High Genetic Similarity Research Articles

Unveiling three novel actinobacterial species (Streptomyces cavernicola sp. nov., Streptomyces solicavernae sp. nov. and Streptomyces luteolus sp. nov.) in soil samples in Phu Pha Phet Cave, Thailand.

Three strains of actinobacteria, designated as B-S-A6T, B-S-A8T and B-S-A12T, were isolated from soil samples collected in the Phu Pha Phet Cave located in the Satun UNESCO Global Geopark, Satun Province, Thailand. A comprehensive polyphasic approach was used to describe these strains. Strains B-S-A6T, B-S-A8T and B-S-A12T were identified within the genus Streptomyces based on a comparative examination of 16S rRNA gene sequences. Strains B-S-A8T and B-S-A12T showed a high genetic similarity to Streptomyces spectabilis NBRC 13424T (99.0%, for both) and to Streptomyces deserti C63T (98.6 and 98.7 %, respectively). Meanwhile, strain B-S-A6T exhibited 98.6% sequence similarity with S. spectabilis NBRC 13424T and Streptomyces koyangensis VK-A6 T. However, upon further comparison, the 16S rRNA gene sequence of strain B-S-A6T showed a similarity of 99.6% to B-S-A8T and 99.7% to B-S-A12T. Contrastingly, B-S-A8T showed a very high similarity of 99.8% with B-S-A12T. The use of digital DNA-DNA hybridization, along with the analysis of average nt identities and aa identities, comparing the three strains to their closest known type strains, validated that each of these strains represents a new and distinct species. Three newly identified strains exhibited phenotypic characteristics and chemotaxonomic properties consistent with the members of the genus Streptomyces. The primary menaquinones identified in these strains were MK-9(H6) and MK-9(H8). The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Their polar lipid profiles included diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The comprehensive phenotypic and genomic analyses of the Streptomyces strains strongly suggest that strains B-S-A6T, B-S-A8T and B-S-A12T represent three new species for which the names Streptomyces cavernicola sp. nov. (type strain B-S-A6T =TBRC 17074T =NBRC 116118T), Streptomyces solicavernae sp. nov. (type strain B-S-A8T =TBRC 17072T =NBRC 116117T) and Streptomyces luteolus sp. nov. (type strain B-S-A12T =TBRC 17060T =NBRC 116116T) are proposed.

Genetic variability of abundant littoral species of mesostigmatic mites (Acari, Mesostigmata) with different distributions from the seashores of Eurasia

The marine littoral acarofauna is of interest both in relation to the history of seas and as biological indicators of water quality, but it remains poorly studied. For the first time, we characterize the molecular genetic variability of four widespread, common and abundant species of littoral mesostigmatic mites: Phorytocarpais kempersi, Parasitidae; Halolaelaps celticus and Halolaelaps orientalis, Halolaelapidae; and Thinoseius spinosus, Eviphididae. Based on the nucleotide sequence analysis of nuclear ribosomal repeats (ITS), we studied mite collections from the coasts of the Caspian, Azov, Black, Baltic, White, Barents, Norwegian, Bering, Okhotsk, and Japan seas. The molecular identification of the species studied, based on DNA barcoding using ITS sequences, appears to be clear. We obtained genetic evidence for the separation of Halolaelaps celticus and H. orientalis as two distinct species, based both on clustering their ITS genotypes (separated by 6 parsimony-informative substitutions) and the geographic distributions of their genotypes. The high genetic similarity of the western and eastern Palaearctic populations in both arctic-adapted species, Phorytocarpais kempersi and Thinoseius spinosus, is explicable in terms of their rather recent contact on the northern coast of Eurasia during the last interglacial or Holocene climatic optimum. The high genetic similarity of Halolaelaps orientalis, a relatively thermophilous species, from the Mediterranean region (the Azov, Black, and Caspian seas) with a sample from the very distant Sea of Japan suggests a recent connection between the European and Pacific populations via the Indian Ocean.

Reclassification of two Nocardiopsis species using whole genome analysis.

This study revisits the taxonomic classification of the genus Nocardiopsis through the application of advanced genome-based methodologies, representing a notable advancement beyond traditional approaches that primarily rely on 16S rRNA gene sequences and phenotypic traits. The advent of Next-Generation Sequencing (NGS) and sophisticated bioinformatic tools has enabled a more precise framework for prokaryotic classification. However, many recognized species still lack complete genome sequences. In this study, we employed overall genome-related indices (OGRI), particularly Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH), to reassess the phylogenetic relationships within the genus. Comparative analyses of complete 16S rRNA sequences demonstrated high genetic similarity between N. umidischolae 66/93T and N. tropica VKMAc-1457T (99.61% similarity), as well as between N. rhodophaea JCM15313T and N. rosea JCM15314T (100% identity). The dDDH, ANI%, FastANI%, ANIm, and ANIb values further supported these results, with 73.2%, 96.94%, 96.15%, 97.19%, and 96.74% for the former pair, and 93.6%, 99.13%, 99.97%, 99.98%, and 99.27% for the latter pair, respectively. All values surpassed the species delineation thresholds of 70% for dDDH and 95-96% for ANI. Consequently, we propose reclassifying N. umidischolae as a heterotypic synonym of N. tropica, and N. rosea as a heterotypic synonym of N. rhodophaea, in accordance with the International Code of Nomenclature of Prokaryotes (ICNP).

Species Identification and Genotyping of Cutaneous Leishmaniasis in Clinical Samples Based on ITS1-PCR-Sequencing in Southeast Iran.

Cutaneous leishmaniasis (CL) is one of the most common parasitic diseases in many regions of Iran. It has a major role in deprived societies. We aimed to identify Leishmania species based on molecular as ITS1-rDNA-PCR internal transcribed spacer 1 (ITS1) region, microscopy, and culture techniques in diagnosing cutaneous leishmaniasis. From April 2018 to May 2020, we conducted a cross-sectional study involving 32 patients with suspected CL lesions in Sistan and Baluchistan Province, located in southeast Iran. Samples were subjected to microscopic examination, culture, and PCR amplification targeting the internal transcribed spacer 1 (ITS1) region. DNA sequencing was performed on PCR-positive samples for species identification and phylogenetic analysis. PCR demonstrated superior sensitivity (93.75%, 30/32) compared to culture (56.25%, 18/32) and microscopic examination (53.1%, 17/32). Molecular analysis revealed that L. major was the predominant causative agent of CL in the study area, with L. tropica occurring less frequently. Sequencing and phylogenetic analysis of the ITS1 region showed high intraspecies similarity among L. tropica isolates, while L. major isolates exhibited greater genetic diversity. This study shows the co-existence of L. major and L. tropica in Mirjaveh, southeast Iran, with L. major as the primary cause. While L. tropica isolates displayed high genetic similarity, L. major samples were more diverse, indicating different epidemiological patterns. These findings highlight the importance of molecular methods for accurately identifying Leishmania species and understanding CL epidemiology in the region.

Caenorhabditis elegans as an Outstanding Model to Explore Flavonoids Under Stress Conditions

Abstract: Plants produce promising chemicals called secondary metabolites in response to stress, which protect against oxidative damage in both plants and humans. Reactive oxygen species (ROS) levels combined with an imbalance in the antioxidant responses can trigger oxidative stress that is related to many conditions such as Alzheimer's disease, diabetes, and cancer. One way to counteract or avoid the stress excess is by flavonoid administration, a class of plant metabolites with a consistent antioxidant action and the ability to inactivate the free radical excess. The mechanisms, as well as the benefits and toxicity of antioxidant products, can be tested in alternative animal models. The mechanisms, as well as the benefits and toxicity of antioxidant products, can be tested in alternative animal models. In this review, we explored how Caenorhabditis elegans, a nematode with high genetic similarity to human genes and the antioxidant response pathway conserved, can be considered an attractive model organism for testing flavonoid compounds. Here, we emphasize the crucial results regarding C. elegans and the flavonoid quercetin, focusing on oxidative stress and aging investigations. Also, this review highlights the quercetin benefits in C. elegans lifespan, healthspan, neurodegeneration, and impacts on insulin/IGF-1 signaling (IIS).

Sexual Trauma, Polygenic Scores, and Mental Health Diagnoses and Outcomes

Leveraging real-world clinical biobanks to investigate the associations between genetic and environmental risk factors for mental illness may help direct clinical screening efforts and evaluate the portability of polygenic scores across environmental contexts. To examine the associations between sexual trauma, polygenic liability to mental health outcomes, and clinical diagnoses of schizophrenia, bipolar disorder, and major depressive disorder in a clinical biobank setting. This genetic association study was conducted using clinical and genotyping data from 96 002 participants across hospital-linked biobanks located at Vanderbilt University Medical Center (VUMC), Nashville, Tennessee (including 58 262 individuals with high genetic similarity to the 1000 Genomes Project [1KG] Northern European from Utah reference population [1KG-EU-clustered] and 11 047 with high genetic similarity to the 1KG African-ancestry reference population of Yoruba in Ibadan, Nigeria [1KG-YRI-clustered]), and Mass General Brigham (MGB), Boston, Massachusetts (26 693 individuals with high genetic similarity to the combined European-ancestry superpopulation [1KG-EU-clustered]). Clinical data analyzed included diagnostic billing codes and clinical notes spanning from 1976 to 2023. Data analysis was performed from 2022 to 2024. Clinically documented sexual trauma disclosures and polygenic scores for schizophrenia, bipolar disorder, and major depressive disorder. Diagnoses of schizophrenia, bipolar disorder, and major depressive disorder, determined by aggregating related diagnostic billing codes, were the dependent variables in logistic regression models including sexual trauma disclosure status, polygenic scores, and their interactions as the independent variables. Across the VUMC and MGB biobanks, 96 002 individuals were included in analyses (VUMC 1KG-EU-clustered: 33 011 [56.7%] female; median [range] age, 56.8 [10.0 to >89] years; MGB 1KG-EU-clustered: 14 647 [54.9%] female; median [range] age, 58.0 [10.0 to >89] years; VUMC 1KG-YRI-clustered: 6961 [63.0%] female; median [range] age, 44.6 [10.1 to >89] years). Sexual trauma history was associated with all mental health conditions across institutions (ORs ranged from 8.83 [95% CI, 5.50-14.18] for schizophrenia in the VUMC 1KG-YRI-clustered cohort to 17.65 [95% CI, 12.77-24.40] for schizophrenia in the VUMC 1KG-EU-clustered cohort). Sexual trauma history and polygenic scores jointly explained 3.8% to 8.8% of mental health phenotypic variance. Schizophrenia and bipolar disorder polygenic scores had greater associations with mental health outcomes in individuals with no documented disclosures of sexual trauma (schizophrenia interaction: OR, 0.70 [95% CI, 0.56-0.88]; bipolar disorder interaction: OR, 0.83 [95% CI, 0.74-0.94]). Sexual trauma and mental health polygenic scores, while correlated with one another, were independent and joint risk factors for severe mental illness in a large, diverse hospital biobank population. Furthermore, associations of schizophrenia and bipolar disorder polygenic scores with respective diagnoses were greater in those without disclosures, suggesting that genetic predisposition to mental illness as measured by polygenic scores may be less impactful in the presence of this severe environmental risk factor.

Phylogenetic Study of Several Parasitic Plant Species Based on The atp-1 Gene Sequence

The distinction between parasitic and non-parasitic plants can be determined by analyzing the atp-1 gene, which plays a vital role in respiration and is known for its high mutation rate. This study analyzed the kinship of parasitic plant subclass species through the construction of a phylogenetic tree based on atp-1 gene sequences. The atp-1 gene sequences of parasitic and non-parasitic plants with a total of 29 species were obtained from NCBI. The sequences were then aligned with ClustalW and analyzed for mutation patterns. Sequences that have been aligned, phylogenetic trees were made with MEGA11 software with the Maximum Likelihood method and analyzed using the iTOL website. The sequences were analyzed for similarity and kinship with Matrix Coefficient and Haplotype Construction. The atp-1 gene proved that parasitic plants (hemiparasites) are furthermore related to non-parasitic plants compared to holoparasite parasitic plants. Besides that, the kinship of parasitic plants can be analyzed by several methods, namely matrix coefficient to measure similarity, DnaSP to analyzing haplotype, and haplotype network to find out detailed information on mutations that occur. Matrix coefficients can also be used to measure specific similarities between species. It was found that the same subclass had high similarities, for example the species Santalum album and Heisteria parvifolia with a genetic distance value of 0.00574. Meanwhile, different subclasses have low similarity, such as Cassytha filiformis and Ombrophytum with a genetic distance value of 0.07871. This study shows that the atp-1 gene is effective in analyzing the kinship between parasitic and non-parasitic plants. Hemiparasites are genetically closer to non-parasitic plants than holoparasites, with higher genetic similarity within the same subclass.

Exome sequencing identifies a novel FBN1 variant in a Chinese family with Marfan syndrome that includes aberrant right subclavian artery

Abstract Background Marfan syndrome (MFS) is an inherited autosomal dominant disorder that affects connective tissue with an incidence of about 1 in 5,000 to 10,000 people. Ninety percent of MFS is caused by mutations in the fibrillin-1 (fbn1) gene. We recruited a family with MFS phenotype in South China and identified a novel variant in fbn1 by whole exome sequencing (WES). The zebrafish share high genetic similarity to humans. This study aimed to generate this novel mutation in the fbn1 gene of zebrafish using the CRISPR/Cas9 technology and researched whether this variant is pathogenic. Methods A three-generation consanguineous family was recruited in this study, which was visited and interviewed for the clinical data and family history. Peripheral blood samples were collected from family members for DNA isolation and WES. The 3D structure of the protein was predicted by Alphafold. CRISPR/Cas9 was applied to generate an fbn1 nonsense mutation (fbn1+/−) in zebrafish. Morphological abnormalities were assessed in F2 fbn1+/− zebrafish by comparing with the wild-type (WT) controls at different development stages. Results Our study recruited a family with MFS phenotype in South China and identified a novel variant [NM_000138.5; c.7764C>G: p.(Y2588*)] in fbn1. Through Sanger sequencing, we found that family members Ⅲ-1 (son) and Ⅲ-2 (daughter) had the fbn1 variant segregated with MFS in the family. The p.Y2588* mutation resulted in the absence of 283 amino acids, thereby leading to the deficiency of 17 β-folded structures, 4 α-helix structures, and various loop structures. Compared with WT zebrafish, F2 fbn1+/− zebrafish exhibited aortic arches bleeding, abnormal angiogenesis, decreased cardiac volume, cardiac function defects, curly tail, and cartilage malformations. Conclusion A novel variant [NM_000138.5; c.7764C>G: p.(Y2588*)] was identified in fbn1 gene, which has not been reported in previous literature. The variant caused loss of function through premature protein truncation or nonsense-mediated mRNA decay. In zebrafish, we identified functional evidence of the detected nonsense mutation, which aligns with the clinical significance, suggesting a pathogenic variant of fbn1. Zebrafish as a novel, efficient tool to allow for the quick classification of unknown variants in fbn1 and improve the clinical diagnosis and treatment of MFS. It has brought the implementation of personal and precision medicine in the clinic within reach and made it possible to find patient-specific treatments.Marfanoid symptoms of the patient.Phenotypic Spectrum of fbn1+/− Zebrafish

An Outbreak of Acute Hemorrhagic Conjunctivitis Caused by Coxsackievirus A24 in Eastern Uttar Pradesh, India 2023

Introduction: Acute hemorrhagic conjunctivitis (AHC) outbreaks are caused mostly by viruses. During July-August 2023, there was a sudden spike in acute hemorrhage conjunctivitis cases in Eastern Uttar Pradesh, India. To identify the etiological and gain molecular epidemiology of the agent, the study was conducted. Methodology: Conjunctival swabs were collected from patients (n = 128) with presumed acute hemorrhage conjunctivitis visiting two tertiary care hospitals. Results: Enteroviruses infection was identified in 96 (75%) patients. In these patients, coxsackievirus A24 (CV-A24) infection was further confirmed by targeting the genetic regions of 3C protease and VP1. Furthermore, the study established the outbreak was caused by the genotype IV of CV-A24 with the highest genetic similarity with CV-A24 reported from Northeast India, China, and Pakistan circulating during the same period. The comparison of our study sequences with earlier Indian outbreak strains (2007) revealed four amino acid substitutions at the 3C region (“S21N,” “V30I,” “S66I,” and “V75I”) and three non-synonymous mutations at the VP1 region (“L16I,” “P21S,” and “N301D”). Conclusion: The study findings revealed that the AHC outbreak was caused by genotype IV of CV-A24 in this region. Molecular identification accompanied by phylogenetic analysis will be useful in studying the enterovirus epidemiology associated with AHC outbreaks.

Genetická charakterizace tisu červeného (Taxus baccata L.) v širší oblasti Podyjí/Thayatal a na Svitavsku s vazbou na ochranářský management

The aim of the work is to determine the genetic diversity, genetic differentiation and genetic structure of subpopulations of the specially protected common yew in the area of South Moravian Podyjí (Czech Republic), Thayatal (Austria) and in the Svitavy region (Czech Republic) using DNA analyses (nSSR-nuclear Simple Sequence Repeats). The subjects of the analyses were yews of 1) natural occurrences in the territory of the Podyjí National Park (NP), 2) cultural origin in the Podyjí NP, 3) natural occurrences in the Thayatal NP (Austria), 4) natural occurrences outside the Podyjí NP, and 5) cultural origin in the Podyjí region outside the NP. For the comparison and better interpretation of results there also were analysed geographically more distant subpopulations, 6) natural occurrences in the Hřebečský ridge (NW Moravia), 7) cultural yew occurrences in the Svitavy region (NE Bohemia & NW Moravia), 8) natural occurrences in the Jílovské yews (N Bohemia), and 9) natural occurrences in the Moravian Karst (S Moravia). We observed higher level of genetic diversity (Ho = 0.54; He = 0.77), the FST with ENA correction ranged from 0.007 to 0.123. According to a STRUCTURE analysis, high genetic similarity was observed between samples from the Podyjí NP and Hřebečský ridge. The impact of the analysis results on the conservation management of tested populations was outlined.

Avian Metapneumovirus Subtype B Circulation in Poultry and Wild Birds of Colombia.

The global poultry industry, as a leading producer of animal protein, faces significant challenges related to animal health and production due to high bird density and disease risks. A major concern is the Avian Respiratory Complex (ARC), a multifactorial health issue involving pathogens such as avian metapneumovirus (aMPV), an often-underdiagnosed component of the ARC. Wild birds are seen as reservoirs and spreaders of the virus. This study aimed to detect the presence and subtypes of aMPV in samples from breeders, broilers, laying hens, and wild birds in Colombia. A total of 273 samples, including swabs from the upper respiratory and reproductive tracts, were collected from commercial poultry and wild birds. Using nested RT-PCR targeting the G gene, aMPV subtype B was identified in 23 samples (8.42%). Sequencing revealed high genetic similarity to vaccine strains, classifying all viruses as vaccine-like. In the commercial birds, aMPV-B appeared in 21 samples, regardless of symptoms, often in tests for other ARC agents, indicating diagnostic bias. In the wild birds, two samples tested positive, suggesting potential transmission between wild and domestic birds. These findings highlight the need for broader diagnostics and further research into aMPV's impact on avian health.

Integrated characterization and in vitro biocontrol of Fusarium sp. using Trichoderma asperellum

Pepper is a crop of great economic importance in Mexico. However, it is affected by multiple diseases. The aim of this research was to identify through morphological and molecular methods the causal agent of both foliar and root wilting in jalapeño pepper plants (Capsicum annuum L.), and the ability of Trichoderma asperellum to control these diseases in vitro. The causal agent of the disease was isolated from soil and foliar samples of jalapeño pepper fields in Delicias, Chihuahua, Mexico. The fungus was cultured on solid PDA medium to study its morphology. The CTAB method was used to extract DNA from Fusarium sp. The ITS1 and ITS4 primer pair was used to amplify a 850 bp DNA fragment by PCR. The sequence was deposited in Genbank (acc. no. OR801070) and used for phylogenetic analysis using Bayesian inference. The analysis revealed five clades and the isolate was placed in clade 4, which showed high genetic similarity with F. oxysporum (99.28% identity). Based on these molecular, morphological and phylogenetic data, the isolate was identified as Fusarium oxysporum Schltdl. The biocontrol potential of T. asperellum (accession No. MN95047) against F. oxysporum was tested in vitro and it showed 40% to 87.5% inhibition of the pathogen. These findings are important for managing this pathogen and reducing the use of chemical fungicides.

Genetic diversity and population structure of Botryosphaeria dothidea and Neofusicoccum parvum on English walnut (Juglans regia L.) in France

Botryosphaeriaceae species are the major causal agents of walnut dieback worldwide, along with Diaporthe species. Botryosphaeria dothidea and Neofusicoccum parvum are the only two Botryosphaeriaceae species associated with this recently emergent disease in France, and little is known about their diversity, structure, origin and dispersion in French walnut orchards. A total of 381 isolates of both species were genetically typed using a sequence-based microsatellite genotyping (SSR-seq) method. This analysis revealed a low genetic diversity and a high clonality of these populations, in agreement with their clonal mode of reproduction. The genetic similarity among populations, regardless of the tissue type and the presence of symptoms, supports the hypothesis that these pathogens can move between fruits and twigs and display latent pathogen lifestyles. Contrasting genetic patterns between N. parvum populations from Californian and Spanish walnut orchards and the French ones suggested no conclusive evidence for pathogen transmission from infected materials. The high genetic similarity with French vineyards populations suggested instead putative transmission between these hosts, which was also observed with B. dothidea populations. Overall, this study provides critical insight into the epidemiology of two important pathogens involved in the emerging dieback of French walnut orchards, including their distribution, potential to mate, putative origin and disease pathways.

Detection and characterization of hemotropic Mycoplasmas in Iberian wolves (Canis lupus signatus) of Cantabria, Spain

Hemoplasmas (hemotropic mycoplasmas) are uncultivable wall-less bacteria able to infect mammalian erythrocytes. Hemoplasmas can cause anemia, especially in immunocompromised hosts, predisposing to secondary infections and even leading to death. Between 2017 and 2023, spleen samples of 131 wild Iberian wolves (Canis lupus signatus) of Cantabria (Spain) were screened for Mycoplasma spp. using a real-time PCR able to amplify a 360 bp fragment of the 16S rRNA gene and confirmed by direct Sanger sequencing. Additional conventional PCRs were performed to screen for coinfections by different Mycoplasma species and to discriminate between Mycoplasma haemocanis/haemofelis (Mhc/Mhf). Overall, 24/131 (18.3%) animals were PCR-positive. Biological and environmental factors potentially promoting hemoplasma infection in this species were analyzed. Two different hemoplasma species were detected: Mhc/Mhf (18/131; 13.7%) and Candidatus Mycoplasma haematoparvum (CMhp) (3/131; 2.3%), each with one nucleotide sequence type (ntST); three other sequences were not classified. No Mhc/Mhf and CMhp coinfection were observed. The 12 Mhc/Mhf suitable for ribonuclease P RNA sequencing were confirmed as Mhc. Mhc ntST was 100% identical to a Mhc sequence previously obtained in domestic dogs (Canis lupus familiaris), and in wild Iberian wolves of northwestern Spain (Asturias and Galicia) at a similar prevalence to the one found herein, suggesting a high Mhc genetic homogeneity in this wild population. CMhp ntST was 100% identical to CMhp sequences from domestic dogs. To our knowledge, this is the first description of CMhp in the Iberian wolf. The high genetic similarity observed in Mhc and CMhp sequences, as well as their high similarity with domestic dog sequences, suggest its recent introduction, a high level of intraspecific transmission within the wild wolf population, and likely, interspecific transmission between wolves and domestic dogs.

Pathogenomic profile and clonal diversity of potential zoonotic MRSA-CC7-ST789-t091-SCCmecV from human skin and soft tissue infections

The whole genome sequence (WGS) of prevalent MRSA strains harboring mecA gene obtained from skin and soft tissue infections (SSTIs) in Nigerian hospitals were profiled for pathogenomic structure and evaluated for clonal diversity. The two MRSA strains identified among 66 isolated multi-drug resistant S. aureus from a collection of 256 clinical samples were phenotyped for antibiotic resistance and genotyped for mecA, SCCmec, and spa types. The mecA positive MRSA was analysed using whole-genome sequencing for resistomes, virulomes, phylogenomic profiles and clonal diversity. The identified MRSA-CC7-ST789-t091-SCCmecV strains from a female child (aged 1 year) with severe otorrhea and an adult male (aged 23) with purulent wound abscess showed high-level resistance to streptomycin, vancomycin, kanamycin, sulfamethoxazole and ciprofloxacin. Both strains harbored abundant resistomes, inherent plasmids, chromosomal replicons and typical seven housekeeping genes (arc3, aroE4, glpF1, gmk4, pta4, tpi6, yqiL3). The most abundant putative virulomes were pathogenesis-associated proteins (included hemolysin gamma, leucocidins, proteases, staphylococcal superantigen/enterotoxin-like genes (Set/Ssl), capsule- and biofilm-associated genes, and hyaluronate lyase). Comparative phylogenomic analysis revealed the relatedness of the two clonal strains with prevalent MRSA-CC7 pathotypes observed in Italy (2013 and 2014), Denmark (2014), Thailand (2015 and 2016), USA (2018), and Nigeria (2016 and 2020); and share high genetic similarities with livestock strains from cow milk and cattle. Identified MRSA-CC7-ST789-t091-SCCmecV pathotypes implicated in SSTIs from Nigeria harboring repertoires of antibiotic resistance and virulence genes, and genetic relatedness with livestock strains; show the possibility of gene transfer between animal and human. Adequate hospital MRSA infection control and geno-epidemiological surveillance for animal and human transfer is required.

Molecular evaluation of several wheat varieties of Triticum aestivum L.

This study was carried out with the aim of determining the extent of genetic variation among 10 varieties of wheat. In this work, 5 primers were used to do the PCR to detect the band patterns of ISSR markers. Within the molecular weight range of 100-1500 bp, the 5 primers combined to generate 42 bands, at a rate of 8 bands per primer. Polymorphic bands accounted for 37 of the totals and the ratio of polymorphic bands was 87.97 %. The highest percentage of divergent bands reached 88.88 %, shown by primers HPS13, 842F and HBG20. The starters 1955A recorded a lower rate of efficiency and distinctive ability of the starter reaching 16.22 %. According to the UPGMA method, a phylogenetic tree of the genetic affinity between the varieties was obtained, varieties were separated into 2 major groups: There were 2 varieties in the first major group, namely S7 and S6, 2 minor groups were formed from the division of the second major group. The S3 variant made up the first secondary group, as opposed to the second secondary group. Additionally, it was split into 2 sub-secondary groups: classes S5, S10, S9, S8 and S1 made up the first sub-secondary group and classes S4 and S2 made up the second. Based on the Nei and Li coefficient, the values of genetic similarity between the varieties were estimated, because the S6 variety and the S3 variety had the largest genetic divergence (lowest genetic similarity), with a value of 0.7073 and with the S4 variety, its value was 0.6829, while the highest genetic similarity was (least genetic divergence) between variety S9 and variety S8, where its value reached 0.9268. The findings of this study showed the high efficiency of ISSR makers in detecting genetic variation among several wheat varieties.

Genetic Variation among Rare Florida Endemic Hymenocallis henryae Populations and the Implication for Conservation and Management

Hymenocallis henryae is a rare, charismatic spider lily endemic to the Florida panhandle. Currently under review to determine if listing under the Endangered Species Act is warranted, this species has undescribed genetic diversity, information crucial to the listing process. We conducted field observations of 21 historic populations across the species’ geographical range and performed genomic analyses of 279 individuals from 19 extant populations. Most populations had fewer than 40 individuals, while populations with >100 individuals were found exclusively on managed lands. Genetic diversity was uniformly low within populations (HE: 0.074–0.093), with low to moderate inbreeding coefficients (FIS: 0.068–0.431). Genetic differentiation was relatively low among most populations (FST: 0–0.098), although there was statistical support for isolation by distance. In addition, we found high genetic similarity and lack of population structure across the species range. Clonal propagation through fused bulbs is a common reproductive strategy. We confirmed current threats (habitat change, residential development, fire suppression) and identified several coastal populations threatened by sea level rise. It is recommended to continue with in situ protection and management as well as the establishment of ex situ living collections to preserve populations most at risk of extirpation from habitat loss and degradation.

SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity.

Circulating bat coronaviruses represent a pandemic threat. However, our understanding of bat coronavirus pathogenesis and transmission potential is limited by the lack of phenotypically characterized strains. We created molecular clones for the two closest known relatives of SARS-CoV-2, BANAL-52 and BANAL-236. We demonstrated that BANAL-CoVs and SARS-CoV-2 have similar replication kinetics in human bronchial epithelial cells. However, BANAL-CoVs have impaired replication in human nasal epithelial cells and in the upper airway of mice. We also observed reduced pathogenesis in mice and diminished transmission in hamsters. Further, we observed that diverse bat coronaviruses evade interferon and downregulate major histocompatibility complex class I. Collectively, our study demonstrates that despite high genetic similarity across bat coronaviruses, prediction of pandemic potential of a virus necessitates functional characterization. Finally, the restriction of bat coronavirus replication in the upper airway highlights that transmission potential and innate immune restriction can be uncoupled in this high-risk family of emerging viruses.

Taxonomy of the genus Ctenomys (Rodentia: Ctenomyidae) in central Argentina: Redefining the limits of Ctenomys bergi Thomas, 1902

Ctenomys Blainville, 1826 (known as tuco-tucos) is considered one of the most diverse genus within mammals; however, its taxonomy is far from resolved. In recent years, new species have been described, and many other forms have been synonymized, while other lineages remain as candidate species. In this work, based on molecular and morphological evidence, we proposed that C. “rosendopascuali”, a taxon considered as a nomen nudum, is in fact a synonym of C. bergi Thomas, 1902. The molecular phylogeny based on the mitochondrial cytochrome b gene showed that individuals from populations a priori assigned to C. bergi and C. “rosendopascuali” were not reciprocally monophyletic. Additionally, geometric morphometric analyses based on cranial morphology showed significant overlap in the morphospace of these two taxa. Our results also show a high genetic similarity among C. bergi, C. “yolandae”, and C. bonettoi Contreras and Berry, 1982, questioning the taxonomic status of the latter two taxa and highlighting the need for exhaustive comparison with C. bergi. We also identified a second locality for a highly divergent lineage within the Mendocinus group (Quijadas lineage). Our study confirms the divergence of this lineage and highlights the need to further taxonomic studies in order to evaluate whether it represents a possible undescribed Ctenomys species.

Complete mitochondrial genomes of Bactrocera (Bulladacus) cinnabaria and B. (Bactrocera) propinqua (Diptera: Tephritidae) and their phylogenetic relationships with other congeners

Bactrocera (Bulladacus) cinnabaria and B. (Bactrocera) propinqua are tephritid fruit flies of the subfamily Dacinae, tribe Dacini. The whole mitogenomes of these two species (first report for the subgenus Bulladacus) possess 37 genes (13 protein-coding genes – PCGs, 2 rRNA and 22 tRNA genes). The mitogenome of B. cinnabaria (15,225 bp) is shorter than that of B. propinqua (15,927 bp), mainly due to the smaller size of the control region and intergenic spacers in B. cinnabaria. Molecular phylogeny based on mitochondrial genes (mt-genes) reveals two clades of the genus Bactrocera: one comprising the subgenus Bactrocera and the other comprising the subgenera Bulladacus, Daculus, Tetradacus and unassigned Bactrocera sp. ‘yunnanensis’. The subgenera represented by two or more taxa are monophyletic. B. (Bulladacus) cinnabaria forms a sister group with the subgenus Tetradacus (B. minax and B. tsuneonis) and B. sp. ‘yunnanensis’, in a clade containing also the basal sister lineage of the subgenus Daculus (B. oleae and B. biguttula). B. propinqua forms a sister group with B. ritsemai and B. limbifera in a subclade containing also B. umbrosa, B. curvifera and B. moluccensis of the monophyletic subgenus Bactrocera. The present study supports the synonymy of B. ruiliensis with B. thailandica. It also shows a high genetic similarity between (a) B. melastomatos and B. rubigina, (b) B. papayae and B. philippinensis, (c) B. dorsalis and B. invadens, (d) B. tryoni and B. neohumeralis, and (e) B. cheni and B. tuberculata; and B. cheni is distinct from and not a synonym of B. tsuneonis or B. lombokensis.