Clustering Of Genotypes Research Articles

Exploring the synergy of enzymes, nutrients, and gene networks in rice starch granule biogenesis

IntroductionRice is a primary food source almost for more than 50% of the total world's population. Glycemic index (GI) is high in most of the rice varieties, limiting their consumption by diabetic and obese people. As a result, developing new rice varieties with low GI necessitates a thorough understanding of starch biogenesis gene expression and its interrelationship.MethodsA total 200 rice genotypes were analyzed for total starch content (TSC), amylopectin content (APC), and amylose content (AC). The clustering of these rice genotypes was done based on their AC. Further, these genotypes were categorized into three groups up to 10% amylose-low, 10–26% amylose-medium, and more than 26% amylose-high. Among them, six genotypes 1 from low AC (NJ-72), 2 from medium AC (UPRI-2003-18, PRR-126), and 3 from high AC (RNRM-7, Urvashi and Ananga) were selected. The genotypes selected from the medium and high AC groups were having 2% amylose variation among themselves respectively and they were further used to study the level of RS, protein content (PC), fatty acid (FA) profiles, and granule morphology along with low group sample.ResultsResistant starch (RS) content ranged from 0.33–2.75%, and fatty acid profiling revealed high levels of palmitic, linoleic, and oleic acids. The degree of crystallinity and APC% were found to be positively correlated. Ananga, the genotype with the highest RS, displayed compact starch granules. Further, NJ-72 showing low RS and Ananga with high RS were selected for investigation of enzymatic activities of starch biosynthesis, metabolites accumulation, and expressions of 20 starch biogenesis genes in developing endosperm. Starch branching enzymes (SBE) and starch synthase (SS) activities peaked at 13 days after anthesis (DAA), while starch debranching enzymes (DBE) were most active at 18 DAA. In Ananga, TSC, AC, APC, and RS levels progressively increased from 3 to 23 DAA. Ananga showed 1.25-fold upregulation of granule-bound starch synthase I (GBSSI) at 18DAA. Higher expressions of SSI and SBEIIb were observed in NJ-72 at 13DAA. PUL2 was predominantly expressed followed by ISA1. GBSSI was positively correlated with both AC and RS while SS, SBE, and DBE were positively related to APC.ConclusionThis research could lead to the development of rice varieties with improved nutritional qualities, such as higher RS content, which is beneficial for human health due to its role in lowering glycemic response and promoting gut health. Additionally, the study provides insights into how the modulation of key genes and enzymes can affect starch composition, offering strategies to breed rice varieties tailored for specific dietary needs or industrial applications.

MitoSort: Robust Demultiplexing of Pooled Single-cell Genomics Data Using Endogenous Mitochondrial Variants.

Multiplexing across donors has emerged as a popular strategy to increase throughput, reduce costs, overcome technical batch effects, and improve doublet detection in single-cell genomic studies. To eliminate additional experimental steps, endogenous nuclear genome variants are used for demultiplexing pooled single-cell RNA sequencing (scRNA-seq) data by several computational tools. However, these tools have limitations when applied to single-cell sequencing methods that do not cover nuclear genomic regions well, such as single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq). Here, we demonstrate that mitochondrial germline variants are an alternative, robust, and computationally efficient endogenous barcode for sample demultiplexing. We propose MitoSort, a tool that uses mitochondrial germline variants to assign cells to their donor of origin and identify cross-genotype doublets in single-cell genomics datasets. We evaluate its performance by using in silico pooled mitochondrial scATAC-seq (mtscATAC-seq) libraries and experimentally multiplexed data with cell hashtags. MitoSort achieves high accuracy and efficiency in genotype clustering and doublet detection for mtscATAC-seq data, addressing the limitations of current computational techniques tailored for scRNA-seq data. Moreover, MitoSort exhibits versatility and can be applied to various single-cell sequencing approaches beyond mtscATAC-seq, provided the mitochondrial variants are reliably detected. Furthermore, we demonstrate the application of MitoSort in a case study where B cells from eight donors were pooled and assayed by single-cell multi-omics sequencing. Altogether, our results demonstrate the accuracy and efficiency of MitoSort, which enables reliable sample demultiplexing in various single-cell genomic applications. MitoSort is available at https://github.com/tangzhj/MitoSort.

Wine metabolome and sensory analyses demonstrate the oenological potential of novel grapevine genotypes for sustainable viticulture in warm climates.

Genetic breeding is essential to develop grapevine genotypes adapted to warm climates and resistant to pathogens. Traditionally cultivated Vitis vinifera is susceptible to biotic and abiotic stresses. Winemakers and consumers, however, perceive wines from non-vinifera or hybrid cultivars as inferior. In this study, sensory analyses and comprehensive metabolite profiling by targeted and untargeted approaches were used to investigate the oenological potential of wines from grapes of genotypes developed throughout four breeding cycles to improve climate adaptation, sugar contents and berry color. Novel genotypes had higher yields and the wines exhibited increased contents of polyphenols, including anthocyanins. Volatile monoterpenes in the wines decreased throughout breeding cycles in the absence of selective pressure. Polyphenol contents were higher in intermediate wines, with hydroxytyrosol contents reaching up to three times reported values. Mouthfeel attributes astringency, leafy taste, flavor and body, and persistency showed significant correlation with untargeted features. Supervised model-based analyses of the metabolome effectively discriminate wines from distinct genetic origins. Taken together, the results demonstrate the potential of novel grapevine genotypes to a more sustainable viticulture and quality wine production in warm climates. Comprehensive metabolite profiling of the wines reveals that genotype clustering is dependent on the chemical class and that traits not submitted to selective pressure are also altered by breeding. Supervised multivariate models were effective to predict the genetic origin of the wines based on the metabolic profile, indicating the potential of the technique to identify biomarkers for wines from sustainable genotypes. © 2024 Society of Chemical Industry.

Correlation and Clustering for Yield and Its Attributing Traits in Maize (Zea mays L.) Hybrids

Present investigation was conducted in 144 maize hybrids of CIMMYT, Hyderabad along with 6 checks at ICRISAT, Hyderabad. The genotypes were evaluated for six quantitative traits: plant height, ear height, anthesis days, silking days, ear per plant and grain yield. Correlation among the traits came to a conclusion that anthesis days and silking are positively correlated with grain yield genotypically and plant height, ear height and ear per plant are positively correlated with grain yield phenotypically. Hence selection on five traits plays a vital role in increasing the grain yield. Clustering of genotypes based on the six traits divide the germplasm into two clusters. Each cluster has 85 and 65 genotypes respectively. Clustering the genotypes based the quantitative traits helps in understanding the relatedness between the genotypes.

Prion protein gene (PRNP) variation in German and Danish cervids

The structure of cellular prion proteins encoded by the prion protein gene (PRNP) impacts susceptibility to transmissible spongiform encephalopathies, including chronic wasting disease (CWD) in deer. The recent emergence of CWD in Northern European reindeer (Rangifer tarandus), moose (Alces alces alces) and red deer (Cervus elaphus), in parallel with the outbreak in North America, gives reason to investigate PRNP variation in European deer, to implement risk assessments and adjust CWD management for deer populations under threat. We here report PRNP-sequence data from 911 samples of German red, roe (Capreolus capreolus), sika (Cervus nippon) and fallow deer (Dama dama) as well as additional data from 26 Danish red deer close to the German border and four zoo species not native to Germany. No PRNP sequence variation was observed in roe and fallow deer, as previously described for populations across Europe. In contrast, a broad PRNP variation was detected in red deer, with non-synonymous polymorphisms at codons 98, 226 and 247 as well as synonymous mutations at codons 21, 78, 136 and 185. Moreover, a novel 24 bp deletion within the octapeptide repeat was detected. In summary, 14 genotypes were seen in red deer with significant differences in their geographical distribution and frequencies, including geographical clustering of certain genotypes, suggesting “PRNP-linages” in this species. Based on data from North American CWD and the genotyping results of the European CWD cases, we would predict that large proportions of wild cervids in Europe might be susceptible to CWD once introduced to naive populations.

Association and Diversity Studies for Yield and Its Attributing Traits in Maize (Zea mays L.) Hybrids

Present investigation was conducted in 144 maize hybrids of CIMMYT, Hyderabad along with 6 checks at ICRISAT, Hyderabad. The genotypes were evaluated for six quantitative traits that are plant height, ear height, anthesis days, silking days and grain yield. Correlation among the traits came to a conclusion that plant height and ear height are positively correlated with grain yield. Path analysis revealed there is highest direct association of plant height on grain yield and ear height had a highest indirect positive association with grain yield. Hence selection plant height and ear height days plays a vital role in increasing yield. Clustering of genotypes based on the six traits divide the germplasm into two clusters. 85 and 65 genotypes were found in each clusters. Clustering the genotypes based the quantitative traits revealed close relatedness between the genotypes. Knowledge on association and diversity identified in our study help in plant breeding process.

Salmonella Typhi genotypic diversity, cluster identification and antimicrobial resistance determinants in Mukuru settlement, Nairobi Kenya

BackgroundUnderstanding the source of typhoid infections and the genetic relatedness of Salmonella Typhi (S. Typhi) by cluster identification in endemic settings is critical for establishing coordinated public health responses for typhoid fever management. This study investigated the genotypic diversity, antibiotic resistance mechanisms, and clustering of 35 S.Typhi strains isolated from cases and carriers in the Mukuru Informal Settlement.MethodsWe studied 35 S.Typhi isolates, including 32 from cases and 3 from carriers, from study participants in the informal settlement of Mukuru, Nairobi, Kenya. Genomic DNA was extracted, and whole-genome sequencing (WGS) was performed to determine the phylogenetic relatedness of strains and detect antimicrobial resistance determinants (AMR). WGS data were analyzed using bioinformatics tools available at the Center for Genomic Epidemiology and Pathogenwatch platforms.ResultsGenotype 4.3.1.2 EA3 was found to be dominant at 46% (16/35), followed by 4.3.1.2 EA2 at 28% (10/35), and 4.3.1.1 EA1 at 27% (9/35). A comparison of the isolates with global strains from Pathogenwatch identified close clustering with strains from Uganda, Tanzania, Rwanda, and India. Three isolates (9%) distributed in each cluster were isolated from carriers. All genotype 4.3.1.2 EA3 isolates were genotypically multidrug-resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole. Single mutations in the quinolone resistance-determining region were identified in the gyrA (S83Y) and gyrB (S464F) genes. All isolates associated with multidrug resistance showed the presence of the IncQ1 plasmid with the following genes: blaTEM-1B, catA1, sul1, sul2, and dfrA7.ConclusionThe close phylogenetic relatedness between antimicrobial-resistant case isolates and carriage isolates indicates that typhoid carriage is a possible source of infection in the community. Comparative analysis with global isolates revealed that the Kenyan isolates share common lineages with strains from neighboring East African countries and India, suggesting regional dissemination of specific MDR clones. AMR was a major feature of the isolates. Surveillance and testing for antimicrobial susceptibility should inform options for the management of cases.

Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic.

Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.

Identifying the strains of dengue circulating in the western province of Sri Lanka during 2019-2022.

A study conducted from July 2019 to May 2022 at several hospitals in the Western Province, Sri Lanka, focused on dengue virus strains during the COVID-19 pandemic. Among 417 febrile patients, 47% were PCR-positive for dengue. Serotyping revealed DENV-1 (12.8%), DENV-2 (46.4%), DENV-3 (37.2%), and DENV-4 (3.6%). Sequencing identified two genotypically distinct variants of DENV-3 and two genotypically distinct variants of DENV-1, while DENV-2 showed a single genotype cluster. Notably, the study found concurrent circulation of two DENV-3 and two DENV-1 genotypes, along with DENV-2, during the pandemic in the area. This data suggests the presence of multiple dengue strains, including several DENV-1 and DENV-3 variants, without major epidemic outbreaks reported in the Western Province. Continuous monitoring and research are essential to understand the dynamics of these dengue strains in the context of the COVID-19 pandemic.

The Genomic Epidemiology of Clinical Burkholderia pseudomallei Isolates in North Queensland, Australia.

Background:Burkholderia pseudomallei, the causative agent of melioidosis, is highly genetically recombinant, resulting in significant genomic diversity. Multiple virulence factors have been associated with specific disease presentations. To date, there are limited data relating to genomic diversity and virulence factors associated with melioidosis cases in North Queensland, Australia. Aim: To describe the genetic diversity of B. pseudomallei and identify virulence factors associated with clinical risk factors and patient outcomes. Methods: Whole genome sequencing of clinical isolates was performed and analysed with clinical data obtained from a retrospective melioidosis cohort study. Results: Fifty-nine distinct sequence types (STs) were identified from the 128 clinical isolates. Six STs comprised 64/128 (50%) isolates. Novel STs accounted for 38/59 (64%) STs, with ST TSV-13 as the most prevalent (n = 7), and were less likely to possess an LPS A genotype or YLF gene cluster (p < 0.001). These isolates were most likely to be found outside the inner city (aOR: 4.0, 95% CI: 1.7-9.0, p = 0.001). ST TSV-13 was associated with increased mortality (aOR: 6.1, 95% CI: 1.2-30.9, p = 0.03). Patients with a history of alcohol excess were less likely to be infected by fhaB3 (aOR 0.2, 95% CI: 0.1-0.7, p = 0.01) or YLF (aOR: 0.4, 95% CI: 0.2-0.9, p = 0.04) positive isolates. Conclusions: There are a significant number of novel sequence types in Townsville, Australia. An emerging novel ST appears to have an association with geographic location and mortality. Ongoing investigation is required to further understand the impact of this ST on the Townsville region.

Genomic epidemiology and evolution of rhinovirus in western Washington State, 2021-22.

Human rhinoviruses (RV) primarily cause the common cold, but infection outcomes vary from subclinical to severe cases, including asthma exacerbations and fatal pneumonia in immunocompromised individuals. To date, therapeutic strategies have been hindered by the high diversity of serotypes. Global surveillance efforts have traditionally focused on sequencing VP1 or VP2/VP4 genetic regions, leaving gaps in our understanding of RV genomic diversity. We sequenced 1,078 RV genomes from nasal swabs of symptomatic and asymptomatic individuals to explore viral evolution during two epidemiologically distinct periods in Washington State: when the COVID-19 pandemic affected the circulation of other seasonal respiratory viruses except for RV (February - July 2021), and when the seasonal viruses reemerged with the severe RSV and influenza outbreak (November-December 2022). We constructed maximum likelihood and BEAST-phylodynamic trees to characterize intra-genotype evolution. We detected 99 of 168 known genotypes and observed inter-genotypic recombination and genotype cluster swapping from 2021 to 2022. We found a significant association between the presence of symptoms and viral load, but not with RV species or genotype. Phylodynamic trees, polyprotein selection pressure, and Shannon entropy revealed co-circulation of divergent clades within genotypes with high amino acid constraints throughout polyprotein. Our study underscores the dynamic nature of RV genomic epidemiology within a localized geographic region, as more than 20% of existing genotypes within each RV species co-circulated each studied month. Our findings also emphasize the importance of investigating correlations between rhinovirus genotypes and serotypes to understand long-term immunity and cross-protection.

Response of selected scion and rootstock grape (&lt;i&gt;Vitis &lt;/i&gt;spp.) genotypes to induced drought stress

Climate change is expected to elevate drought frequency, straining agricultural freshwater resources. Developing drought-tolerant grapevine varieties is crucial. This study examined grape scion and rootstock genotypes under well-watered (WW) and induced-drought (ID) conditions. ID treatment reduced vine length by 11.34-35.15%, with Vitis parviflora, 110R, and Male Hybrid rootstocks showing superior growth. Root length increased under ID, indicating an adaptive moisture-seeking response. The ID treatment led to substantial reduction in leaf count and average leaf area, especially in Flame Seedless (27.71 and 19.07 cm2, respectively). Drought stress elevated chlorophyll a:b ratio, affecting chlorophyll degradation in different genotypes. Significant variations were observed in leaf and root iron (Fe) and zinc (Zn) contents. Enzyme activities particularly peroxidase and polyphenol oxidase especially rose under drought, particularly in V. parviflora (3.39 μM guaiacol min-1 mg-1 protein and 1.33EU/ml/min respectively) likely to be contributing in drought tolerance mechanism. Principal component analysis (PCA) highlighted impact of traits on genotypes, emphasizing V. parviflora, Male Hybrid and Pusa Navrang as superior drought stress tolerant genotypes. Genotype clustering confirmed distinct groupings, while, correlation analysis unveiled intricate trait interactions.

Avian Orthoreoviruses: A Systematic Review of Their Distribution, Dissemination Patterns, and Genotypic Clustering.

Avian orthoreviruses have become a global challenge to the poultry industry, causing significant economic impacts on commercial poultry. Avian reoviruses (ARVs) are resistant to heat, proteolytic enzymes, a wide range of pH values, and disinfectants, so keeping chicken farms free of ARV infections is difficult. This review focuses on the global prevalence of ARVs and associated clinical signs and symptoms. The most common signs and symptoms include tenosynovitis/arthritis, malabsorption syndrome, runting-stunting syndrome, and respiratory diseases. Moreover, this review also focused on the characterization of ARVs in genotypic clusters (I-VI) and their relation to tissue tropism or viral distribution. The prevailing strains of ARV in Africa belong to all genotypic clusters (GCs) except for GC VI, whereas all GCs are present in Asia and the Americas. In addition, all ARV strains are associated with or belong to GC I-VI in Europe. Moreover, in Oceania, only GC V and VI are prevalent. This review also showed that, regardless of the genotypic cluster, tenosynovitis/arthritis was the predominant clinical manifestation, indicating its universal occurrence across all clusters. Globally, most avian reovirus infections can be prevented by vaccination against four major strains: S1133, 1733, 2408, and 2177. Nevertheless, these vaccines may not a provide sufficient defense against field isolates. Due to the increase in the number of ARV variants, classical vaccine approaches are being developed depending on the degree of antigenic similarity between the vaccine and field strains, which determines how successful the vaccination will be. Moreover, there is a need to look more closely at the antigenic and pathogenic properties of reported ARV strains. The information acquired will aid in the selection of more effective vaccine strains in combination with biosecurity and farm management methods to prevent ARV infections.

Genotypic cluster analysis of Neisseria gonorrhoeae reveals a spectrum of sexual mixing including among HIV-serodiscordant men who have sex with men

Background Men who have sex with men (MSM) are more vulnerable to acquiring sexually transmitted infections (STIs). In 2019, for instance, 74% of European Neisseria gonorrhoeae (Ng) cases among males affected MSM. A recent report by the World Health Organization showed that most of the 2020’ interim targets to end STIs by 2030 had not been met. A broadened understanding of STI transmission networks could guide future elimination strategies and reduce the STI burden. Therefore, we used whole-genome sequencing (WGS) to determine Ng-clusters and assess sexual mixing. Methods WGS was performed on Ng-isolates collected at the Medical University of Vienna, Austria and was used for core genome multi-locus sequencing typing cluster analysis. Epidemiologic and infection-specific details were extracted from medical records. Results Genomic analysis and demographic data were available for 415 isolates, and 43.9% (182/415) were allocated to 31 Ng-clusters. Nine clusters comprised samples from heterosexual individuals only (women N = 4, human immunodeficiency virus (HIV)-negative men N = 49, HIV-positive man N = 1), nine clusters included MSM only (HIV-negative N = 22, HIV-positive N = 13) and 13 clusters included both heterosexuals and MSM (HIV-negative N = 75, HIV-positive N = 18). Current use of HIV pre-exposure prophylaxis (PrEP) was reported by 22.8% of MSM. In multivariate analysis, only ‘MSM’ predicted clustering with isolates from HIV-positive individuals (adjusted odds ratio 10.24 (95% CI 5.02–20.90)). Conclusions Sexual mixing of HIV-positive, HIV-negative MSM and non-MSM was frequently observed. Furthermore, HIV-serodiscordant clustering highlights the importance of PrEP rollout to avert HIV transmission. Our findings can inform future STI prevention strategies and continuous surveillance efforts are required to keep up with transmission dynamics.

Genetic Divergence and Cluster Studies for Different Morphological Traits in Bread Wheat (Triticum aestivum L.em.Thell)

A field experiment was conducted on 135 wheat (Triticum aestivum L.em.Thell) genotype under timely sown condition, in order to determine the genetic variability and genetic diversity. The experimental findings indicated highly significant differences in genotypes for all 12 morphological traits taken under study. Clustering of genotypes revealed that Cluster VI had highest genotypes followed by cluster VIII, V, II, III. The lowest genotypes were noted in cluster I. The average inter cluster D2 values indicated that the most diverse groups were V and IV followed by cluster IV and I, VI and I. The lowest inter cluster value was found among VIII and V. The genotypes bearing desired values from different clusters can be exploited in future breeding programme for improving the yield and physiological traits. Such differences in genetic component of traits studied can be applied as a new source of variation in other breeding programs and crossing nurseries for wheat improvement.

Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes.

Pseudomonas aeruginosa is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic diversity and the functional metabolic landscape of P. aeruginosa clinical isolates. To better understand the metabolic repertoire of P. aeruginosa in infection, we deeply profiled a representative set from a library of 971 clinical P. aeruginosa isolates with corresponding patient metadata and bacterial phenotypes. The genotypic clustering based on whole-genome sequencing of the isolates, multilocus sequence types, and the phenotypic clustering generated from a multi-parametric analysis were compared to each other to assess the genotype-phenotype correlation. Genome-scale metabolic network reconstructions were developed for each isolate through amendments to an existing PA14 network reconstruction. These network reconstructions show diverse metabolic functionalities and enhance the collective P. aeruginosa pangenome metabolic repertoire. Characterizing this rich set of clinical P. aeruginosa isolates allows for a deeper understanding of the genotypic and metabolic diversity of the pathogen in a clinical setting and lays a foundation for further investigation of the metabolic landscape of this pathogen and host-associated metabolic differences during infection.

Grouping of Bulgarian and foreign cotton varieties by cluster analysis

Abstract. During the period 2016-2019, 21 Bulgarian and 10 foreign cotton varieties were included in a trial set by the block method design in four replicates and a harvest plot of 20 m2. A cluster analysis was applied to the most important economic traits. It was found that based on the clustering by individual years and on average for four years, the varieties were divided into two or three main clusters, mainly on the traits of seed cotton yield, fiber length and lint percentage. The year conditions have influenced the phenotypic manifestation of the studied traits and have had a significant impact on the genotypes clustering by the individual years. The clustering of the varieties based on the average data for four years showed different degrees of genetic similarity and distance between them and with the standard variety – Chirpan-539. The varieties Helius, Trakia, Philipopolis and Plovdiv, which were highly productive, were genetically very similar and it is appropriate to include them in one selection program together with the varieties Natalia, Dorina, Vega, Perla-267, Kolorit, (Bulgarian selection), Stoneville 112, Deltapine 30 (American) and 791-169 (Greek), which were genetically more distant from them and have shown other valuable traits.

Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022.

The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.

Genome Sequence Comparisons between Small and Large Colony Phenotypes of Equine Clinical Isolates of Arcanobacterium hippocoleae.

Arcanobacterium hippocoleae is a Gram-positive fastidious bacterium and is occasionally isolated from the reproductive tract of apparently healthy mares (Equus caballus) or from mares with reproductive tract abnormalities. Apart from a few 16S rRNA gene-based GenBank sequences and one recent report on complete genome assembly, detailed genomic sequence and clinical experimental data are not available on the bacterium. Recently, we observed an unusual increase in the detection of the organism from samples associated with mare reproductive failures in Atlantic Canada. Two colony morphotypes (i.e., small, and large) were detected in culture media, which were identified as A. hippocoleae by MALDI-TOF mass spectrometry and 16S rRNA gene sequencing. Here, we report the whole genome sequencing and characterization of the morphotype variants. The genome length of the large phenotypes was between 2.42 and 2.43, and the small phenotype was 1.99 Mbs. The orthologous nucleotide identity between the large colony phenotypes was ~99%, and the large and small colony phenotypes was between 77.86 and 78.52%, which may warrant the classification of the two morphotypes into different species. Phylogenetic analysis based on 16S rRNA genes or concatenated housekeeping genes grouped the small and large colony variants into two different genotypic clusters. The UvrA protein, which is part of the nucleotide excision repair (NER) system, and 3-isopropoylmalate dehydratase small subunit protein expressed by the leuD gene were identified as potential virulence factors in the large and small colony morphotypes, respectively. However, detailed functional studies will be required to determine the exact roles of these and other identified hypothetical proteins in the cellular metabolism and potential pathogenicity of A. hippocoleae in mares.

Morpho-Physiological Characterization of Potato (Solanum Tuberosum) Genotypes of the Andigenum and Phureja Group from the Working Collection of the Universidad De Nariño

This study presents the morpho-physiological characterization of potato (Solanum tuberosum) genotypes from the Andigenum and Phureja groups, cultivated at the Nariño, Colombia. The research addresses the vital role of genetic diversity in agricultural sustainability and food security, highlighting the importance of genetic resources for crop improvement and ecosystem stability. The study utilized a comprehensive morphological characterization based on both qualitative and quantitative descriptors to assess genetic variability within the university's potato collection. This approach allowed for the identification of duplicates, the enhancement of a morphological database, and insights into the genetic diversity of the collections. Using techniques like Multiple Correspondence Analysis (ACM) and Principal Component Analysis (PCA), distinct clusters of genotypes were identified, which were highly influenced by their ploidy levels. Results indicated significant morphological variation between diploid Phureja and tetraploid Andigenum genotypes. Phureja genotypes showed greater similarity among themselves compared to the more diverse Andigenum group. This morphological diversity is importante for the identification of specific traits beneficial for breeding programs, such as resistance to environmental stresses and diseases. The study underscores the importance of maintaining genetic diversity within potato germplasm collections, facilitating the selection of genotypes with desirable agronomic traits. The findings contribute significantly to the understanding of the genetic and morphological foundations necessary for the future genetic improvement of the potato, a staple food crop with profound implications for global food security. The geographic distribution of the genotypes also suggested a correlation between morphological traits and geographic locations, reinforcing the role of local adaptation in crop diversity and resilience.