Estimates Of Genetic Diversity Research Articles

Assessment of Genetic Variability and Population Structure of Betula utilis subsp. jacquemontii in the Western Himalayan Region of India.

Betula utilis subsp. jacquemontii (Spach) Ashburner & McAll. is a medicinally and ecologically important tree species in the Western Himalayan Region (WHR) of India. Estimation of genetic variability and population structure of 11 populations of B. utilis subsp. jacquemontii in the WHR were carried out using 15 ISSR and 10 DAMD markers. The cumulative analyses of the markers (ISSR + DAMD) revealed a moderate level (49.47%) of polymorphism at the species level. Khilanmarg, Gangotri, and Khaliya top populations showed the highest polymorphism, while the Bhyundar Valley and Chatru-Kaza road populations showed the lowest polymorphism across 11 populations. Mantel test revealed a positive correlation between pair-wise genetic and geographical distances in wild populations of B. utilis subsp. jacquemontii in theWHR. The AMOVA analysis showed that majority of variation of the species exists among populations (54%), followed by within populations (20%). The clustering pattern obtained from UPGMA, PCoA, and STRUCTURE analyses revealed that 11 natural populations of B. utilis subsp. jacquemontii separated into two distinct genetic clusters. The genetic differentiation is notably high (GST = 0.74) among populations with a low gene flow (Nm = 0.16), which could be attributed to geographic isolation, high mountain ranges, regional climatic conditions, and habitat destruction in theWHR. The genetically diverse populations recognized in this study could be a valuable genetic resource for conservation and management of this important timberline tree species.

Genomic exploration of Thuja plicata indicates no loss of diversity from adults to offspring in UK Woodlands

Thuja plicata is a conifer tree that is valued for its cultural, ecological and wood quality features in its natural range in western North America and is used in Europe as an exotic timber species. It is increasingly used in mixed species forests in the UK that are managed using natural regeneration, raising questions about genetic diversity of both the adult trees and offspring of the species in these stands. We studied population structure and genetic diversity in four UK woodlands of both adults and naturally regenerated offspring of T. plicata. We discovered 194,154 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 655 SNPs across 598 genome sequence scaffolds for analysis. The majority of these scaffolds included only one SNP, suggesting that; the selected SNPs were widely distributed within the genome. We found many monomorphic sites, most of which were restricted to adults in a single woodland, indicative of a genetic differentiation among woodlands. We found three ancestral populations (K = 3) and low levels of admixture across the four sites, indicating that the starting materials were largely from single populations. Estimates of genetic diversity using heterozygosity (Ho) and nucleotide diversity (π) were low (overall Ho = 0.174, π = 0.00226) across all sites but slightly higher in juveniles at two sites. Our genotyping methods and results on standing genetic diversity in this important conifer provide insight into the ability of planted woodlands in the UK to face environmental shifts and disease threats.

Genetic diversity and selection signatures in sheep breeds.

Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.353 and 0.355, respectively. Suffolk had the least genetic variation and, along with Texel, had slower linkage disequilibrium decay. iHS and Tajima's D detected selection signatures for all breeds, with some regions overlapping, thus forming longer segments of selection signatures. Common selection signatures were identified across iHS and Tajima's D methods for all breeds, with Belclare and Texel having several common regions under positive selection. Several genes were detected within the selection signature regions, including ITGA4, TLR3, and TGFB2 related to the immune system against endoparasites; DLG1, ROBO2, MXI1, MTMR2, CEP57, and FAM78B related to reproductive traits; WDR70 related to milk traits; SCHM1 and MYH15 related to meat traits; and TAS2R4, TAS2R39, and TAS2R40 related to adaptive traits. In conclusion, our results demonstrated moderate genetic diversity in the sheep breeds and detected and characterized selection signatures harboring genes associated with reproductive traits, milk production, meat production, and adaptive traits such as endoparasite resistance.

Population viability of the orchid Gymnadenia conopsea increases with population size but is not related to genetic diversity

Abstract Population size is a main indicator of conservation potential, thought to predict both current and long‐term population viability. However, few studies have directly examined the links between the size and the genetic and demographic properties of populations, using metrics that integrate effects across the whole life cycle. In this study, we combined 6 years of demographic data with SNP‐based estimates of genetic diversity from 18 Swedish populations of the orchid Gymnadenia conopsea. We assessed whether stochastic growth rate increases with population size and genetic diversity, and used stochastic life table response experiment (SLTRE) analysis to evaluate how underlying vital rates contribute to among‐population variation in growth rate. For each population, we also estimated the probability of quasi‐extinction (shrinking below a threshold size) and of a severe (90%) decline in population size, within the next 30 years. Estimates of stochastic growth rate indicated that 10 populations are declining, seven increasing and one population is approximately stable. SLTRE decomposition showed that low mean adult survival and growth characterized strongly declining populations, whereas high mean fecundity characterized strongly increasing populations. Stochastic growth rate increased with population size, mainly due to higher survival in larger populations, but was not related to genetic diversity. One third of the populations were predicted to go extinct and eight populations to undergo a 90% decrease in population size in the coming 30 years. Low survival in small populations most likely reflects a positive association between local environmental conditions and population size. Synthesis: The association between G. conopsea population size and viability was driven by variation in survival, and there was no sign that ongoing declines are due to genetic erosion. This suggests that large populations occur in favourable habitats that buffer effects of climatic variation. The results also illustrate that demographic metrics can be more informative than genetic metrics, regarding conservation priority.

Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada

Abstract The Wolverine (Gulo gulo) is a cold-adapted species of conservation interest because it is sensitive to human development, disturbance, exploitation, and climate warming. Wolverine populations have been studied across much of their distributional range to evaluate patterns of genetic diversity, genetic structure, and gene flow. Little population structure has been detected in northwestern North America with microsatellite loci, but low genomic diversity in wolverines may limit detection of genetic differences in this highly vagile species. Here, we genotyped a relatively large sample of wolverines from across Alaska (US) and adjacent Yukon (Canada) with 12 microsatellite loci (n = 501) and 4,222 single nucleotide polymorphisms (SNPs; n = 201) identified using restriction-site associated DNA sequencing. We compared the relative ability of our microsatellite and SNP datasets to evaluate population genetic structure, genetic diversity, differentiation, and isolation by distance (IBD). We predicted that the SNP dataset would detect a higher degree of genetic structure and provide more significant support for IBD. We found evidence for multiple genetic clusters, including genetic distinctiveness of wolverines in southeast Alaska and on the Kenai Peninsula. The SNP dataset detected additional genetic clusters that align largely with ecoregions, and the SNP dataset showed stronger evidence of IBD, while the 2 datasets were generally consistent in estimates of genetic diversity and differentiation among regional groups. Our results highlight the importance of genomic methods to assess gene flow in wolverines. Identifying population genetic structure allows an assessment of the potential impacts of conservation threats and is an important precursor for designing population monitoring programs.

Hybridization and Introgression in Black Hakes (Merluccius polli and M. senegalensis): Evolutionary Dynamics and Conservation Implications in the Contact Zone Exploited by Multi-Species Fisheries.

Hybridization is relatively common between closely related species that share part of their distribution. Understanding its dynamics is important both for conservation purposes and to determine its role as an evolutionary mechanism. Here we have studied the case of black hakes (Merluccius polli and Merluccius senegalensis) in its contact zone. The area of study is located in the FAO fishing area 34, in Mauritania and Senegal waters, where both species are exploited jointly in multi-species fisheries involving national and foreign fleets. Using a ddRADSeq approach and based on a set of 5820 SNPs and a total of 240 individuals, we identified one F1 hybrid and several backcrossed individuals among 90 M. polli samples and none in 90 M. senegalensis samples obtained in 2020, suggesting unidirectional introgression towards M. polli. Hybridization signals were not found in any of the 60 historical samples from 2000. Excluding the hybrids and developing two separate sets of SNPs (5093 SNPs for M. polli and 2794 SNPs for M. senegalensis), our results detected two distinct genetic clusters within M. polli that show different genetic diversity estimates, with one of the clusters showing a higher potential vulnerability to exploitation. This pattern was observed in both contemporary and historical samples, and both groups presented subtle depth segregation. Moreover, 109 outlier loci were identified between the two groups, that could be developed into molecular markers to further study differentiation between both clusters and contribute to improved stock assessment and management of these important demersal resources.

Estimation of genetic variability, heritability, and genetic advance for drought-tolerant traits in an F2 mapping population of rice

Estimation of genetic variability, heritability, and genetic advance for drought-tolerant traits in an F2 mapping population of rice

Genetic improvement in Colombian cattle, a reality or an intention? A review

Background: Genetic improvement programs in domestic species require a set of steps involving the definition of breeding objectives, information systems, variance component estimation, genetic evaluations, selection indexes, and the estimation of genetic progress and variability. Objective: To identify strengths and weaknesses in the design and implementation of genetic improvement programs in Colombian cattle through scientific and academic contributions derived from research. Conclusion: The greatest challenges in the design and implementation of genetic improvement programs in Colombian cattle are currently related to the absence of consensus breeding objectives among farmers and associations. Additionally, there is a need in the short term to improve both the quality and quantity of information available in databases. Finally, conducting economic analyses that consider genetic parameters is essential for optimizing the response to genetic selection, considering the different productive systems and environmental conditions that Colombia offers.

Unravelling the Genetic Complexity: Enhancing MYMV Resistance in Blackgram [Vigna mungo (L.) Hepper] Through Trait-based Selection

Background: Limited genetic diversity in blackgram, stemming from its common ancestry with greengram, presents challenges in combating Mungbean Yellow Mosaic Virus (MYMV), leading to yield stagnation. To address this, genetic screening and selection of segregating generations in F2 are essential for refining resistance traits with enhancing productivity. Methods: A two-season experiment was conducted in Panpoli, Tamil Nadu, during the Kharif 2021 and Kharif 2022 in a randomized block design using, F2 seeds from specific crosses (MDU 1 × Mash 114 and ADT 3 × PU 31), along with F1 and parent plants. MYMV disease scores were recorded using the infector row method for all the genotypes studied. Result: The study unveiled a complex genetic basis of MYMV resistance in blackgram, characterized by di-genic dominant genes displaying duplicative dominance type of epistatic interaction. This complexity underscores the insufficiency of simple selection methods. Estimates of genetic variability for “number of pods per plant” exhibited high genetic advance and moderate heritability, indicating control by additive genes. Positive correlations were observed between plant height, number of clusters per plant and number of pods per plant with yield. Path analysis revealed that traits like number of seeds per pod, 100 seed weight and number of pods per plant directly and positively influenced yield, which exhibit minimal influence from MYMV. These traits offer crucial selection criteria for enhancing MYMV resistance in blackgram.

Genetic Characterization of HIV-1 tat Gene from Virologically Controlled Aging Individuals with HIV on Long-Term Antiretroviral Therapy.

Despite advancements in antiretroviral therapy (ART) that reduces the viral load to undetectable levels and improve CD4 T cell counts, viral eradication has not been achieved due to HIV-1 persistence in resting CD4+ T-cells. We, therefore, characterized the tat gene, which is essential for HIV-1 replication and pathogenesis, from 20 virologically controlled aging individuals with HIV (HIV+) on long-term ART and improved CD4+ T-cell counts, with a particular focus on older individuals. Peripheral blood mononuclear cell genomic DNA from HIV+ were used to amplify tat gene by polymerase chain reaction followed by nucleotide sequencing and analysis. Phylogenetic analysis showed that each HIV+ tat sequences were confined to their own subtrees and well discriminated from other HIV+ sequences. Moreover, there was a low degree of viral heterogeneity and lower estimates of genetic diversity within these individuals' tat sequences, which decreased with increasing CD4 T counts in these HIV+. Most HIV+ Tat deduced amino acid sequences showed intact open reading frames and maintained the important functional domains for Tat functions, including transactivation, TAR binding, and nuclear localization. Furthermore, Tat-deduced amino acid sequences showed variation in previously characterized cytotoxic T lymphocytes (CTL) epitopes, suggesting escape mutants. In conclusion, a low degree of genetic variability and conservation of functional domains and variations in CTL epitopes were the features of tat sequences that may be contributing to viral persistence in these 20 aging individuals with HIV on long-term ART.

Estimates of genetic variability and interplay of germination and seedling traits conferring salinity tolerance in rice (Oryza sativa L.)

This study estimates genetic variability and correlations among germination and seedling traits conferring salinity tolerance in rice accessions. Five rice accessions were screened under salinity levels of 0, 50, 100, and 200 mM NaCl in a controlled laboratory setting. Traits such as germination energy, capacity, shoot and root length, and biomass were measured. Data were analyzed for variance and correlations to assess variability and trait relationships. Significant genetic variability was found among accessions for all traits. Germination energy showed the highest coefficient of variation (CV) at 22.29% under control conditions, while fresh shoot weight had the highest CV (34.35%) under 200 mM salinity. Accessions ACC2 and ACC5 consistently demonstrated higher performance in germination energy (23.33 to 53.33% and 10.00 to 41.67%), germination capacity (40.00 to 60.00% and 28.33 to 46.67%), and shoot length (0.67 to 2.97 cm and 0.40 to 3.93 cm) under various salinity stress levels. ACC1, ACC3, and ACC4 showed more variability but maintained some consistency in specific traits, with ACC4 generally showing lower performance across most traits. Genetic parameter estimates indicated high heritability (˃60%) for all traits, with the highest in germination capacity (96.88%). High genetic advance (GAM) was observed for all traits (˃20%), with germination energy showing the highest (107.00%). Traits with high heritability and genetic advance, such as germination energy, germination capacity, and root length, suggest strong genetic control and potential for improvement through selective breeding. Significant correlations were found between germination energy and capacity (r= 0.89 to 0.96) and between shoot length and leaf length (r= 0.92) under stress conditions. Stress tolerance indices identified accessions ACC2 and ACC5 as the most tolerant, with ACC1 showing consistent performance across traits. This study underscores the importance of identifying resilient traits and accessions to enhance salinity tolerance in rice, contributing to improved productivity in saline-affected regions.

Estimation of Genetic Diversity for Yield and Yield Components in Pearl Millet

Pearl millet [Pennisetum glaucum (L.) R. Br.] is one of the most significant cultivated cereals. It demonstrates remarkable genetic diversity due to its wide distribution across the globe and its adaptability to harsh environmental conditions. A multi-location experiment was conducted in Srikakulam (Location 1), Vizianagaram (Location 2), and Patancheru (Location 3) during Kharif 2021 to investigate genetic diversity in a world diversity panel of pearl millet based on grain yield and its component traits using principal component analysis (PCA). The PCA revealed that first three principal components with eigen values greater than one accounted for about 69% of the total variation in location 1, 66% in location 2, and two components accounted for 62% in location 3. The first principal component showed high positive loadings for HI and PHI in locations 1 and 2 and for PWT and GYLD in location 3. Traits such as TGWT, PH, and PL contributed positively to the total variation in all three locations. This genetic variability can thus be effectively utilized in pearl millet breeding programs.

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Coffee breeding programs aim at developing superior genotypes, which entail exploring the genetic variability existing in conilon/robusta coffee. This study aimed at examining the variability and estimate genetic param of physical and physiological nature in Coffea canephora seeds in order to provide bases for the selection of genotypes for superior seeds quality. Forty-three C. canephora genotypes were evaluated for 11 physical and physiological seed traits. Estimates of genetic param, environmental variance, phenotypic variance, genotypic variance, broad-sense heritability, variation index and Pearson's correlation were obtained. The Dissimilarity between genotypes was obtained by generalized Mahalanobis distance. The dendrogram was constructed using unweighted pair group method with arithmetic mean (UPGMA). C. canephora genotypes presented high germination potential and exhibited genetic diversity for all seed traits, with estimates of genetic variance greater than environmental variance. Heritability reached values above 96.0% and all genetic variation indices found were higher than unity. The UPGMA hierarchical method grouped the genotypes in three groups. The physical traits (circumference, area and roundness) were those that contributed the most to explaining the dissimilarity between genotypes. Genotypes Alecrim, AP, Bamburral, Z39 and Tardio C were the most divergent. The results revealed the presence of genetic variability between C. canephora genotypes and greater genetic than environmental influence on the characters of seeds, indicating that selection for the studied traits showed favorable conditions in terms of immediate gain.

Prioritizing Conservation Areas for the Hyacinth Macaw (Anodorhynchus hyacinthinus) in Brazil From Low-Coverage Genomic Data.

Estimates of current genetic diversity and population connectivity are especially important for endangered species that are subject to illegal harvesting and trafficking. Genetic monitoring can also ensure that management units are sustaining viable populations, while estimating genetic structure and population dynamics can influence genetic rescue efforts and reintroduction from captive breeding and confiscated animals. The Hyacinth Macaw (Anodorhynchus hyacinthinus) is a charismatic endangered species with a fragmented (allopatric) distribution. Using low coverage genomes, we aimed to investigate the dynamics across the remaining three large disjunct populations of Hyacinth Macaws in Brazil to inform conservation strategies. We obtained low coverage DNA data for 54 individuals from seven sampling sites. Our results showed that Hyacinth Macaws have four genetically structured clusters with relatively high levels of diversity. The Pantanal biome had two genetically distinct populations, with no obvious physical barriers that might explain this differentiation. We detected signs of gene flow between populations, with some geographical regions being more connected than others. Estimates of effective population size in the past million years of the species' evolutionary history showed a decline trend with the lowest Ne in all populations reached within the last few thousand years. Our findings suggest that populations from the Pantanal biome are key to connecting sites across its distribution, and maintaining the integrity of this habitat is important for protecting the species. Given the genetic structure found, we also highlight the need of conserving all wild populations to ensure the protection of the species' evolutionary potential.

Assessment of Genetic Variability in Groundnut (Arachis hypogaea L.)

The present study was carried out with thirty advanced breeding lines of groundnut for estimation of genetic variability, heritability and genetic advance. Analysis of variance revealed highly significant differences among genotypes for all the studied characters indicating that there is substantial variability among the genotypes for these traits. High estimates of GCV and PCV was observed for pod yield per plant, kernel yield per plant, dry haulm yield per plant and number of mature pods per plant. High heritability coupled with high genetic advance as per cent of mean were recorded for number of mature pods per plant, pod yield per plant, kernel yield per plant, dry haulm yield per plant, number of immature pods per plant, plant height, harvest index and hundred kernel weight indicating the preponderance of additive gene action in expression of these traits and hence simple phenotypic selection would be effective for improvement of these characters.

Inclusion of imputed genotypes from non-genotyped dairy cattle in a Thai multibreed genomic-polygenic evaluation.

This study assessed the impact of incorporating imputed SNP information from non-genotyped animals on genomic-polygenic evaluations in a Thai multibreed dairy population under various levels of imputation accuracy. Data encompassed pedigree and phenotypic records for 305-day milk yield (MY), 305-day fat (Fat), and age at first calving (AFC) from 12,859 first-lactation cows, and genotypic records of various densities from 4,364 animals. A set of 64 animals genotyped with GeneSeek Genomic Profiler 80K and with four or more genotyped progenies was defined as target animals to simulate imputation scenarios for non-genotyped individuals. Actual and imputed genotypes were utilized to construct three SNP sets. All SNP Sets contained actual and imputed SNP markers from genotyped animals. SNP Set 1 contained no SNPs from target animals, whereas SNP Set 2 incorporated imputed SNPs from target animals, and SNP Set 3 added actual SNPs from target animals. Genomic-polygenic evaluations were conducted using a 3-trait single-step model that included contemporary group, calving age, and heterozygosity as fixed effects and animal additive genetic and residual as random effects. The imputation accuracy was similar across non-genotyped animals irrespective of the number of genotyped progenies (average: 40.55%; range: 34.68% to 53.82%). Estimates of additive genetic and environmental variances and covariances for MY and AFC varied across SNP sets. SNP Sets 1 and 2 had slightly higher additive genetic and lower environmental variances and covariances than SNP Set 3. Heritabilities and additive genetic, environmental, and phenotypic correlations between MY, Fat, and AFC were similar across all SNP Sets. Spearman rank correlations between genomic-polygenic EBVs from SNP Sets 2 and 3 were high for all traits (0.9990±0.0003). Utilization of phenotypic and pedigree data from imputed non-genotyped animals enhanced the efficiency and cost-effectiveness of the genetic improvement program in the Thai multibreed dairy cattle population.

Estimation of Genetic Variability for Yield and Its Component Traits in Chickpea (Cicer arietinum L.)

The present investigation was conducted with 12 chickpea genotypes, raised in randomized block design with three replications during the Rabi season 2023-2024 at at Organic Research Farm, Karguanji, Institute of Agricultural Sciences, Bundelkhand University, Jhansi (U.P.). The experiment was laid-out in randomized block design with three replications of the plant geometry was maintained at 30 cm x 10 cm. The present experimental material showed a wide range of phenotypic variation for number of seed per pod, number of primary branches per plant, biological yield per plant and seed yield per plant, number of secondary branches per plant, number of pods per plant and harvest index whereas, low phenotypic coefficient of variation was observed for plant height, 100-seed weight, days to 50 per cent flowering and days to maturity as revealed by high values of Coefficient of Range. The estimates of high heritability coupled with high genetic advance expressed as a per cent of mean were observed for biological yield per plant, seed yield per plant and number of pods per plant manifesting the preponderance of additive gene action on the expression of these traits. In the investigation, genotypes viz., RSG-44 and Aruna were superior not only for seed yield per plant but also related traits like 100-seed weight, biological yield per plant, number of pods per plant and number of primary branches per plant.

Estimation of genetic variability, heritability and genetic advance of yield and related traits in F4 and F5 generations of okra (Abelmoschus esculentus [L.] Moench)

Estimation of genetic variability, heritability and genetic advance of yield and related traits in F4 and F5 generations of okra (Abelmoschus esculentus [L.] Moench)

Genetic Variability, Heritability, Genetic Advance, Path Coefficient Analysis, and Inter-Character Relationships in Colocynth (Citrullus colocynthis [L.] Schrad.) from Southeastern Villages of the Benin Republic

Genetic improvement of crops for important traits requires reliable estimates of genetic variability. heritability and genetic advance of intending parent materials to identify traits useful in planning an efficient breeding program through selection. Hence, the effectiveness of genetic improvement of a crop depends on the variability in the morpho-agronomic traits of individual genotypes. Understanding the variation that exists will allow the breeder to determine strategies to be adopted in his breeding program. The objectives of the present study were to estimate the magnitude of genetic variability and advance, heritability and inter-character relationships by simple correlations and path coefficient analysis in 40 local colocynth genotypes from Southeastern Benin. The experiment was carried out in a randomized complete block design with three replications in three locations for three years. 34 morpho-agronomic traits were observed in each genotype. Analysis of variance revealed that effects of genotype, genotype by year or location and genotype by year by location interactions were significant (p ≤ 0.01 or 0.05) for all the characters. Phenotypic coefficients of variation (PCV) values were relatively greater than genotypic coefficients of variation (GCV) for all traits. High magnitude of phenotypic and genotypic coefficients of variation as well as high heritability along with high genetic advance were recorded particularly for qualitative traits. All yield components, except time to emergence, time to tailspins, leaf limb width, fruit number per plant, fruit width, seed length, seed tegument percentage and stem pubescence texture, had significant and positive correlations with yield attributes represented by thousand-seed weight (TSW) and seed number per plant (SNP). Path coefficient analysis indicated that all the characters (except leaf pubescence texture, stem pubescence texture, fruit design produced by secondary skin color and male flower size) had positive direct effects on TSW and partly SNP. Results suggested that most of the 34 quantitative and qualitative traits studied could be effectively used as selection criteria in the breeding program of Citrullus colocynthis varieties with high yield.

VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.

RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.