Genetic Distance Research Articles

Molecular transmission clusters in newly HIV-1 diagnosed migrants in Portugal from 2014 to 2019

Abstract Background Portugal has an important HIV burden with a total of 804 diagnosed cases in 2022. Migrants remain a significant source of HIV infections, with 45% of newly reported cases. We aimed to evaluate the characteristics of HIV-1 molecular transmission clusters (MTCs) among migrants followed in Portugal, diagnosed between 2014 and 2019. Methods 265 migrants, newly HIV-1 diagnosed were included in the BESTHOPE project with clinical, socio-behavioral and genomic data. Pol nucleotide-based phylogenetic analyses were used to infer HIV-1 MTC. Those were constructed using ClusterPickerGUI_1.2.3 considering SH-aLRT higher than 90 of branch support and a pairwise genetic distance of ≤ 4.5. Logistic regression analyses were used to examine the relationship between the sociodemographic and clinical data associated with HIV-1 clustering. Results 66.8% of the migrants included in the study were males with a median age at diagnosis of 36.0 years old (IQR:29-45). Most migrants were from African countries (50.6%) followed by Brazil (39.6%). Sixty-eight (33%) of the migrants were included in clusters. Being in cluster was significantly associated with region of origin, with individuals from South America more likely to be in cluster (OR = 14.85, 95%CI:1.52-144.79), compared to individuals from Africa; with transmission route, with men who have sex with men (MSM) more likely to be in cluster (OR = 23.52, 95%CI:2.35-235.10), compared to the heterosexuals and with subtype, with subtypes B less likely to be in cluster (OR = 0,017, 95%CI:0,001-0,254) compared with subtype non-B. Conclusions Migrants HIV transmission clusters in Portugal are associated with specific health determinants, such as region of origin, transmission route and subtype. Targeted prevention health strategies are needed to mitigate transmission of HIV within this population. Funded by FCT to GHTM - UID/04413/2020 and LA-REAL - LA/P/0117/2020; BESTHOPE (HIVERA:249697); and MARVEL (PTDC/SAU-PUB/4018/2021). Key messages • HIV transmission clusters in migrant are associated with their region of origin, transmission route and subtype. • Targeted prevention health strategies are needed for the migrant population.

Virulence perspective genomic research unlocks the secrets of Rhizoctonia solani associated with banded sheath blight in Barnyard Millet (Echinochloa frumentacea).

Banded sheath blight (Bsb) disease, caused by Rhizoctonia solani, is an emerging problem in barnyard millet cultivation. One of the significant goals of pathogenomic research is to identify genes responsible for pathogenicity in the fungus. A virulence profiling-based approach was employed and six R. solani isolates were collected from various ecological zones of India. The morphological parameters and virulence of all of the six R. solani isolates were investigated. The most virulent strain was designated as RAP2 and its genome has been sequenced, assembled, and annotated. The RAP2 genome is 43.63 megabases in size and comprises 10.95% repetitive DNA, within which 46% are retroelements, 8% are DNA transposons, and 46% are unidentified DNA. The Gene Ontology (GO) annotation of RAP2 proteins revealed that "phosphorylation", "membrane", and "ATP binding" have the highest gene enrichment in the "biological process", "cellular component" and "molecular function" domains, respectively. The genome comprises a majority of secretory proteins in the pectin lyase fold/virulence factor superfamily, which break down plant cell wall polymers to extract saccharides. The RAP2 genome is comparable to R. solani, which infects maize and rice, but it diverges further from soybean in terms of nucleotide-level genetic similarity. Orthologous clustering of RAP2 protein sequences with R. solani infecting maize, rice, and soybean yields 5606 proteins shared across all genomes. GO analysis of 25 proteins specific to the RAP2 genome found enrichment in the ethylene response, which can cause spore germination and infection in host plants. Interestingly, a 28-bp deletion in the RAP2 strain's cutinase domain was discovered in the cutinase protein, which might be important in the infection process, perhaps rendering the enzyme inactive or allowing the pathogen to infect barnyard millet while avoiding host defense. This study sheds light on the genetic makeup of R. solani, allowing researchers to discover critical genes related with pathogenicity as well as potential targets for fungicide development.

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

NEW RECORD SPECIES OF GIANT FRESH WATER SHRIMP FROM THE DOWNSTREAM OF SERAYU RIVER

Indonesia is characterized by great diversity of freshwater shrimp, consisting of several islands due to the geographical location on the equator. A recent investigation conducted in Central Java has identified Serayu River as the major habitat of freshwater shrimp genus Macrobrachium. Therefore, this research aimed to determine the type of giant freshwater shrimp found downstream of Serayu River using explanatory method. The experiment was conducted for one year (January - December 2023) and the results found two freshwater giant prawn species, namely Macrobrachium rosenbergii and Macrobrachium spinipes. Moreover, this research is the first record of M. spinipes based on the Cytochrome C oxidase Subunit I (CO1) gene. The mtDNA segment of M. rosenbergii was 631 bp (base pairs) (GenBank accession: LC813231.1), while M. spinipes was 616 bp (GenBank accession: PP735157.1). M. spinipes and M. rosenbergii downstream of Serayu River showed similar locations and characteristics. Genetic distance conducted on 15 species of the genus Macrobrachium showed that giant freshwater prawn serayu had a matrix value of 0.09 - 0.18. Genetic analysis conducted with GenBank indicated that M. spinipes showed significant differences from other species, suggesting the natural dispersal of juvenile through currents across Wallace Line. This research also found that M. rosenbergii was similar to M. dacqueti and related to M. malcolmsonii, while M. spinipes was close to M. suphanense. To support these results, recommendation was made to explore further the rivers in the western part of Java, Indonesia.

First support for phylogenetically segregated ecotypes and delineating thresholds for inter‐ and intraspecific ranks in phytophagous Central Asian beetles (Coleoptera)

AbstractAs defining various taxonomic ranks, especially at and within a specific level, can often be difficult, we used an evolutionarily young group of Central Asian beetles, the genus Anoplistes, to examine the limits between species, subspecies and ecotype. The molecular data (COI genetic distance, haplotype network and species delimitation) and detailed morphology (using SEM) of taxa assigned to the rank of species, subspecies and ecotype were used to verify their taxonomic status and attempt to more precisely establish the boundaries between these concepts. The minimum threshold for the COI genetic distance between species was found to be approximately 3%, while at the threshold of 4%–5% the morphology left no doubt as to the species distinctiveness. The threshold of approximately 2% was accepted as adequate for a subspecies rank, whereas intraspecific variability among individuals of the same subspecies (including its ecotypes) ranged from 0% to 2%. A newly presented colour/elytral pattern form, possibly another ecotype of A. halodendri distributed in western Mongolia, exemplifies adaptation to different environmental conditions via ecological speciation. Our results provide support that ecotypes can form phylogenetically distinct clades. Based on the results of the haplotype network, it can be tentatively concluded that the sand ecotype was the incipient form from which further ecotypes and subspecies developed.

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

The Saccharomyces cerevisiae cell lysis mutant cly8 is a temperature-sensitive allele of ESP1.

The Saccharomyces cerevisiae mutants designated cly ( c ell ly sis) cause cell lysis at elevated temperatures. The cly8 mutation, previously localized to an 80 kilobase region between GCD2 and SPT6 on the right arm of chromosome VII, has been used for mutation mapping and in recombination assays, but its genetic identity has remained unknown. Whole genome sequencing of cly8 mutant and CLY8 wild-type strains revealed four missense mutations specific to the cly8 mutant strain in the GCD2 - SPT6 interval, three of these missense mutations affected essential genes. The esp1-G543E mutation, but not the two other missense mutations, recapitulated the temperature-sensitive growth, the cell lysis phenotype, and recessive nature of the cly8 mutation. The ESP1 gene encodes S. cerevisiae separase and is required for normal chromosome segregation during mitosis. Shifting cells containing the esp1-G543E mutation to the non-permissive temperature caused chromosome missegregation based on the analysis of DNA content by flow cytometry analysis. Taken together, these results indicate that the temperature-sensitive cly8 mutation is an allele of the essential ESP1 gene.

Characterisation of Tomato (Solanum lycopersicon Mill.) Genotypes for Morphological and Disease Resistance Traits through Cluster Analysis

The characterization of germplasm is crucial for breeding and developing improved seed varieties. In this study, seed material was collected from M/s. Noble Seeds Pvt. Ltd., Yelhanka, focusing on genotypes with varying resistance to Tomato Leaf Curl Virus (ToLCV). The research was conducted during the Kharif seasons of 2021 and 2022 in Kestur Village, Doddballapura. Morphological characterization was performed according to DUS guidelines set by PPV&FRA, assessing 20 qualitative and 22 quantitative traits. The genotypes were grown in a randomized complete block design for reliability. Multivariate cluster analysis was employed to group the genotypes based on the morphological traits assessed, enabling the identification of patterns and relationships among them. This analysis facilitated the formation of distinct clusters, highlighting the genetic diversity and similarities among the genotypes, which are crucial for targeted breeding strategies. Through multivariate cluster analysis, two main clusters (A and B) were identified, each further divided into two sub-clusters (C and D). Overall, 66.67% of the 30 genotypes (20 in total) were grouped in Cluster E, while 5 genotypes were placed in Cluster C, 3 in Cluster D, and only 2 in Cluster F. The analysis revealed that NBLTM-22 and NBLTM-11 exhibited the highest variation between them, while genotypes within clusters demonstrated greater similarity. These findings underscore the importance of genetic diversity in breeding programs, highlighting that closer proximity in clustering correlates with trait similarity among genotypes. This information can guide further breeding efforts aimed at developing ToLCV-resistant varieties.

Genetic Diversity of Maize (Zea mays L.) Genotypes under Low Level of Nitrogen

Maize (Zea mays L.) is India's second most significant crop, behind rice. As a cross-pollinated crop, hybrid vigour is commonly used to achieve the best production potential. The selection of various genotypes is a primary goal in the maize hybrid breeding programme. Maize is a voracious feeder and requires a lot of fertiliser. The biggest limits on maize production in India are low soil nitrogen and high fertiliser costs. Jharkhand consumes only 82.5 kg of total fertiliser nutrients per acre. In order to discover genetically varied maize genotypes for nitrogen usage efficiency, the current study evaluated 121 maize genotypes in a randomised block design with two replications at low nitrogen levels. Plant height, days to 50% pollen shed, days to 50% silk, anthesis-silking interval (ASI), days to75% maturity, number of leaves per plant, root length, stover yield per plant, grain yield per plant, and harvest index were all recorded. Statistical analysis was performed using the morphological trait data. Analysis of variance revealed substantial (p≤0.05) variations in morphological features between maize genotypes. For statistical analysis, a clustering method was used to locate various genotypes with greater genetic distance in order to develop good heterotic combinations. One hundred twenty one genotypes were divided into six clusters using the dendogram-by-ward minimum variance approach. Cluster III and V had the greatest inter-cluster distance (79.26), followed by cluster III and VI (74.77) and cluster II and III (73.80). The many heterotic combinations developed from these clusters can be employed in subsequent breeding programmes to produce low nitrogen-requiring hybrids with a low yield penalty.

Multiple Maternal Lineages of <i>Strauchbufo raddei</i> (Strauch, 1876) in Mongolia Revealed by Mitochondrial DNA

The Mongolian toad Strauchbufo raddei (Strauch, 1876) is one of widely distributed and dominated amphibian species in eastern Asian, including Mongolia. In this study, we amplified and sequenced a total of 50 samples of S. raddei, from three main regions in its Mongolian distribution range namely, Northern, Eastern, and Gobi regions. Our phylogenetic trees (Bayesian inference; BI and time-calibrated) and network analysis clearly support presence of multiple maternal mitochondrial DNA lineages for S. raddei in Mongolia. As expected, samples from these three regions were clustered separately in BI tree (Bayesian posterior probability (BPP 0.52). In addition, the population specific haplotypes, estimated genetic distances (e.g. uncorrelated p distance; ranged from 1% to 25%) and hierarchical AMOVA suggested relatively strong population genetic structure of S. raddei across Mongolia. Time-calibrated tree and ancestral range analysis showed that the first colonization of S. raddei may have occurred in Northern part of Mongolia approximately 9.63 mya, then dispersed over other parts of the country. Estimated approximate time for crossing event of S. raddei over dry steppe and semi-desert regions in Mongolia was 5.02 – 2.50 mya. Finally, high level of genetic diversity (overall; haplotype diversity, Hd = 0.93; nucleotide diversity, π = 0.011) of S. raddei were observed in Mongolia. Importantly, through this study, we contributed to closing sampling gaps in distribution range of S. raddei in Eastern Asia, which is key to better understanding species history, as well as describing cryptic lineages.

Studies on Genetic Divergence in Faba Bean (Vicia faba L.)

Background: The genetic divergence in faba bean genotypes is critical for breeding programs aiming to improve yield and other agronomic traits. Understanding the extent of genetic variability among different genotypes can guide the selection of superior varieties and enhance crop improvement efforts. This study was conducted to evaluate the genetic diversity among 47 faba bean genotypes grown under the specific agro-climatic conditions of Chhattisgarh. Methods: The experiment was conducted during the Rabi season of 2022-23 at the Hi-Tech-Nursery, Dau Kalyan Singh College of Agriculture and Research Station, Bhatapara, under Indira Gandhi Krishi Vishwavidyalaya, Chhattisgarh. A total of 47 faba bean genotypes were evaluated for genetic divergence using Mahalanobis D2 statistics and Tocher’s method. Ten quantitative characters, including marketable pod yield per plant and marketable pod weight appearance, were measured and analyzed. The genotypes were grouped into clusters based on their genetic distances. Result: The clustering pattern indicated that genetic diversity was independent of geographical diversity. Cluster II contained the highest number of genotypes (19), followed by Cluster I (13), while Cluster IV had the least (1). Among the ten quantitative characters studied, marketable pod yield per plant contributed most to genetic divergence, followed by marketable pod weight appearance. The maximum intra-cluster D2 value was observed in Cluster IV (477.35), followed by Cluster III (250.07). The highest inter-cluster D2 value was between Cluster I and Cluster IV (7917.34), followed by Cluster IV and Cluster V (6156.43).

A haplogroup-based methodology for assigning individuals to geographical regions using Y-STR data

Y chromosome markers are essential tools in forensic genetics, offering valuable insights for genetic identification. This study seeks to develop a forensic prediction model using machine learning techniques to improve the efficiency of genetic identification processes. Specifically, the model aims to predict an individual's nearest geographical area of residence based on Y chromosome marker analysis. The methodology involved four key steps: haplogroup determination, primary branch identification, geographical region assignment, model stratification, and fine-tuning. Once developed, the model can be integrated into decision support systems, providing forensic geneticists with a reliable knowledge source to enhance decision-making during investigations.

Morpho–Molecular Characterization of Brazilian Common Bean Landraces Varieties and Commercial Cultivars

This study aimed to characterize forty genotypes (31 landrace varieties and nine commercial cultivars) of common bean (Phaseolus vulgaris L.) morphologically and molecularly. Morphological descriptors were evaluated during seedling, flowering, physiological maturation and post-harvest stages. Ten microsatellite markers were used for molecular screening. The markers were analyzed according to the number of alleles per locus, the allele frequency per locus and the polymorphism in content (PIC). Genetic distances and cluster analysis were performed using Bayesian inference and the UPGMA method. All black beans evaluated have anthocyanin in the cotyledons, hypocotyls and stems, and their flowers are purple. For the growth habit, 50% of the evaluated genotypes belong to type III, and at the physiological maturation stage, yellow color is predominant in the pods (85%). Through the genetic dissimilarity, three groups were observed for the likelihood reason, and five groups were observed through the UPGMA method, a strong indication of the wide genetic diversity among the evaluated genotypes. All genotypes from the Andean center of origin were grouped into the same cluster.

Diversity of Improved Diploids and Commercial Triploids from Musa spp. via Molecular Markers

Banana breeding consists of obtaining diploid, triploid, and tetraploid intra- and interspecific hybrids by conventional breeding methods with the objective of aggregating characteristics of agronomic and commercial interest. Given the narrow genetic base of bananas, Embrapa’s Banana Genetic Breeding Program (BGBP) aims at crosses between improved diploids (ID) (ID × ID) and between improved diploids (ID) and commercial triploids (ID × CTP) and tetraploids (ID × CTT), in order to increase the genetic base and variability in bananas regarding agronomic traits of interest and resistance to main biotic and abiotic factors. These improved diploids are resistant to main fungal diseases such as yellow (YSD) and black Sigatoka (BSD) disease and Fusarium wilt (race 1 and subtropical race 4), the latter being one of the most devastating diseases in bananas. The genetic diversity between 22 improved diploids and seven commercial banana triploids was analyzed using DNA molecular markers. Five IRAP (Inter-Retrotransposon Amplified Polymorphism, 7 ISSR (Inter-Simple Sequence Repeats) and 12 SSR (Simple Sequence Repeat) markers were used. The genetic dissimilarity matrix was based on the Jaccard dissimilarity index; clusters were separated using the UPGMA (Unweighted Pair Group Method With Arithmetic Mean) method and cophenetic correlation of 0.8755. This study of the genetic diversity between improved diploids and commercial triploids, based on the genetic dissimilarity matrix, revealed that the most dissimilar diploids were DM23 and DM15 (74%) and DM16 and DM15 (74%). The smallest genetic distances between the improved diploids and commercial triploids were between TCGN25 and DM17 (50%) and TCN26 and DM17 (50%). The genetic distance matrix also revealed important genotypes to be used in crosses in order to maintain good characteristics in commercial triploids when crossed with improved diploids. The results of our study provide better breeding strategies for one of the largest banana-breeding programs worldwide focused on the development of banana varieties resistant to main biotic and abiotic factors.

Assessment of Genetic Diversity and Population Structure of Exotic Sugar Beet (Beta vulgaris L.) Varieties Using Three Molecular Markers.

Sugar beet (Beta vulgaris L.) is a biennial herb belonging to the Amaranthaceae family. It contributes to approximately 30% of the world's total sucrose production and is an economically important crop. In this study, we analyzed the genetic diversity and population structure of 132 exotic sugar beet varieties using three molecular makers: four pairs of simple sequence repeat (SSR) primers, three pairs of insertion-deletion sequence (InDel) primers, and 20 cis-element amplification polymorphism (CEAP) primers. The results indicated that the number of alleles (Na) was 298, among which the number of effective alleles (Ne) was 182.426 (accounting for approximately 61.2%). The mean value of the genetic diversity index was 0.836. The polymorphic information content (PIC) was 0.639-0.907 (mean = 0.819), indicating a high level of polymorphism. These sugar beet varieties were classified into six clusters using the UPGMA method of cluster analysis. Population structure analysis revealed that the most ideal K value was 6. This indicated that the test materials could be divided into six categories, consistent with the clustering results. The clustering results indicated that most sugar beet varieties from the same breeding company clustered together, and the genetic distance between them was small, indicating that they may share the same male and/or female parent. Some varieties from different companies clustered together, indicating a narrow genetic base and potential exchange of germplasm resources between breeding companies. This study revealed the genetic differences among exotic sugar beet varieties and characteristics of the population structure. It provided a scientific basis for the identification of sugar beet varieties and markers-assisted breeding in China in the future.

Genotyping Error Detection and Customised Filtration for SNP Datasets.

A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non-invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.

Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene

The Asteraceae family is a prominent group of flowering plants found across the globe, with the exception of Antarctica. The Asteraceae family is a largest flowering family pivotal group in plant evolution and diversification. Despite its importance, the genetic diversity within this family remains understudied. We focused on the rps-11 gene, a chloroplast marker previously utilized in phylogenetic studies, to investigate its potential in resolving Asteraceae relationships. The focus was on examining genetic diversity within sixteen specifically chosen species from the Asteraceae family. This assessment was based on an analysis of a chloroplast gene responsible for encoding the ribosomal protein of the smaller subunit 11 (rps 11). Nearly 417 bp of rps 11 gene was amplified, sequenced, computationally translated into amino acid sequence and the data was used for phylogenetic analysis as well as for rps 11 protein structure predictions. Based on nucleotide and amino acid sequences phylograms were drawn with the help of Molecular Evolutionary Genetic Analysis (MEGA 6), which exhibited clear genetic relationship among species under investigation. The observed genetic distance was 0.02 for Maximum likelihood tree based on nucleotide sequences whereas it was 0.05 for phylogram based on amino acid sequences. These values revealed that amino acid-based tree has demonstrated greater diversity among selected species in comparison to nucleotides-based tree. On the basis of pair wise distance calculations, genetic divergence values were found within the range of 0.015–0.309. Moreover, 3D protein modeling for rps 11 protein of sixteen selected species was also carried out by iterative threading assembly refinement (I-Tasser) software. The models exhibiting the highest C-score were picked with satisfactory plot statistics (> 90%) and structurally validated by PROCHECK. Furthermore, Ramachandran plots displayed that the rps 11 protein structures of Tagetes minuta, Xanthium strumarium, Lactuca sativa and Chrysanthemum indicum have best feature models with > 90% of residues in the allowed region and ≤ 2% in the disallowed region. The research is not enough to stand alone to validate the viability of the rps11 gene as a prospective contender for phylogenetic analysis. İn future we will focus on the maximum genetic diversity theory for phylogenetic analysis of this family.

Variabilitas Genetik pada Beberapa Varietas Unggul Baru Padi (Oryza sativa L.) Berdasarkan Penanda Morfologi Biji

Rice (Oryza sativa L.) is known to have a very diverse genetic diversity. The target of rice variety improvement is to produce new varieties that have superior traits in accordance with the development objectives in each typological region. This study aims to determine the level of similarity formed in a number of new superior varieties. The method used is descriptive experimental, with 51 treatments, namely new superior varieties, repeated 3 times so that there are 132 experimental units. Each agronomic character observation data was analyzed by clustering using the UPGMA method. The analysis used NTSYS 2.02i and 2.11a software. The results showed that the genetic variability of 51 new superior varieties of rice (Oryza sativa L.) has a similarity coefficient value of 0.81 based on clustering analysis. This shows a high level of similarity of genetic variability, however, the clustering results form 5 main groups with genetic distances ranging from 0.0000 - 0.5593. Keywords: genetic variability, seed morphology, new improved varieties, clustering.

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.

Whole-genome sequencing of toxigenic Clostridioides difficile reveals multidrug resistance and virulence genes in strains of environmental and animal origin

BackgroundClostridioides difficile has been recognized as an emerging pathogen in both humans and animals. In this context, antimicrobial resistance plays a major role in driving the spread of this disease, often leading to therapeutic failure. Moreover, recent increases in community-acquired C. difficile infections have led to greater numbers of investigations into the animal origin of the disease. The aim of this study was to evaluate the genetic similarities between 23 environmental and animal isolates by using whole-genome sequencing and to determine antimicrobial resistance and virulence factor genes in toxigenic C. difficile strains to provide important data for the development of diagnostic methods or treatment guidelines.ResultsThe most common sequence type was ST11 (87%), followed by ST2 (9%) and ST19 (4%). In addition, 86.95% of the strains exhibited multidrug resistance, with antimicrobial resistance to mainly aminoglycosides, fluoroquinolones, tetracycline and B-lactams; nevertheless, one strain also carried other resistance genes that conferred resistance to lincosamide, macrolides, streptogramin a, streptogramin b, pleuromutilin, oxazolidinone and amphenicol. In addition, a wide range of virulence factor genes, such as those encoding adherence factors, exoenzymes and toxins, were found. However, we observed variations between toxinotypes, ribotypes and sequence types.ConclusionsThe results of this study demonstrated significant genetic similarity between ST11 strains isolated from environmental sampling and from animal origin; these strains may represent a reservoir for community-acquired C. difficile infection, which is becoming a growing public health threat due to the development of multridug resistant (MDR) bacteria and the number of virulence factors detected.