health risks. Despite its importance, current genomic resources are heavily biased toward Microcystis aeruginosa, limiting comprehensive understanding of genomic diversity within the genus. In this study, we present the first complete genome sequences of two morphospecies, M. ichthyoblabe FBCC-A1114 and M. protocystis FBCC-A270. Using long-read sequencing, both genomes were assembled into single circular chromosomes of 5.84 Mb and 5.76 Mb, respectively. Phylogenetic analyses placed both strains within genospecies G, alongside M. aeruginosa and M. viridis. Comparative analysis of biosynthetic gene clusters revealed that, while most genospecies G members harbor aeruginosin, cyanobactin, and microviridin gene clusters, the two newly sequenced strains lack cyanobactin and microcystin clusters but retain the microginin cluster. Synteny analysis demonstrated high structural conservation between the two genomes, while notable structural variations were observed when compared with M. aeruginosa NIES-298. These findings reveal both functional and structural plasticity within the genospecies, suggesting ecotype diversification driven by environmental adaptation. The newly assembled genomes provide critical resources to refine classification frameworks and advance our understanding of Microcystis genomic diversity. Full article

Sugarcane (Saccharum spp.) is crucial for sweetener production but is highly susceptible to diseases such as orange rust, caused by Puccinia kuehnii. In the northwestern Colombian Amazon, sugarcane is increasingly cultivated, mainly for panela production, a traditional sweetener. However, the introduction of sugarcane has occurred without systematic planning, resulting in limited knowledge about cultivars’ characteristics and disease susceptibility. This study aimed to characterize sugarcane cultivars in the region and assess the occurrence and field-level impact of orange rust, while also confirming the identity of the pathogen using molecular and morphological analysis. We identified five sugarcane cultivars, with only CP 57-603 having an official designation, while the others were known by local names: Regional Without Fuzz, Hairy Purple, and two unnamed genotypes (Cultivar-1 and -2). CP 57-603 and Regional Without Fuzz were the most commonly cultivated (by 49.2% and 74.5% of farms, respectively), while Cultivar-1 (11.8%), Cultivar-2 (7.8%), and Hairy Purple (1.96%) were less frequent. Orange rust was detected in 72% of farms with CP 57-603, 66% with Regional Without Fuzz, and 50% with Cultivar-1, but was absent in farms growing Cultivar-2 and Hairy Purple. Molecular analysis of the ITS1/2 region revealed a single haplotype within the P. kuehnii population, indicating low diversity at this locus in the region. Phylogenetic analysis grouped our ITS1/2 haplotype within a clade alongside isolates from the Americas. Morphological characterization of the pathogen showed no significant trait variation among samples. These findings confirm the presence of P. kuehnii in the region and highlight the urgent need for cultivar diversification and improved disease management to safeguard sugarcane production. Full article

Plant triterpenoids are structurally diverse specialized metabolites with significant ecological, medicinal, and agricultural importance. Oxidosqualene cyclases (OSCs) catalyze the crucial cyclization step in triterpenoid biosynthesis, generating the fundamental carbon skeletons that determine their structural diversity and biological functions. Genome-wide identification of OSC genes was performed using bioinformatics tools, including HMMER and BLASTP, followed by phylogenetic analysis, gene structure analysis, conserved domain and motifs identification, cis-regulatory element prediction, protein–protein interaction analysis, and expression profiling using publicly available transcriptome data from UV-B treated A. annua six-week-old seedlings. We identified 24 AaOSC genes, classified into CAS, LAS, LUS, and unknown subfamilies. Phylogenetic analysis revealed evolutionary relationships with OSCs from other plant species. Gene structure analysis showed variations in exon–intron organization. Promoter analysis identified cis-regulatory elements related to light responsiveness, plant growth and development, hormone signaling, and stress response. Expression profiling revealed differential expression patterns of AaOSC genes under UV-B irradiation. This genome-wide characterization provides insights into the evolution and functional diversification of the OSC gene family in A. annua. The identified AaOSC genes and their regulatory elements lay the foundation for future studies aimed at manipulating triterpenoid biosynthesis for medicinal and biotechnological applications, particularly focusing on enhancing stress tolerance and artemisinin production. Full article

Serine hydroxymethyltransferases (SHMTs) are key enzymes in one-carbon metabolism, with vertebrates possessing two paralogs, cytosolic SHMT1 and mitochondrial SHMT2, implicated in nucleotide biosynthesis and glycine metabolism. In this study, we investigate the evolutionary history of animal Shmt genes and analyze the expression patterns of Shmt genes in developing amphioxus (Branchiostoma lanceolatum). Phylogenetic analyses indicate the presence of Shmt1 and Shmt2 orthologs in deuterostomes, spiralians and placozoans, which is consistent with an ancient Shmt gene duplication event predating bilaterian diversification. Gene expression analyses in developing amphioxus show that Shmt2 expression is confined to the somites and absent from neural tissues. In contrast, Shmt1 is broadly expressed across germ layers, but its transcription is restricted to tissues characterized by strong cell proliferation. Notably, Shmt1 expression in the nervous system does not match the distribution of glycinergic neuron populations, implying a negligible role in glycine neurotransmitter synthesis. Instead, the spatial correlation of Shmt1 expression with mitotically active domains suggests a primary function in nucleotide biosynthesis via one-carbon metabolism. These findings indicate that SHMTs predominantly support cell proliferation rather than neurotransmission in amphioxus. Full article

Avian metapneumovirus subtype B (aMPV/B) is an economically significant pathogen in poultry, causing respiratory and reproductive disorders. In this study, 167 clinical samples were collected from commercial poultry farms across Thailand to investigate the prevalence, genetic diversity, and evolutionary dynamics of aMPV/B. Nested RT-PCR targeting the G gene revealed a positivity rate of 34.13% (57/167). Phylogenetic and Median-joining network analyses of sequenced amplicons identified two distinct Thai lineages: one genetically similar to vaccine strains and another of unknown origin. Divergence time analysis using a Bayesian framework estimated the time to the most recent common ancestor (tMRCA) of these lineages around 2006, with further sub-lineage diversification occurring around 2009 and 2016. These findings suggest that the circulating Thai aMPV/B strains likely stem from limited introduction events followed by local evolution. Lineage-specific amino acid substitutions within the G gene were identified, which may affect antigenic properties and immune recognition. This study highlights the molecular heterogeneity and ongoing diversification of aMPV/B in Thailand and underscores the need for sustained genomic surveillance and regionally tailored vaccination strategies. Full article

This study conducted a spatiotemporal review of the coelacanth fossil record and explored its distribution and diversity patterns. Coelacanth research can be divided into two distinct periods: the first period, which is based solely on the fossil record, and the second period following the discovery of extant taxa, significantly stimulating research interest. The distribution and research intensity of coelacanth fossils exhibit marked spatial heterogeneity, with Europe and North America being the most extensively studied regions. In contrast, Asia, South America, and Oceania offer substantial potential for future research. Temporally, the coelacanth fossil record also demonstrates significant variation across geological periods, revealing three diversity peaks in the Middle Devonian, Early Triassic, and Late Jurassic, with the Early Triassic peak exhibiting the highest diversity. With the exception of the Late Devonian, Carboniferous, and Late Cretaceous, most periods remain understudied, particularly the Permian, Early Jurassic, and Middle Jurassic, where the record is notably scarce. Integrating the fossil record with phylogenetic analyses enables more robust estimations of coelacanth diversity patterns through deep time. The diversity peak observed in the Middle Devonian is consistent with early burst models of diversification, whereas the Early and Middle Triassic peaks are considered robust, and the Late Jurassic peak may be influenced by taphonomic biases. The low population abundance and limited diversity of coelacanths reduce the number of specimens available for fossilization. The absence of a Cenozoic coelacanth fossil record may be linked to their moderately deep-sea habitat. Future research should prioritize addressing gaps in the fossil record, particularly in Africa, Asia, and Latin America; employing multiple metrics to mitigate sampling biases; and integrating a broader range of taxa into phylogenetic analyses. In contrast to the widespread distribution of the fossil record, extant coelacanths exhibit a restricted distribution, underscoring the urgent need to increase conservation efforts. Full article

Plant protein phosphatase 2C (PP2C) represents the largest and most functionally diverse group of protein phosphatases in plants, playing pivotal roles in regulating metabolic processes, hormone signaling, stress responses, and growth regulation. Despite its significance, a comprehensive genome-wide analysis of the PP2C gene family in oat (Avena sativa L.) has remained unexplored. Leveraging the recently published oat genome, we identified 194 AsaPP2C genes, which were unevenly distributed across all 21 chromosomes. A phylogenetic analysis of PP2C classified these genes into 13 distinct subfamilies (A-L), with conserved motif compositions and exon-intron structures within each subfamily, suggesting evolutionary functional specialization. Notably, a promoter analysis revealed an abundance of stress-responsive cis-regulatory elements (e.g., MYB, MYC, ARE, and MBS), implicating AsaPP2Cs in hormones and biotic stress adaptation. To elucidate their stress-responsive roles, we analyzed transcriptomic data and identified seven differentially expressed AsaPP2C (Asa_chr6Dg00217, Asa_chr6Ag01950, Asa_chr3Ag01998, Asa_chr5Ag00079, Asa_chr4Cg03270, Asa_chr6Cg02197, and Asa_chr7Dg02992) genes, which were validated via qRT-PCR. Intriguingly, these genes exhibited dynamic expression patterns under varying stress conditions, with their transcriptional responses being both time-dependent and stress-dependent, highlighting their regulatory roles in oat stress adaptation. Collectively, this study provides the first comprehensive genomic and functional characterization of the PP2C family in oat, offering valuable insights into their evolutionary diversification and functional specialization. Full article

Potyviruses (family Potyviridae, genus Potyvirus), including emerging ones, pose a growing threat to cucurbit production. This study presents the first virome analysis of severely symptomatic cucurbits in continental Croatia, combining high-throughput sequencing (HTS) and RT-PCR diagnostics. Zucchini, cucumber, and butternut squash plants with severe virus-like symptoms sampled in 2021–2022 were found to consistently host a complex of potyviruses, including watermelon mosaic virus (WMV), zucchini yellow mosaic virus (ZYMV), and Moroccan watermelon mosaic virus (MWMV)—the latter being newly reported in Croatia and representing likely its northernmost detection in Europe. Phylogenetic analysis classified WMV isolates as emerging strains of subgroup EM3 and ZYMV as subgroup A1, consistent with European lineages. Croatian MWMV isolates formed a distinct subclade within the Mediterranean group, raising questions about its diversification trajectory. The findings highlight the expanding range of MWMV and underscore the value of HTS for early detection of emerging threats. These results have critical implications for cucurbit disease management, indicating the need to re-evaluate resistance claims in commercial cultivars and implement stricter phytosanitary surveillance in Croatia. The potential role of climate change in facilitating virus spread via aphid vectors is discussed, warranting further risk assessment and international monitoring efforts. Full article

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. Full article

The plant-specific PLATZ transcription factors play crucial roles in plant growth, development, and responses to abiotic stresses. However, despite their functional significance, PLATZ genes remain poorly characterized in soybeans. In this study, we conducted a genome-wide analysis of the GmPLATZ gene family and investigated their expression profiles under salt stress. We identified a total of 29 GmPLATZ genes in the soybean genome and systematically analyzed their physicochemical properties, conserved domains, evolutionary relationships, cis-acting elements, and expression regulation patterns. Subcellular localization predictions indicated nuclear localization for most GmPLATZs, except for GmPLATZ5 and GmPLATZ14, which showed dual chloroplast–nuclear localization. A gene family expansion analysis indicated that 21 segmental duplication events were the primary driver of GmPLATZ diversification. A phylogenetic analysis classified the GmPLATZ genes into four subgroups, while gene structure and motif analyses revealed conserved zinc-binding domains and identified multiple cis-acting elements associated with light responsiveness, hormone signaling, and stress responses. Expression profiling showed tissue-specific expression patterns, with 13 GmPLATZ genes differentially expressed under salt stress, including root-preferential members (e.g., GmPLATZ1, GmPLATZ10) and leaf-preferential members (e.g., GmPLATZ8, GmPLATZ9). This study provides a theoretical basis for further investigation of GmPLATZ gene functions in soybean development and stress tolerance. Full article

Soil salinization threatens agriculture by inducing osmotic stress, ion toxicity, and oxidative damage. SnRK2 genes are involved in plant stress responses, but their roles in salt stress response regulation of tobacco remain unclear. Through genome-wide analysis, we identified 54 SnRK2 genes across four Nicotiana species (N. tabacum, N. benthamiana, N. sylvestris, and N. tomentosiformis). Phylogenetic reconstruction clustered these genes into five divergent groups, revealing lineage-specific expansion in diploid progenitors (N. tomentosiformis) versus polyploidy-driven gene loss in N. tabacum. In silico promoter analysis uncovered regulatory networks involving light, hormones, stress, and developmental signals, with prevalent ABA-responsive elements (ABREs) supporting conserved stress-adaptive roles. Structural analysis highlighted functional diversification through variations in intron–exon architecture and conserved kinase motifs. This study provides a genomic atlas of SnRK2 evolution in Nicotiana, offering a foundation for engineering salt-tolerant crops. Full article

Adaptive radiations are characterized by increases in rates of lineage and trait evolution, typically due to the opening of new ecological opportunities such as may follow from dispersal to a new region or the evolution of a trait that allows exploitation of new niches. This results in clades that have accumulated unusually high biological diversity within a relatively short evolutionary timespan and hence the phenomenon has attracted longstanding interest amongst evolutionary biologists. Natricidae is a family of snakes with a primarily Old World distribution but which have colonized the New World on a single occasion. This dispersal event coincides with an increased speciation rate that has led to a species-rich New World clade. Herein, we take a phylogenetic comparative approach to investigate a likely adaptive radiation of New World natricids. We first confirmed previously reported findings of a single origin (providing new ecological opportunity) coinciding with a burst of lineage diversification. We then estimate the rates of evolution for three ecologically important traits (body size and broad categories of diet and habitat) separately for New World and Old World natricids. Of these three traits, our results provide evidence that only transition rates between terrestrial and (semi-)aquatic habitats are higher in the New World clade. Taken together, this supports a scenario of an adaptive radiation in natricids primarily associated with differentiation by habitat as the clade spread across the New World following its arrival there. Considering other adaptive radiations alongside our evidence for Natricidae, we propose the hypothesis that there is a common distinction between spatially constrained ‘island’ adaptive radiations (which often diverge along trophic axes) and continental adaptive radiations, which diverge as the clade spreads across a larger spatial scale and adapts to different habitats. Full article

Forests harbor most of the world’s terrestrial biodiversity; however, traditional conservation frameworks prioritize species richness over evolutionary diversity. Phylogenetic diversity (PD) reflects the complete evolutionary history contained within a community, offering a more comprehensive understanding of biodiversity. This review examines the theoretical foundations of PD, highlights methodological advancements in its assessment, and discusses its conservation applications in forest ecosystems. We discuss key metrics, including Faith’s PD, mean pairwise distance (MPD), mean nearest taxon distance (MNTD), and indices, including the net relatedness index (NRI) and nearest taxon index (NTI), as well as analytical tools (Picante, Phylocom, Biodiverse) and frameworks like the categorical analysis of neo- and paleo-endemism (CANAPE) and the evolutionarily distinct and globally endangered (EDGE) index, evaluating their effectiveness in identifying evolutionarily significant conservation areas. We examine global and regional forest PD patterns, including elevational and latitudinal gradients, using case studies from the Pan-Himalayan region, Tibetan Plateau, and northern Pakistan, along with the environmental and anthropogenic drivers, e.g., soil pH, precipitation, land-use change, and invasive species, and historical biogeographic forces that shape lineage diversification. We emphasize the need for data standardization, regional research expansion, and the inclusion of PD in national biodiversity strategies and global policy frameworks. This review highlights the transformative potential of shifting from species-centric to evolutionarily informed conservation, and provides a critical framework for enhancing the long-term resilience and adaptive capacity of forest ecosystems. Full article