Search Results (14)

The degree of informational redundancy is often examined in genetic studies but not yet detailed for taxa conceived as minimally monophyletic groups (microgenus). Evolutionary processes in microgenera were reviewed, detailing critical sets of traits, the novon, the immediate ancestron, and the ancestron. Calculations were made from known intra-genus character state changes for maximum entropy, Shannon entropy, and entropic redundancy. Additional evaluations of contrived data sets were intended to evaluate the range of informational variation in small, medium, and large numbers of species and traits. Results indicate that measures of Shannon information and redundancy are rather similar in all but microgenera with the smallest number of species and traits per species. Hypothetically, this similarity is due to the fairly constant balance between numbers of newly evolved traits and traits monothetically redundant because all are shared with all species in the genus. This balance may be explained by a selective construct or emergent property that balances innovation leading to the colonization of new niches and conservation of proven ancestral traits for survival sympatricially and peripatrically in the particular challenges of the ancestor’s niche. The entropic redundancy calculations indicate that 0.20 to 0.30 of the information in a microgenus serves as flexibility in survival adaptation at the genus level. Full article

To date, the only probiotic yeast with evidence of health-promoting effects is Saccharomyces cerevisiae var. boulardii. The expanded market including dietary supplements and functional foods supplemented with Saccharomyces cerevisiae var. boulardii creates an environment conductive to food adulterations, necessitating rapid testing to verify product probiotic status. Herein, qPCR-HRM analysis was tested for probiotic yeast identification. The effectiveness of the primer pairs’ set was examined, designed to amplify heterogeneous regions in (a) rDNA sequences previously designed to identify food-derived yeast and (b) genes associated with physiological and genotypic divergence of Saccharomyces cerevisiae var. boulardii. Preliminary tests of amplicons’ differentiation power enabled the selection of interspecies sequences for 18SrRNA and ITS and genus-specific sequences HO, RPB2, HXT9 and MAL11. The multi-fragment qPCR-HRM analysis was sufficient for culture-dependent Saccharomyces cerevisiae var. boulardii identification and proved effective in the authentication of dietary supplements’ probiotic composition. The identification of S. cerevisiae var. boulardii in complex microbial mixtures of kefir succeeded with more specific intragenus sequences HO and RPB2. The predominance of S. cerevisiae var. boulardii in the tested matrices, quantitatively corresponded to the probiotic-enriched food, was crucial for identification with qPCR–HRM analysis. Considering the reported assumptions, qPCR-HRM analysis is an appropriate tool for verifying probiotic-enriched food. Full article

Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species. Full article

The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges. Full article

Urban heat islands (UHIs) and global warming will unavoidably have a negative impact on human health in urban areas, making urban forests much more susceptible to the risk of heat waves than forests. It is pivotal for urban forest management to understand tree species’ adaptation mechanisms by focusing on the species-dependent variability of polyamines (PAs), significant players in the amelioration of biotic and abiotic stress in plants, to mitigate the negative effects of UHIs and global warming on human health. Based on this background, the content of major polyamines (PAs) (putrescine, spermidine, and spermine) and total phenolics and the corresponding antioxidant capacities were determined and analyzed in the 24 most prevalent deciduous and coniferous tree species found in urban areas, namely Futoški Park in Novi Sad (Serbia). High-performance liquid chromatography (HPLC) coupled with fluorometric detection (HPLC-FD) was used to separate and quantify major PAs from tree species. Results showed a species-specific level variation in polyamines, total phenolic, and antioxidant capacity in coniferous and deciduous woody plant species in inspected urban areas. In terms of total PA content, the most notable deciduous tree species were Betula pendula, Junglans regia, and Quercus rubra, while the coniferous tree species Thuja occidentalis, Taxodium distichum, Pinus nigra, and Abies concolor stand out. The most dominant foliar PA in most of the inspected species was putrescine (ranging from 527.67 to 10,049.3 nmol g⁻¹ DW), followed by spermidine (from 250.56 to 2015.92 nmol g⁻¹ DW) and spermine (from 168.8 to 718.41 nmol g⁻¹ DW). Furthermore, significant intra-genus variability in terms of PA content was recorded within the genera Pinus, Thuja, and Picea. This study demonstrated that the PA and phenolic compounds, in combination with antioxidant assays, can serve as reliable and trustworthy criteria and descriptors for the selection of adaptable tree species in the context of urban climate–smart forestry. Full article

The Almadén mining district is known to be one of the richest mercury areas in the world. Despite the high concentrations of this metal, this territory has well-established vegetation that provides a wide range of mercury-tolerant plants that can be used as ecosystem services. This is the case of some species of Cistus that grow wild and spontaneously as part of the natural flora of Almadén. The objective of this study was to evaluate if there were differences between the absorption and distribution of Hg of five species of the genus Cistus in spontaneous growth and to evaluate their potential application in phytotechnologies. The work has been carried out with plant samples collected under field conditions in the “Fuente del Jardinillo” located in the old mining area of Almadén (Ciudad Real). The experimental plot was divided into three previously characterised subplots to ensure that all the sampled plants had grown in similar soil conditions (pH, organic matter content, EC, CEC, total Hg and available Hg). Additionally, the experiment was carried out in triplicate. The results showed that despite the homogeneity of the soil, the absorption of Hg in the aerial part of the plants showed significant differences related to Cistus species. The values in the bioaccumulation of mercury in the aerial part were also different. Based on the uptake of mercury by the plants sampled in this study, its potential use in phytotechnologies was established, classifying them as phytoextractors (Cistus albidus, C. ladanifer and C. monspeliensis) and phytostabilisers (C. crispus and C. salviifolius). Full article

Saxifraga species are widely distributed in alpine and arctic regions in the Northern hemisphere. Highly morphological diversity within this genus brings great difficulties for species identification, and their typical highland living properties make it interesting how they adapt to the extreme environment. Here, we newly generated the chloroplast (cp) genomes of two Saxifraga species and compared them with another five Saxifraga cp genomes to understand the characteristics of cp genomes and their potential roles in highland adaptation. The genome size, structure, gene content, GC content, and codon usage pattern were found to be highly similar. Cp genomes ranged from 146,549 bp to 151,066 bp in length, most of which comprised 130 predicted genes. Yet, due to the expansion of IR regions, the second copy of rps19 in Saxifraga stolonifera was uniquely kept. Through sequence divergence analysis, we identified seven hypervariable regions and detected some signatures of regularity associated with genetic distance. We also identified 52 to 89 SSRs and some long repeats among seven Saxifraga species. Both ML and BI phylogenetic analyses confirmed that seven Saxifraga species formed a monophyletic clade in the Saxifragaceae family, and their intragenus relationship was also well supported. Additionally, the ndhI and ycf1 genes were considered under positive selection in species inhabiting relatively high altitudes. Given the conditions of intense light and low CO₂ concentration in the highland, the products of these two genes might participate in the adaptation to the extreme environment. Full article

Morphologically similar to Synechococcus, a large number of Parasynechococcus strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 Synechococcus-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as Parasynechococcus-like strains and showing considerably intragenus genetic divergence among the subclades identified. Further, bioinformatics analysis disclosed diversified patterns of distribution, abundance, density, and diversity of microsatellites (SSRs) and compound microsatellites (CSSRs) in genomes of these Parasynechococcus-like strains. Variations of SSRs and CSSRs were observed amongst phylotypes and subclades. Both SSRs and CSSRs were in particular unequally distributed among genomes. Dinucleotide SSRs were the most widespread, while the genomes showed two patterns in the second most abundant repeat type (mononucleotide or trinucleotide SSRs). Both SSRs and CSSRs were predominantly observed in coding regions. These two types of microsatellites showed positive correlation with genome size (p < 0.01) but negative correlation with GC content (p < 0.05). Additionally, the motif (A)_n, (AG)_n and (AGC)_n was a major one in the corresponding category. Meanwhile, distinctive motifs of CSSRs were found in 39 genomes. This study characterizes SSRs and CSSRs in genomes of Parasynechococcus-like strains and will be useful as a prerequisite for future studies regarding their distribution, function, and evolution. Moreover, the identified SSRs may facilitate fast acclimation of Parasynechococcus-like strains to fluctuating environments and contribute to the extensive distribution of Parasynechococcus species in global marine environments. Full article

Rats, including those of the Sprague Dawley strain, may kill mice. Because of this muricidal behavior, it is standard practice in many research animal housing facilities to separate mice from rats (i.e., the predators) to minimize stress for the mice. We tested the effect of cohousing on the stress levels of mice from either the C57BL/6J (BL6) or the CD1 strain and Sprague Dawley rats (SD rat) by quantifying their fecal corticosterone and metabolites (FCM) concentration. We also investigated cohousing impacts a behavioral assay, i.e., conditioned place preference for intragenus (i.e., mouse–mouse or rat–rat) dyadic social interaction (DSI CPP) that was shown be sensitive to social factors, especially to handling by humans. We found that the two delivery batches of BL6 mice or SD rats, respectively, had different stress levels at delivery that were statistically significant for the BL6 mice. Even so, the BL6 mice cohoused with rats had significantly increased FCM concentrations, indicative of higher stress levels, as compared to (1) BL6 mice housed alone or (2) BL6 mice at delivery. In contrast to their elevated stress levels, the attractiveness of contextual cues associated with mouse–mouse social interaction (DSI CPP) even increased in rat-cohoused BL6 mice, albeit non-significantly. Thus, cohousing BL6 mice and rats did not impair a behavioral assay in BL6 mice that was proven to be sensitive to handling stress by humans in our laboratory. SD rats cohoused with BL6- or CD1 mice, and CD1 mice cohoused with SD rats, showed DSI CPP that was not different from our previously published data on SD rats and BL6 mice of the Jackson- or NIH substrain obtained in the absence of cohousing. CD1 mice cohoused with rats did not show an increased FCM concentration compared to delivery. Our findings suggest that the effect of cohousing rats and mice under the conditions described above on their stress levels as opposed to their behavior might be less clearcut than generally assumed and might be overriden by conditions that cannot be controlled, i.e., different deliveries. Our findings can help to use research animal housing resources, which are usually limited, more efficiently. Full article

Clubroot disease caused by the obligate parasite Plasmodiophora brassicae is a serious threat to cabbage production worldwide. Current clubroot control primarily relies on a fungicide, but this has a negative impact on the environment and the use of a single biocontrol agent cannot efficiently control the disease. Thus, the combined application of different biocontrol agents has been proposed as a promising alternative. In this study, we used bacterial biocontrol agents as a co-culture (inter-genus and intra-genus) and mono-culture to mitigate the clubroot disease of Chinese cabbage. We evaluated their biocontrol effect and plant growth promoter (PGP) traits in in vitro and in vivo experiments. This study revealed that the inter-genus bacterial co-culture significantly suppresses the incidence of clubroot disease and enhances plant growth compared with intra-genus and mono-culture. In pairwise interaction, we observed that Bacillus cereus BT-23 promotes the growth of Lysobacter antibioticus 13-6 (inter-genus bacterial co-culture), whereas L. capsici ZST1-2 and L. antibioticus 13-6 (intra-genus microbial co-culture) are antagonists to each other. Furthermore, a total of 5575 metabolites, 732 differentially expressed metabolites (DEMs), and 510 unique metabolites were detected through the LC-MS/MS technique in the bacterial co-culture. The number of unique metabolites in inter-genus bacterial co-culture (393 metabolites) was significantly higher than in the intra-genus bacterial co-culture (117 metabolites). Further analysis of DEMs showed that the DEMs were mainly involved in four kinds of metabolism pathways, i.e., carbohydrate metabolism, amino metabolism, nucleotide metabolism, and metabolism of cofactors and vitamins. The contents of some secondary metabolites with biocontrol activity and plant growth-promoting functions were increased in inter-genus bacterial co-culture, indicating that inter-genus bacterial co-culture has a solid potential to suppress clubroot disease. We conclude that the inter-genus bacterial interaction changes the community metabolism and improves several secondary metabolites functions with respect to disease control and PGP ability. Full article

Sequencing of whole microbial genomes has become a standard procedure for cluster detection, source tracking, outbreak investigation and surveillance of many microorganisms. An increasing number of laboratories are currently in a transition phase from classical methods towards next generation sequencing, generating unprecedented amounts of data. Since the precision of downstream analyses depends significantly on the quality of raw data generated on the sequencing instrument, a comprehensive, meaningful primary quality control is indispensable. Here, we present AQUAMIS, a Snakemake workflow for an extensive quality control and assembly of raw Illumina sequencing data, allowing laboratories to automatize the initial analysis of their microbial whole-genome sequencing data. AQUAMIS performs all steps of primary sequence analysis, consisting of read trimming, read quality control (QC), taxonomic classification, de-novo assembly, reference identification, assembly QC and contamination detection, both on the read and assembly level. The results are visualized in an interactive HTML report including species-specific QC thresholds, allowing non-bioinformaticians to assess the quality of sequencing experiments at a glance. All results are also available as a standard-compliant JSON file, facilitating easy downstream analyses and data exchange. We have applied AQUAMIS to analyze ~13,000 microbial isolates as well as ~1000 in-silico contaminated datasets, proving the workflow’s ability to perform in high throughput routine sequencing environments and reliably predict contaminations. We found that intergenus and intragenus contaminations can be detected most accurately using a combination of different QC metrics available within AQUAMIS. Full article

Salmonellosis is a zoonotic infection caused by Salmonella enterica serotypes contracted from contaminated products. We hypothesized that competitive exclusion between Salmonella serotypes in neonatal broilers would reduce colonization and affect the host immune response. Day of hatch broilers were randomly allocated to one of six treatment groups: (1) control, which received saline, (2) Salmonella Kentucky (SK) only on day 1 (D1), (3) Salmonella Typhimurium (ST) or Salmonella Enteritidis (SE) only on D1, (4) SK on D1 then ST or SE on day 2 (D2), (5) ST or SE on D1 then SK on D2, and (6) SK and ST or SE concurrently on D1. Salmonella gut colonization and incidence were measured from cecal contents. Livers and spleens were combined and macerated to determine systemic translocation. Relative mRNA levels of interleukin-1β (IL-1β), IL-6, IL-10, IL-18, and gamma interferon (IFN-γ) were measured in cecal tonsils and liver to investigate local and systemic immune responses. When a serotype was administered first, it was able to significantly reduce colonization of the following serotype. Significant changes were found in mRNA expression of cytokines. These results suggest competitive exclusion by Salmonella enterica serotypes affect local and systemic immune responses. Full article

Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological processes important for preservation of the health status of the host. The most widespread microbiota profiling method is based on amplification and sequencing of a variable portion of the 16S rRNA gene as a universal taxonomic marker among members of the Bacteria domain. Despite its popularity and obvious advantages, this 16S rRNA gene-based approach comes with some important limitations. In particular, the choice of the primer pair for amplification plays a major role in defining the accuracy of the reconstructed bacterial profiles. In the current study, we performed an in silico PCR using all currently described 16S rRNA gene-targeting primer pairs (PP) in order to assess their efficiency. Our results show that V3, V4, V5, and V6 were the optimal regions on which to design 16S rRNA metagenomic primers. In detail, PP39 (Probio_Uni/Probio_Rev), PP41 (341F/534R), and PP72 (970F/1050R) were the most suitable primer pairs with an amplification efficiency of >98.5%. Furthermore, the Bifidobacterium genus was examined as a test case for accurate evaluation of intra-genus performances at subspecies level. Intriguingly, the in silico analysis revealed that primer pair PP55 (527f/1406r) was unable to amplify the targeted region of any member of this bacterial genus, while several other primer pairs seem to rather inefficiently amplify the target region of the main bifidobacterial taxa. These results highlight that selection of a 16S rRNA gene-based PP should be done with utmost care in order to avoid biases in microbiota profiling results. Full article

Plant-infecting viruses of the genera Alpha- and Betacryptovirus within the family Partitiviridae cause no visible effects on their hosts and are only transmitted by cell division and through gametes. The bipartite dsRNA genome is encoding a RNA-dependent RNA polymerase (RdRp) and a coat protein (CP). Aside from sequence and structural analysis, the investigation of protein interactions is another step towards virus characterization. Therefore, ORFs of two type members White Clover Cryptic Virus 1 and 2 (WCCV-1 and WCCV-2), as well as the related viruses from Red Clover and Dill were introduced into a bimolecular fluorescence complementation assay. We showed CP-CP dimerization for all tested viruses with localization for alphacryptoviruses at the nuclear membrane and for betacryptoviruses close to cell walls within the cytoplasm. For CPs of WCCV-1 and WCCV-2, deletion mutants were created to determine internal interaction sites. Moreover, RdRp self-interaction was found for all viruses, whereas CP-RdRp interactions were only detectable for the alphacryptoviruses. An intra-genus test of CPs was successful in various virus combinations, whereas an inter-genus interaction of WCCV-1CP and WCCV-2CP was absent. This is the first report of in vivo protein interactions of members in the family Partitiviridae, indicating distinct features of the alpha- and betacryptoviruses. Full article