Limited Genetic Diversity Research Articles

Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae)

The southeastern United States harbors one of the most diverse temperate freshwater fish faunas of the world. Unfortunately, due to improper land use practices and habitat degradation, many of the species in this region are imperiled and may become extinct without appropriate conservation efforts. This study examined the population dynamics of an endangered endemic darter of southwest Kentucky, the Relict Darter (Etheostoma chienense) and its sister taxon, the undescribed Clarks Darter (Etheostoma cf. oophylax). Mitochondrial sequence data coupled with SNP data were used to infer population structure, gene flow, genetic variation, and effective population sizes of both species. The results from this study, based on 160 individuals from nine localities, indicate that the endangered Relict Darter possesses limited genetic variation based on mitochondrial DNA haplotypes (N = 4). In addition, SNP data (6.8 k markers) further indicates limited genetic structure (K = 1), as well as a low effective population size (143–918), suggesting that the Relict Darter can be managed as a single, panmictic conservation unit. It is suggested that conservation efforts be taken to protect remaining habitats, augment the system with artificial spawning substrates, and, as a last resort (if needed), supplement the natural population with captive reared individuals. Ethesotoma cf. oophylax showed some genetic variation among distant sites, but more samples are needed throughout the range in order to fully understand the population dynamics of this species.

Adaptation to Water and Salt Stresses of Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme

Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme represent a valuable tool for tomato breeding, particularly for tolerance to abiotic stresses. Water stress and salinity are major constraints to tomato’s cultivation, and for which limited genetic variability has been reported within the cultivated species. We evaluated four accessions of S. pimpinellifolium and four of S. l. var. cerasiforme for their adaptation to water deficit and salinity. The CO2 assimilation rate, stomatal conductance, substomatal CO2 concentration, transpiration rate, and leaf chlorophyll concentration were evaluated, as well as morphological and agronomic traits. The accessions showed a remarkable inter- and intra-species response variability to both stresses. Two S. pimpinellifolium accessions and one S. l. var. cerasiforme showed unaltered physiological parameters, thus indicating a good adaptation to water deficit. Two S. l. var. cerasiforme accessions showed an interesting performance under salt stress, one of which showing also good adaptation to water stress. In general, both stresses showed a negative impact on leaf size and fruit fresh weight, especially in the big-sized fruits. However, flowering, fruit setting and earliness remained unaltered or even improved when compared to control conditions. Stressed plants yielded fruits with higher ° Brix. Response to stresses seemed to be linked to origin environmental conditions, notwithstanding, variability was observed among accessions of the same region.

Determining Genetic Diversity of Deshi Jute (Corchorus capsularis) for the Improvement of Fibre Yield and Associated Traits

Commercially important natural fibres considered as fiber of the future are cultivated in different south-east Asian countries including India and Bangladesh. Unfortunately, they are characterized by limited genetic variation in terms of yield, quality and susceptibility to diseases and pests. Therefore, genetic deviation studies are crucial to develop a successful cultivation program to develop varieties to meet the growing demand for domestic and foreign jute products. In our study, which was conducted at the Central Jute Research Experiment Station of Bangladesh Jute Research Institute (BJRI), during Kharif seasons of 2014. 44 Thirteen progenies (1546, 1548, 4311, 4328, 4330, 4337, 4339, 5007, 6702/A, 6702/B, 6772, 6787, 6790) and two check varieties CVL-1 and CVE-3 (developed from Bangladesh Jute Research Institute) were investigated to study the genetic variability, genetic diversity and degree of association of different component characters related to fiber yield. The seeds of experimental plant materials were grown in Randomized Complete Block Design with three replications. Statistical analysis was run to find out the genotypic and phenotypic variances, correlations and cluster analysis for fibre yield related traits namely plant height (m), base diameter (cm), stick weight (g), fiber weight (g). Highly significant differences were observed among the genotypes for all the characters. Cluster analysis divided the accessions and varieties into four cluster. From our evaluation it was revealed that the treatment number 4337/06, 4339/06 and 6702/A performed better in most of the cases than the control varieties CVL-1 and CVE-3. These accessions may be used as parents for future variety development program.

Population genomic and genome-wide association analysis of lignin content in a global collection of 206 forage sorghum accessions

Forage sorghum (Sorghum bicolor (L.) Moench) is a wildly cultivated C4 cereal crop in many geographical regions and differs among germplasms in a number of important physiological traits. Lignin is a complex heteropolymer found in plant cell walls that adversely affects economic and environmental benefits of the crop. To understand the genetic basis, we re-sequenced the genomes of 206 sorghum accessions collected around the globe and identified 14,570,430 SNPs and 1,967,033 indels. Based on the SNP markers, we characterized the population structure and identified loci underlying lignin content by genome-wide association studies (GWAS). Analysis of the genetic relationships among the accessions revealed a more diverse spread of sorghum accessions and breeding lines from Asia, America, and their genetically improved variety, but a limited genetic diversity in the European accessions. These findings add new perspectives to the historical processes of crop diffusion within and across agroclimatic zones of America, Asia, and Europe. GWAS revealed 9 quantitative trait loci (QTLs) for lignin content, harboring 184 genes. These genes were significantly enriched into 7 major gene ontology (GO) terms involved in plant-type cell wall organization or bioenergy. The alleles of 9 QTLs in the 206 accessions were geographically distributed. The findings provide us with an understanding of the origin and spread of haplotypes linked to lignin content. The findings will allow improvements to feed quality and adaptation to stresses in sorghum, through the rapid increase of genetic gains for lignin content.

Genetic polymorphism of Plasmodium falciparum circumsporozoite protein on Bioko Island, Equatorial Guinea and global comparative analysis

BackgroundPlasmodium falciparum circumsporozoite protein (PfCSP) is a potential malaria vaccine candidate, but various polymorphisms of the pfcsp gene among global P. falciparum population become the major barrier to the effectiveness of vaccines. This study aimed to investigate the genetic polymorphisms and natural selection of pfcsp in Bioko and the comparison among global P. falciparum population.MethodsFrom January 2011 to December 2018, 148 blood samples were collected from P. falciparum infected Bioko patients and 96 monoclonal sequences of them were successfully acquired and analysed with 2200 global pfcsp sequences mined from MalariaGEN Pf3k Database and NCBI.ResultsIn Bioko, the N-terminus of pfcsp showed limited genetic variations and the numbers of repetitive sequences (NANP/NVDP) were mainly found as 40 (35%) and 41 (34%) in central region. Most polymorphic characters were found in Th2R/Th3R region, where natural selection (p > 0.05) and recombination occurred. The overall pattern of Bioko pfcsp gene had no obvious deviation from African mainland pfcsp (Fst = 0.00878, p < 0.05). The comparative analysis of Bioko and global pfcsp displayed the various mutation patterns and obvious geographic differentiation among populations from four continents (p < 0.05). The global pfcsp C-terminal sequences were clustered into 138 different haplotypes (H_1 to H_138). Only 3.35% of sequences matched 3D7 strain haplotype (H_1).ConclusionsThe genetic polymorphism phenomena of pfcsp were found universal in Bioko and global isolates and the majority mutations located at T cell epitopes. Global genetic polymorphism and geographical characteristics were recommended to be considered for future improvement of malaria vaccine design.

Oral Microbiome Metabarcoding in Two Invasive Small Mammals from New Zealand

All multicellular organisms host a wide diversity of microorganisms in and on their bodies, which are collectively known as their microbiome. Characterising microbial communities that inhabit different body niches in wild animals is critical to better understand the dynamics of microbiome diversityand its functional significance. The current study is the first to apply massively parallel sequencing of 16S rRNA to characterise the microbial diversity and functional content of oral microbiota in two of New Zealand’s most important invasive mammals, the omnivorous common brushtail possum (Trichosurus vulpecula) and the carnivorous stoat (Mustela erminea). In total, strains of bacteria belonging to 19 different phyla, 27 classes, 52 orders, 103 families, 163 genera and 51 known species were identified from the oral cavities of the study species. Strains of the phyla Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria dominated the core oral microbial diversity in both species, while other taxa were comparatively less abundant. Despite invasive populations typically demonstrating limited genetic variation, intraspecific variation of the core bacterial taxa in the oral microbiota was considerable. This suggests that a complex interaction between genetic, physiological, and environmental factors determines the diversity of the study species’oral microbiome.

Genetic Sequencing of Influenza A (H1N1) pdm09 Isolates from South India, Collected between 2011 and 2015 to Detect Mutations Affecting Virulence and Resistance to Oseltamivir

AbstractBackground: Influenza A viruses evolve continuously and the two surface antigens, hemagglutinin (HA) and neuraminidase (NA) have been the target proteins for research as they are vital components in determining the virulence, immune effectiveness, pathogenicity, transmission and resistance. Methods: Both HA and NA (partial genes) of 45 pandemic influenza A(H1N1)pdm09 isolates were sequenced. Phylogenetic analysis was performed with reference to representative global isolates retrieved from Influenza Virus Resource (IVR), GISAID EpiFluTM and GenBank and evolutionary analyses. Nucleotide and amino acid sequences were aligned using ClustalW/Clustal Omega/MEGA version 6 with reference to vaccine strain (A/California/07/2009). Results: All the isolates clustered along with the clade 7 virus, irrespective of the year of isolation. The study isolates exhibited 98.5% and 98.8% nucleotide homology to the reference strain A/California/07/2009(H1N1) for HA and NA, respectively. Overall, there was limited genetic diversity observed over a period of 3 years (2012-2015). Two samples collected from expired patients had D239N (D222G or D225G) mutation in HA. This mutation which is associated with dual-binding specificity of the virus has been well-correlated with severe disease outcomes. All the study isolates possessed H274 residue and 7 strains had N295S, the next most common mutation found in oseltamivir-resistant variants. Conclusion: In this study, although H274Y mutation associated with oseltamivir resistance has not been noted, significant mutations have been noted in both HA and NA genes including D239N, N295S, V106I, Q136K, N248D, V267A. In both HA and NA gene analysis, multiple mutations were found more in 2015 strains when compared to 2012 strains. Hence such accumulation of mutations has to be monitored continuously to determine the efficacy of annual flu vaccines and anti-influenza drugs.

Grain hardness in triticale: a physical and molecular evaluation

Grain hardness is an important quality trait of cereals. In the present work, the particle size index (PSI) was used to assess the variability in grain hardness of thirteen triticale genotypes, three wheat genotypes and one rye genotype grown in two subsequent seasons. The PSI values of the triticale samples ranged between 7.7 to 19.2%, representing a medium hard to a very hard grain. Moreover, the sequencing of genes in the Hardness (Ha) locus revealed a limited genetic variability in the grain hardness genes, namely secaloindoline-a (Sina) and secaloindoline-b (Sinb). Two possible new allelic variants were identified, one for each of the secaloindoline genes. The existing variability in the grain hardness as well as polymorphisms in its candidate genes are a good starting point for efforts in breeding new varieties of triticale with improved grain hardness.

Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine.

It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at >17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, FST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (He ) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.

Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize.

Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.

Rickettsialpox — a rare but not extinct disease: review of the literature and new directions

Rickettsialpox is an urban zoonosis caused by Rickettsia akari. To date R. akari is the only well-characterized mite-borne member of the spotted fever group. It is transmitted by the mouse mite, Liponyssoides sanguineus, commonly found on peridomestic rodents. While the disease was first discovered in New York City in 1946, a few years later a similar outbreak occurred in the Ukraine SSR. Numerous serosurveys and diagnosis of sporadic cases of rickettsialpox suggest its global distribution; however, the actual contemporary geography of rickettsialpox and its incidence are unknown. Rickettsialpox is characterized by the classic clinical triad found in rickettsioses of a black eschar, high fever, and rash but the latter is atypical as it is papulovesicular. Dermatological manifestations and the progression of rickettsialpox may mimic other infectious and noninfectious syndromes, including sexually transmitted diseases. The purpose of this review is to increase awareness of this unique disease through reanalysis of classic and contemporary clinical descriptions of rickettsialpox, evaluation of its worldwide distribution, and updates on the public health importance of the disease as well as the ecology and vector associations of R. akari. Our review data suggests that only limited genetic diversity exists among the available isolates of R. akari associated with previous outbreaks; additional effort is still required to define specific genetic markers permitting direct surveillance, accurate and reliable diagnosis, tracking and studying of the vector and host associations of contemporary isolates. The potential of R. akari to cross into other vector species emphasizes the necessity for detection of outbreaks of the disease in new regions of the world and in novel ecological settings. We describe existing gaps and limitations in our current understanding of the pathogenesis of rickettsialpox, the epidemiology of this disease and the genetic diversity of R. akari. We propose research priorities for what is needed to improve our understanding of this neglected rickettsial disease and its etiologic agent.

Evaluation of intra-cultivar variability in Olea europaea L. cv. Leccino using morphological, biochemical and molecular markers

The phenotypic and genotypic variability of olive tree cv. Leccino (Olea europaea L.), an ancient cultivar from North-Central Italy, was investigated using 44 quantitative and qualitative agro-morphological traits, SDS-PAGE of seed proteins (storage proteins and tegument proteins) and molecular markers such as RAPDs (30 primers) and SSRs (8 primers). Fifteen accessions of Olea europaea catalogued as "Leccino" and one certified tree of "Leccino" (LESt) were examined. The plants were clonally propagated and the measuring of all morphological characteristics was conducted over a period of seven years. The ANOVA analysis showed that all accessions were homogenous for many traits while very few variations were recorded for length of one year old shoots, leaf width, leaf length/leaf width ratio, fruit length, fruit fresh weight, fruit length/fruit width ratio, pit length and pit fresh weight. The PCA analysis and similarity coefficients confirmed a low level of variability of Leccino cultivar. SDS-PAGE analysis of seed proteins showed monomorphic patterns of storage proteins. Protein subunits of teguments revealed a generally high level of similarity as evidenced by Nei-Li coefficient. SSRs and RAPDs markers showed molecular monomorphism among Leccino accessions. The results of agro-morphological, biochemical and molecular nature, taken as a whole, seem to indicate a weakly differentiated/homogeneity of the accessions tested belonging to the Leccino cultivar. The limited morphological and genetic variation could support the assumptions of a monophyletic origin of Leccino cultivar with a genetically restricted base.

Plasmodium vivax HAP2/GCS1 gene exhibits limited genetic diversity among parasite isolates from the Greater Mekong Subregion

BackgroundAntigens expressed in sexual stages of the malaria parasites are targets of transmission-blocking vaccines (TBVs). HAP2/GCS1, a TBV candidate, is critical for fertilization in Plasmodium. Here, the genetic diversity of PvHAP2 was studied in Plasmodium vivax parasite populations from the Greater Mekong Subregion (GMS).MethodsPlasmodium vivax clinical isolates were collected in clinics from the China-Myanmar border region (135 samples), western Thailand (41 samples) and western Myanmar (51 samples). Near full-length Pvhap2 (nucleotides 13–2574) was amplified and sequenced from these isolates. Molecular evolution studies were conducted to evaluate the genetic diversity, selection and population differentiation.ResultsSequencing of the pvhap2 gene for a total of 227 samples from the three P. vivax populations revealed limited genetic diversity of this gene in the GMS (π = 0.00036 ± 0.00003), with the highest π value observed in Myanmar (0.00053 ± 0.00009). Y133S was the dominant mutation in the China-Myanmar border (99.26%), Myanmar (100%) and Thailand (95.12%). Results of all neutrality tests were negative for all the three populations, suggesting the possible action of purifying selection. Codon-based tests identified specific codons which are under purifying or positive selections. Wright’s fixation index showed low to moderate genetic differentiation of P. vivax populations in the GMS, with FST ranging from 0.04077 to 0.24833, whereas high levels of genetic differentiation were detected between the China-Myanmar border and Iran populations (FST = 0.60266), and between Thailand and Iran populations (FST = 0.44161). A total of 20 haplotypes were identified, with H2 being the abundant haplotype in China-Myanmar border, Myanmar and Thailand populations. Epitope mapping prediction of Pvhap2 antigen showed that high-score B-cell epitopes are located in the S307-G324, L429-P453 and V623-D637 regions. The E317K and D637N mutations located within S307-G324 and V623-D637 epitopes slightly reduced the predicted score for potential epitopes.ConclusionsThe present study showed a very low level of genetic diversity of pvhap2 gene among P. vivax populations in the Greater Mekong Subregion. The relative conservation of pvhap2 supports further evaluation of a Pvhap2-based TBV.

Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world's southernmost poplar (Populus ilicifolia).

Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P.ilicifolia, characterize genome-wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P.ilicifolia experienced a more prolonged and severe decline of effective population size (Ne ) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome-wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species.

Analysis of Benzalkonium Chloride Resistance and Potential Virulence of Listeria monocytogenes Isolates Obtained from Different Stages of a Poultry Production Chain in Spain

Listeria monocytogenes can survive in food production facilities and can be transmitted via contamination of food during the various stages of food production. This study was conducted to compile the results of three independent previous studies on the genetic diversity of L. monocytogenes in a poultry production company in Spain and to determine the potential virulence and sanitizer resistance of the strains by using both genotype and phenotype analyses. L. monocytogenes was detected at three production stages: a broiler abattoir, a processing plant, and retail stores marketing fresh poultry products from the same company. These three stages spanned three locations in three provinces of Spain. A set of 347 L. monocytogenes isolates representing 39 subtypes was obtained using pulsed-field gel electrophoresis (PFGE). A total of 28 subtypes (68%) had a full-length internalin A gene, and two subtypes had a phenotype with low potential for virulence because of a mutation in the prfA gene. A total of 32 subtypes (82%) were classified as benzalkonium chloride resistant (BAC-R) and contained the resistance determinant bcrABC (21 subtypes, 54%) or the resistance gene qacH (11 subtypes, 28%). A total of 13 persistent BAC-R subtypes (minimum of 3 months between the first and last sample from with the isolate was recovered) were identified at the abattoir and processing plant. The three production stages shared a unique subtype (PFGE type 1), which had the mutation in the prfA gene and the bcrABC resistance determinant. Whole genome sequencing revealed this subtype to be sequence type 31. Limited genetic diversity was noted in the isolates studied, including some subtypes that were persistent in the environment of the investigated facilities. Given the high prevalence of BAC-R subtypes, these results support the association between resistance to biocides and persistence of L. monocytogenes.

Effects of Genetic Variants on Stroke Risk.

Effects of Genetic Variants on Stroke Risk.

&lt;p&gt;&lt;strong&gt;Genetic diversity and species limits in &lt;em&gt;Veltheimia&lt;/em&gt; (Asparagaceae: Scilloideae): insights from noncoding cpDNA sequence data&lt;/strong&gt;&lt;/p&gt;

Veltheimia is a genus of two species of bulbous flowering angiosperms restricted to southern Africa. Both parsimony and Bayesian analysis of 1829 nucleotides of DNA sequence data, from three non-coding chloroplast regions from multiple samples of both species, indicates that specimens of V. bracteata form a monophyletic clade together with three specimens named as V. capensis. This clade receives low support and is embedded within a paraphyletic grade of specimens of V. capensis. A Median Joining Network analysis of a subset of samples revealed nine haplotypes, the relationships of which mirrored the relationships resolved by the Bayesian analysis. With the exception of the V. capensis members of the V. bracteata clade, the remaining specimens are from the summer rainfall thicket and coastal forests. The samples of the basal V. capensis grade are found in the winter rainfall regions of southern Africa. These results indicate that there is limited genetic diversity within the genus, and there is no clear distinction between these two species based on plastid non-coding DNA data. This may be due to their recent divergence and incomplete lineage sorting, or recent or ongoing hybridisation and / or introgression.

The genetic characteristics of invasive Largemouth Bass in southern Brazil

Largemouth Bass (Micropterus salmoides) have been introduced on a global scale for sport fishing but represent a conservation concern given their documented negative impacts on native faunal diversity and abundance. Recent research using molecular data to characterize invasive Largemouth Bass populations elsewhere has demonstrated that populations are typically characterized by limited genetic diversity, or represent a combination of Largemouth Bass and Florida Bass (Micropterus floridanus). To test whether these traits were consistent with invasive populations in Brazil, we generated mitochondrial sequence data from four established populations of Largemouth Bass collected in southern Brazil as well as a local aquaculture facility to confirm species identity and quantify levels of genetic diversity. We identified the exclusive presence of Largemouth Bass in the region and observed limited levels of haplotype (haplotype diversity = 0.0684, SE = 0.038) and nucleotide diversity (0.0003, SE = 0.0002) which suggested the presence of a founder effect associated with introduction. Each of the four populations were dominated by a single haplotype that was identical to one recovered from a nearby aquaculture facility, which identified this facility as a potential introduction source.

Genetic diversity of Solanum nigrum cultivated in Kenya

Abstract. Wagio RS, Runo S, Muchugi A. 2019. Genetic diversity of Solanum nigrum cultivated in Kenya. Asian J Agric 2: 63-71. Solanum nigrum L., sometimes known as black nightshade, is a worldwide weed found on arable land, in gardens, and garbage dumps. It has been utilized in the pharmaceutical industry to produce analgesics, ointments, and vasodilators. Using morphological and Simple Sequence Repeats (SSR) markers, this study aimed to assess the genetic diversity of S. nigrum populations growing in specific regions of Kenya. One hundres-twenty (120) samples from four populations were evaluated in total. Morphological characterization utilized four aerial characters. leaf surface (smooth and hairy), leaf margin (whole and sinuous), leaf form (ovate, lanceolate, and diamond), fruit color (red, purple small, and purple large). Tukey's HSD test demonstrated substantial variation among the evaluated attributes (P?0.05). Four SSR primers produced 63 polymorphic bands, ranging from 14 to 17 per primer set. The range of Polymorphic Information Content was 0.1429 to 0.1855, with a mean value of 0.1704. Heterozygosity (using SSR markers) averaged out to be He=0.1370. Axis 1 and 2 of the PCoA explained 44.65% of the population distribution variance. The analysis of multi-level variance (AMOVA) showed that there was only 14% variation between populations and 86% variation inside the populations. Nei's genetic distance varied between 0.010 (Kipkaren and Matanya) and 0.020 (Makuyu and Mauche). Using DARwin 6.0.5 and Unweighted Neighbor Joining with 1000 bootstraps, a dissimilarity study was conducted. The absence of morphological and genetic distinctions in the dendrogram is indicative of the absence of genetic divergence between groups. Variance in the Agro-Ecological Zone is not indicative of variation in the S. nigrum cultivars. Comparing morphological and molecular data revealed leaf surface and fruit color grouping with genetic data. Using the same data, however, there was no grouping between leaf shape and leaf margin. The observed physical distinctions are primarily the effect of human selection. This study demonstrates that the S. nigrum complex displays limited genetic diversity but considerable morphological heterogeneity. Low genetic distance and the absence of clustering patterns indicate that S. nigrum is a closely related group of plants. The results of this study will have far-reaching implications for future breeding efforts of the Solanum complex, as they will be utilized to produce markers connected to crucial agronomic features. The findings will contribute further to resolving the taxonomic ambiguity surrounding S. nigrum.

Human pegivirus 2 exhibits minimal geographic and temporal genetic diversity

We applied an NGS based target capture approach to amplify HPgV-2 sequences from metagenomic libraries and enable full genome characterization. Despite expanded geographical sampling, sequence variability remains low, with diversity concentrated in approximately 3.3% of all amino acids. Serial samples from one HPgV-2 positive individual co-infected with comparable titers of HIV, HCV, and GBV-C showed that HPgV-2 remains highly stable over several weeks compared to other RNA viruses, despite a similarly error-prone polymerase. The consistent epidemiological association with and structural similarities to HCV, and the weak positive correlation of HCV and HPgV-2 titers shown here, suggests it may benefit from co-infection. While minimal selective pressure on HPgV-2 to evolve could suggest fitness, the rarity of HPgV-2 and the tight phylogenetic clustering of global strains likely indicates origination from a common source and a virus that is ill-suited to its host. Sporadic infections may explain the limited genetic diversity observed worldwide.