Clustering Of Genotypes Research Articles

Genotypic and antimicrobial resistance characterizations of Cronobacter sakazakii isolated from powdered milk infant formula: A comparison between domestic and imported products.

Cronobacter sakazakii, an opportunistic foodborne pathogen and a main cause of meningitis in neonates, is usually isolated from powdered milk infant formula (PMIF). At the present study, C. sakazakii were isolated from imported and domestically produced PMIF samples and identified by detection of ompA gene using real‐time PCR SYBR green melting curve following the evaluation of antimicrobial susceptibility and genotyping of the isolates employing BOX‐PCR and RAPD methods. We detected totally 5% contamination rate and a significantly higher prevalence of C. sakazakii in bulky imported domestically packaged PMIF samples. Also, our isolates were recognized as multidrug‐resistant pathogen completely resistant to ampicillin and amoxicillin; and intermediately resistant to ciprofloxacin and tetracycline antimicrobials. Genotype clustering patterns of bulky imported and imported product isolates were identical by both genotyping methods. Far genetic relatedness of domestic isolate to other isolates and the reference strain indicated higher genetic diversity of the domestic isolate genome. Multidrug resistance and diverse population genetic make complicated situation for determination of strategies for infectious disease prevention.

Identification and characterization of white onion (Allium cepa L.) genotypes for high total soluble solid content through molecular markers

Onion (Allium cepa L.) is one of the most important bulbous vegetable used in global kitchen. Although it has various important traits but among them the high total soluble solid content (HTSS) of white onion is highly preferred by the industries for processing purpose. Looking into the broader use of the white onion; we utilized a total of 23 polymorphic simple sequence repeats (SSRs) and intron length polymorphic markers (ILPs) to characterize thirty five white onion genotypes for HTSS. Further, we also correlated these DNA fingerprint data with the TSS for identification of HTSS and LTSS lines. The total average numbers of alleles for SSR and ILP locus, heterozygosity (He) and polymorphism information content were found to be 2.4, 0.35 and 0.29 respectively. The UPGMA dendrogram revealed two distinct clusters of genotypes. Based on the TSS and DNA genotype data, our study revealed that Bhima-shweta (LTSS-12.09%, sub-cluster IAa) & WHT-12L-HT-15-Reject-M-7(HTSS- 18.02%, cluster II) are more diverse than the others. Other white onion lines including WHTB-7G-GT-15-SC-M-7 small bulb (HTSS 18.80%), WHT-2B-GT-18-SC-M-7 (HTSS 18.51%), WHTS-4D-GT-18-MC-M-7 (HTSS 18.49%), WHTB-3C-GT-18-MC-M-7 (HTSS 18.27%) and WHTS-11K-Pickle-SC-M-7 (HTSS 17.68%) were identified as superior HTSS lines. These identified diverse HTSS and LTSS lines could be useful for the mapping of HTSS coding genes for the acceleration of molecular breeding of onion through the marker assisted selection (MAS) which could be used by the industries for the larger scale processing of the white onion products required by the global community.

Integrating univariate and multivariate statistical models to investigate genotype × environment interaction in durum wheat

AbstractThere has been a significant trend in the use of different statistical tools to analyse genotype × environment (GE) interaction for grain yield in multi‐environment trials. Several statistical models including 16 univariate stability methods and four multivariate models such as the additive main effects and multiplicative interaction (AMMI), GGE biplot (G+GE biplot), and factorial regression and partial least squares regression were applied to investigate the GE interaction for grain‐yield data of 18 durum wheat genotypes grown in 14 environments (location‐year combinations). The main objectives were to use the different statistical models to evaluate GE interaction for grain yield in durum wheat and to investigate the effect of some climatic variables on the interactions. The main effect of environment, genotype and GE interactions were significant (p < .01), and accounted for 85.1, 0.8 and 6.8% of total variation, respectively. Using the cluster and discriminant analyses, a pattern map developed simultaneously for clustering of stability methods and genotypes, which allowed identifying seven genotypic groups for genotypes and four groups for stability methods. The different stability groups explained genotypic performance differently, with or without respect to yield. The AMMI stability value, Wricke's ecovalence (Wi), Shukla's stability variance (σ2), Perkins and Jinks's (β and Dj) indices, joint regression parameters (bi and S2di, R2) and Tai's stability (σ and λ) methods did not correlate with genotypic mean yields, while the dynamic stability GGE distance and superiority measure (Pi) showed significant positive correlations with genotypic mean yields, showing selection based on these two methods would improve yield stability and performance. Using the applied methods, the breeding lines G12, G13 and G7 showed high mean yield and stability performance. The results also showed that the GE interactions were mostly influenced by the climatic data of rainfall, freezing days, minimum temperature and relative humidity. Although the multivariate methods provided valuable information on GE interaction, the univariate methods seem to be useful alternatives to complement improving screening efficiency.

Genotypic diversity in multi-drug-resistant E. coli isolated from animal feces and Yamuna River water, India, using rep-PCR fingerprinting.

Genotypic diversity among multi-drug-resistant (MDR) aquatic E. coli isolated from different sites of Yamuna River was analyzed using repetitive element PCR (rep-PCR) methods viz. ERIC-PCR and (GTG)5-PCR and compared with the MDR animal fecal isolates. The 97 E. coli isolates belonging to different serotypes, phylogroups, and multi-drug resistance patterns were analyzed. High genetic diversity was observed by both the methods; however, (GTG)5 typing showed higher discriminating potential. Combination of ERIC types (E1-E32) and (GTG)5 types (G1-G46) generated 77 genotypes. The frequency of genotypes ranged from 0.013 to 0.065. The genotype composition of E. coli isolates was highly diverse at all the sampling sites across Yamuna River except at its entry site in Delhi. The sampling sites under the influence of high anthropogenic activities showed an increase in number of unique genotype isolates. These sites also exhibited high multiple antibiotic resistance (MAR) indexes (above 0.25) suggesting high risk of contamination. Principal coordinate analysis (PCoA) showed limited clustering of genotypes based on the sampling sites. The most frequent genotypes were grouped in the positive zone of both the principal coordinates (PC1 and PC2). The genotypes of most of the animal fecal isolates were unique and occupied a common space in the negative PC1 area forming a separate cluster. High genotypic diversity among the aquatic E. coli and the drain isolates, discharging the untreated municipal waste in the river, was observed, suggesting that the sewage effluents contribute substantially to contamination of this river system than animal feces. The presence of such a high diversity among the MDR E. coli isolates in the natural river systems is of great public health significance and highlights the need of an efficient surveillance system for better management of Indian natural water bodies.

Continuous variation and specific interactions in the Pyrenophora teres f. teres–barley pathosystem in Uruguay

The nature of host–pathogen interactions between Pyrenophora teres f. teres and barley has been reported to be as well race-specific as race-non-specific with evidence that the definition of races is tenuous. Infection responses of 266 single-spore isolates of P. teres f. teres collected in Uruguay during regular surveys from 2005 to 2015 to 41 barley genotypes that had been determined on a 1–10 scale and thus allowed for qualitative and quantitative distinction in virulence and aggressiveness were subjected to cluster analysis. A total of four isolate clusters and seven barley clusters based on mean infection responses were determined. Infections reactions of the 266 isolates were continuous, and each isolate had a unique pathogenic spectrum. There were no effects of sampling year and location on the occurrence of similar isolates. Despite some very few and clear isolate-specific interactions, the interactions in this pathosystem can be described as predominately quantitative. For screening purposes, 1–2 isolates from the different clusters with broad aggressiveness to most or all of the respective barley genotype clusters will be the best choice.

Recent Increase in the Prevalence of Fluconazole-Non-susceptible Candida tropicalis Blood Isolates in Turkey: Clinical Implication of Azole-Non-susceptible and Fluconazole Tolerant Phenotypes and Genotyping.

Candida tropicalis is the fourth leading cause of candidemia in Turkey. Although C. tropicalis isolates from 1997 to 2017 were characterized as fully susceptible to antifungals, the increasing global prevalence of azole-non-susceptible (ANS) C. tropicalis and the association between high fluconazole tolerance (HFT) and fluconazole therapeutic failure (FTF) prompted us to re-evaluate azole susceptibility of C. tropicalis in Turkey. In this study, 161 C. tropicalis blood isolates from seven clinical centers were identified by ITS rDNA sequencing, genotyped by multilocus microsatellite typing, and tested for susceptibility to five azoles, two echinocandins, and amphotericin B (AMB); antifungal resistance mechanisms were assessed by sequencing of ERG11 and FKS1 genes. The results indicated that C. tropicalis isolates, which belonged to 125 genotypes grouped into 11 clusters, were fully susceptible to echinocandins and AMB; however, 18.6% of them had the ANS phenotype but only two carried the ANS-conferring mutation (Y132F). HFT was recorded in 52 isolates, 10 of which were also ANS. Large proportions of patients infected with ANS and HFT isolates (89 and 40.7%, respectively) showed FTF. Patients infected with azole-susceptible or ANS isolates did not differ in mortality, which, however, was significantly lower for those infected with HFT isolates (P = 0.007). There were significant differences in mortality (P = 0.02), ANS (P = 0.012), and HFT (P = 0.007) among genotype clusters. The alarming increase in the prevalence of C. tropicalis blood isolates with ANS and HFT in Turkey and the notable FTF rate should be a matter of public health concern.

Genotypic and phenotypic diversity among Lactobacillus plantarum and Lactobacillus pentosus isolated from industrial scale cucumber fermentations

The Lactobacillus plantarum and Lactobacillus pentosus genotypes existing in industrial-scale cucumber fermentations were defined using rep-PCR-(GTG)5. The ability of each genotype to ferment cucumbers under various conditions was evaluated. Rep-PCR-(GTG)5 was the technique capable of illustrating the most intraspecies discrimination compared to the sequencing of housekeeping genes (recA, dnaK, pheS and rpoA), MLST and RAPD with primers LP1, OPL5, M14 and COC. Ten genotypic clusters were defined for the 199 L. pentosus tested and three for the 17 L. plantarum clones. The ability of the 216 clones genotyped and 37 additional cucumber fermentation isolates, of the same species, to rapidly decrease the pH of cucumber juice medium under various combinations of sodium chloride (0 or 6%), initial pH (4.0 or 5.2) and temperatures (15 or 30 °C) was determined using a fractional factorial screening design. A reduced fermentation ability was observed for the L. plantarum strains as compared to L. pentosus, except for clone 3.2.8, which had a ropy phenotype and aligned to genotypic cluster A. L. pentosus strains belonging to three genotypic clusters (B, D and J) were more efficient in cucumber juice fermentation as compared to most L. plantarum strains. This research identified three genetically diverse L. pentosus strains and one L. plantarum as candidates for starter cultures for commercial cucumber fermentations.

A nosocomial cluster of vancomycin resistant enterococci among COVID-19 patients in an intensive care unit

BackgroundCurrently, hospitals have been forced to divert substantial resources to cope with the ongoing coronavirus disease 2019 (COVID-19) pandemic. It is unclear if this situation will affect long-standing infection prevention practices and impact on healthcare associated infections. Here, we report a nosocomial cluster of vancomycin-resistant enterococci (VRE) that occurred on a COVID-19 dedicated intensive care unit (ICU) despite intensified contact precautions during the current pandemic. Whole genome sequence-based typing (WGS) was used to investigate genetic relatedness of VRE isolates collected from COVID-19 and non-COVID-19 patients during the outbreak and to compare them to environmental VRE samples.MethodsFive VRE isolated from patients (three clinical and two screening samples) as well as 11 VRE and six vancomycin susceptible Enterococcus faecium (E. faecium) samples from environmental sites underwent WGS during the outbreak investigation. Isolate relatedness was determined using core genome multilocus sequence typing (cgMLST).ResultsWGS revealed two genotypic distinct VRE clusters with genetically closely related patient and environmental isolates. The cluster was terminated by enhanced infection control bundle strategies.ConclusionsOur results illustrate the importance of continued adherence to infection prevention and control measures during the COVID-19 pandemic to prevent VRE transmission and healthcare associated infections.

Genetic diversity of Indian porcine circovirus type 2 (PCV2) isolates (2006-2018)

Porcine circovirus type 2 (PCV2) is an emerging viral infection in swine population and results in severe economic loss to piggeries worldwide. The present study was conducted to explore the genetic diversity of PCV2 circulating in swine population of India from 2006–2018. A total of 74 heart, lungs, spleen and lymph nodes collected from different regions in Uttar Pradesh, India were subjected to molecular analysis. For studying genetic diversity, the complete nucleotide and ORF2 sequences of 95 PCV2 including 43 nucleotide sequences from India were used. DNA was extracted from samples and positive samples were subjected to full genome sequencing and phylogenetic analysis was done by maximum likelihood method. Phylogenetic analysis of 40 Indian PCV2 genomes downloaded from GenBank along with three new isolates from the current study based on the complete genome and cap gene together with nucleotide sequences of PCV2 isolates from different countries results in a tree in which Indian isolates clustered in 4 different branches includes PCV2b-1C, PCV2a-2D, PCV 2b-1A/B, PCV 2d-2 recombinant group and two new cluster in which one clustered along with unclassified PCV2 viruses from Indonesia and Croatia. The comparison of ORF2 gene among Indian isolates revealed nucleotide identity ranging from 88.6% to 99.6%, indicating the genetic diversity of PCV2 strains circulating in Indian pig. The present work reports for the first time in India the PCV2-1A/B cluster of 2b genotype and all the Indian isolates available in India from 2006–2018 were used in this analysis.

Canola yield and its association with phenological, architectural and physiological traits across the rainfall zones in south-western Australia

• Multiple-environment trials were used to understand yield and associated traits. • Genotype × environment interaction reveals two environment and four genotype clusters. • Flowering time, biomass and harvest index were the main factors determining yield. • Both specific and broad adaption were identified. Understanding genotype and environment interaction (G × E) and the association between yield and phenological, architectural and physiological traits plays a crucial role in successful canola breeding and agronomic management. We investigated yield performance of 20 open-pollinated and hybrid canola across multiple environments over five years and its association with these traits. Heterogenic genetic variance and genetic correlation among the environments demonstrated significant G × E interactions in yield, biomass, but not in harvest index (HI). Flowering time, biomass at maturity and HI are the three most important traits underlying the G × E interaction. Principal component analysis (PCA) based on the yield across the environments identified two mega-environments (the low/medium rainfall zone (LMRZ) and the high rainfall zone (HRZ)) and four genotype clusters (early-flowering, late-flowering, average performing, and broadly adapted varieties). Early flowering genotypes were better adapted to the LMRZ mega-environment and late-flowering ones to the HRZ mega-environment. Despite the G × E interaction, a group of hybrid varieties were identified as broadly adapted, producing either the highest or similar yield to specifically adapted varieties. The genotype by trait PCA revealed that yield was positively associated with biomass and HI but negatively with flowering time in the LMRZ mega-environment. In contrast, yield was positively associated with increased biomass, late-flowering but negatively with HI in the HRZ mega-environment. In both mega-environments, HI was negatively correlated with delay in flowering and increased plant height and biomass. Reducing plant height in late flowering hybrid varieties offers a solution to the trade-off between biomass and HI. It can have the potential to increase yield by increasing HI while maintaining biomass in the HRZ mega-environment.

A network analysis framework of genetic and nongenetic risks for type 2 diabetes.

Both genetic and nongenetic factors have been found to be associated with type 2 diabetes, however, the correlation between them is still unclear. In the present study, we aimed to fully decipher the nongenetic and genetic factor association network for type 2 diabetes. We identified risk factors for type 2 diabetes by systematically searching for related meta-analyses and genome-wide association studies (GWAS) database. Among a total of 27,822 studies screened, 202 articles were eligible, from which 174 nongenetic factors and 210 genetic factors associated with type 2 diabetes were identified. Then, we obtained 584 associations between the nongenetic and genetic factors of type 2 diabetes, based on which a risk factor association network was conducted. The nongenetic factors could be classified into seven categories according to the Global Burden of Diseases (GBD). Of these seven categories of nongenetic factors, five were found to be correlated with genes associated with type 2 diabetes, including environmental risks, behavioral risks, metabolic risks, related disease of type 2 diabetes, and treatments. Specifically, air pollutants of environmental risks, alcohol using of behavioral risks, obesity of metabolic risks, rheumatoid arthritis of related disease risk, and simvastatin of treatment was correlated with the largest number of genes. In summary, the correlation between genetic factors and nongenetic factors identified in this study indicates that there is a common phenotype-genotype association in type 2 diabetes, with the combinations of genotypes ("genetic signature") clustering in phenotypes related to type 2 diabetes. Thus, we should take a systematic approach to explore the relationship of various factors for type 2 diabetes, as well as other noncommunicable diseases.

Staphylococcus aureus From Goats Are Genetically Heterogeneous and Distinct to Bovine Ones.

Staphylococcus aureus is one of the major pathogens responsible for intramammary infections in small ruminants, causing severe economic losses in dairy farms. In addition, S. aureus can contaminate milk and dairy products and produce staphylococcal enterotoxins, being responsible for staphylococcal food poisoning. Currently, data on the population structure and the virulence gene patterns of S. aureus strains isolated from goat milk is limited. Therefore, this study aimed at defining Ribosomal Spacer PCR (RS-PCR) genotypes, clonal complexes (CC), spa types, and virulence gene profiles of S. aureus isolated from goat milk samples from Lombardy region of Italy. A total of 295 S. aureus isolates from 65 goat bulk tank milk samples were genotyped by RS-PCR. spa typing and virulence gene patterns of a subgroup of 88 isolates were determined, and MLST was performed on a further subgroup of 39 isolates, representing all the spa types identified during the analysis. This study revealed 7 major genotypic clusters (CLR, CLAA, CLZ, CLAW, CLBW, CLS, and CLI), of which S. aureus CLR (19.8%) was the most common. A total of 26 different spa types were detected, the most prevalent types were t1773 (24%), t5428 (22.7%), and t2678 (12.5%). Overall, 44.3% of all isolates harbored at least one enterotoxin gene. The most prevalent was the combination of sec-sel genes (35.2%). Based on their MLST, isolates were assigned to 14 different CC, with majority grouped as CC133 (24%), CC130 (19.6%), and CC522 (19.6%). The caprine S. aureus population was depicted with a minimum spanning tree and an evolutionary analysis based on spa typing and MLST, respectively. Then, the variability of such strains was compared to that of bovine strains isolated in the same space-time span. Our results confirmed that S. aureus isolates from goats have wide genetic variability and differ from the bovine strains, supporting the idea that S. aureus from small ruminants may constitute a distinct population.

Influence of CYP3A polymorphisms on tacrolimus pharmacokinetics in kidney transplant recipients.

Tacrolimus is characterized by a highly variable pharmacokinetics (PK) and a small therapeutic window. It is metabolized specifically by the CYP3A isoenzymes. This study aimed to determine, in kidney transplant patients, the influence of different genotypic clusters involving these SNPs CYP3A4*1B, CYP3A4*22, and CYP3A5*3 on Tacrolimus bioavailability during the first (PTP1) and the second (PTP2) posttransplant phase (PT). We included kidney transplant patients who received Tacrolimus and underwent drug monitoring by C0 monitoring. CYP3A4 and CYP3A5 genotyping were performed using PCR-RFLP. We classified the patients into four groups: Slow, Intermediate, rapid, and ultra-rapid metabolizers. We included 80 patients. The Tacrolimus dose-normalized C0 (C0/D ratio) was significantly decreased in intermediate, rapid, and ultra-rapid comparing with slow metabolisers. During PTP1 only CYP3A5*3 and CYP3A4*22 polymorphisms correlate significantly with C0/D ratio. Regardless of the PT phase and during the late one, only the CYP3A4 polymorphisms correlate significantly with the C0/D ratio. We identified that these SNPs are all associated independently with Tacrolimus exposure in different PT phases. Moreover, we are the first to define a genotypic cluster including the three CYP3A SNPs.

Genetic analysis of twenty two selected genotypes of Jatropha curcas L. (physic nut) from Africa, Asia and America, using SSR and AFLP markers

Twenty two genotypes of J. curcas L. from Africa (Senegal, Burkina Faso, Mali, Congo and Madagascar Island), Asia (Cambodia, China and India) and America (Ecuador, Dominican Republic and Brazil) selected for their vigor and their productivity were analyzed with ten SSR primer pairs and six AFLP primer combinations. The two marker approaches showed their ability to effectively reveal polymorphism among the selected genotypes: 94.02 and 56% of polymorphism for AFLPs and SSRs respectively. Among the three groups of selected genotypes, the Asian group was the least diverse while the genetic diversities found in African and American groups were slightly comparable. The Nei’s genetic diversity (He) of all twenty-two selected genotypes was 0.2029 based on combined SSR+AFLP data. The Gst value and the AMOVA analysis indicated that more than 80% of the genetic diversity resided within the groups. The analysis of the genetic relationships between the genotypes using the Nei’s standard dissimilarity matrix gave dissimilarity coefficients ranging from 0.14397 to 0.73943 with an average of 0.3540. The most distant genotypes were found between a genotype from Africa (Congo) and one from America (Ecuador). The clustering of genotypes obtained with the neighbor-joining dendrogram and the PCoA analysis revealed the existence of a certain level of diversity that can be used by breeders. Key words: Biodiesel, genetic diversity, jatropha, molecular markers, AFLP, SSR, plant breeding.

Genetic diversity of exotic and local eggplants (Solanum spp.) cultivated in Côte d’Ivoire based on ISSR markers

Abstract. Konan NO, Akaffou MA, Kouadio L, Akaffou DS, Mergeai G. 2020. Genetic diversity of exotic and local eggplants (Solanum spp.) cultivated in Côte d’Ivoire based on ISSR markers. Biodiversitas 21: 3651-3658. Eggplants are important vegetables in Côte d'Ivoire. Despite an increase in the cultivation of exotic genotypes and their progressive dominance over local cultivars, which could represent a threat of genetic erosion, there are not enough molecular data available on the genetic diversity of the eggplants currently cultivated in this country. This study is a contribution to the knowledge of the genetic diversity of the current eggplant cultivars grown in Côte d’Ivoire. It aimed to assess the genetic variation of nine exotic and local eggplants commonly cultivated in Côte d'Ivoire, using five inter-simple sequence repeat (ISSR) primers. The results revealed for the exotic cultivars 42 ISSR loci of which 31 were polymorphic (73.81 %), and for local cultivars 51 loci of which 49 (96.08%) were polymorphic. The Nei’s genetic diversity and Shannon’s information index of local cultivars (He = 0.3333 and I = 0.4863) were higher than those of exotic cultivars (He = 0.2000 and I = 0.2971). The Gst value and the AMOVA analysis found more than 70% of the total genetic diversity within the groups. The Jaccard’s dissimilarity coefficients between the cultivars, ranged from 0.324 to 0.966 with an average of 0.741. The clustering of genotypes with the neighbor-joining unrooted tree and PCoA analysis differentiated three main clusters with exotic cultivars grouped in cluster I and local cultivars in cluster II and III. In view of these results, the local eggplants had higher genetic diversity and constitute an interesting germplasm which needs to be conserved for potential breeding programs.

Distribution and validation of genotypic and phenotypic glyphosate and PPO-inhibitor resistance in Palmer amaranth (Amaranthus palmeri) from southwestern Nebraska

AbstractFailure to control Palmer amaranth with glyphosate and protoporphyrinogen IX oxidase (PPO)-inhibitor herbicides was reported across southwestern Nebraska in 2017. The objectives of this study were to 1) confirm and 2) validate glyphosate and PPO-inhibitor (fomesafen and lactofen) resistance in 51 Palmer amaranth accessions from southwestern Nebraska using genotypic and whole-plant phenotypic assay correlations and cluster analysis, and 3) determine which agronomic practices might be influencing glyphosate resistance in Palmer amaranth accessions in that location. Based on genotypic assay, 88% of 51 accessions contained at least one individual with amplification (>2 copies) of the 5-enolypyruvyl-shikimate-3-phosphate synthase (EPSPS) gene, which confers glyphosate resistance; and/or a mutation in the PPX2 gene, either ΔG210 or R128G, which endows PPO-inhibitor resistance in Palmer amaranth. Cluster analysis and high correlation (0.83) between genotypic and phenotypic assays demonstrated that EPSPS gene amplification is the main glyphosate resistance mechanism in Palmer amaranth accessions from southwestern Nebraska. In contrast, there was poor association between genotypic and phenotypic responses for PPO-inhibitor resistance, which was attributed to segregation for PPO-inhibitor resistance within these accessions and/or the methodology that was adopted herein. Genotypic assays can expedite the process of confirming known glyphosate and PPO-inhibitor resistance mechanisms in Palmer amaranth from southwestern Nebraska and other locations. Phenotypic assays are also a robust method for confirming glyphosate resistance but not necessarily PPO-inhibitor resistance in Palmer amaranth. Moreover, random forest analysis of glyphosate resistance in Palmer amaranth indicated that EPSPS gene amplification, county, and current and previous crops are the main factors influencing glyphosate resistance within that geographic area. Most glyphosate-susceptible Palmer amaranth accessions were found in a few counties in areas with high crop diversity. Results presented here confirm the spread of glyphosate resistance and PPO-inhibitor resistance in Palmer amaranth accessions from southwestern Nebraska and demonstrate that less diverse cropping systems are an important driver of herbicide resistance evolution in Palmer amaranth.

Evaluation of (GTG) 5-PCR for Genotyping of Klebsiella pneumonia Strains Isolated from Patients with Urinary Tract Infections

Klebsiella pneumonia is one of the common causes of pneumonia and bacteremia in intensive care patients. The present study was aimed to determine the capability of (GTG) 5-PCR assay for molecular typing of K. pneumonia strains isolated from patients with urinary tract infections. In this descriptive-sectional study, K. pneumoniae strains were collected from hospitalized patients with urinary tract infection in Baqiyatallah Hospital, Tehran, Iran during 2017-2018. Isolates were identified by conventional microbiological tests. Bacterial DNA was extracted using boiling method and (GTG) 5-PCR assay was used for subtyping of the isolates. For clustering of isolates, dendrogram was generated according to the un-weighted pair group method with arithmetic (UPGMA). Overall, 88 K. pneumoniae isolates were isolated and subjected to the molecular typing study. The (GTG) 5-PCR assay was able to differentiate the K. pneumoniae strains into 9 clusters including G1-G9. Genotype clusters G4 and G9 consist of highest (26) and lowest (1) number isolate, respectively. The K. pneumonia strains isolated under the study belonged to various clones and the (GTG) 5-PCR assay as simple and rapid method can be a powerful tool for molecular typing of K. pneumoniae strains.

Genetic capitalism and stabilizing selection of antimicrobial resistance genotypes in Escherichia coli.

Antimicrobial resistance (AMR) in pathogenic strains of bacteria, such as Escherichia coli (E.coli), adversely impacts personal and public health. In this study, we examine competing hypotheses for the evolution of AMR including (i) 'genetic capitalism' in which genotypes that confer antibiotic resistance are gained and not often lost in lineages, and (ii) 'stabilizing selection' in which genotypes that confer antibiotic resistance are gained and lost often. To test these hypotheses, we assembled a dataset that includes annotations for 409 AMR genotypes and a phylogenetic tree based on genome-wide single nucleotide polymorphisms from 29 255 isolates of E.coli collected over the past 134years. We used phylogenetic methods to count the times each AMR genotype was gained and lost across the tree and used model-based clustering of the genotypes with respect to their gain and loss rates. We demonstrate that many genotypes cluster to support the hypothesis for genetic capitalism while a few genotypes cluster to support the hypothesis for stabilizing selection. Comparing the sets of genotypes that fall under each of the hypotheses, we found a statistically significant difference in the breakdown of resistance mechanisms through which the AMR genotypes function. The result that many AMR genotypes cluster under genetic capitalism reflects that strong positive selective forces, primarily induced by human industrialization of antibiotics, outweigh the potential fitness costs to the bacterial lineages for carrying the AMR genotypes. We expect genetic capitalism to further drive bacterial lineages to resist antibiotics. We find that antibiotics that function via replacement and efflux tend to behave under stabilizing selection and thus may be valuable in an antibiotic cycling strategy.

Tolerance and determinants of drought character descriptors of the Madurese landrace bambara groundnut (Vigna subterranea)

Abstract. Fatimah S, Ariffin, Rahmi AN, Kuswanto. 2020. Tolerance and determinants of drought character descriptors of the Madurese landrace bambara groundnut (Vigna subterranea). Biodiversitas 21: 3108-3116. Bambara groundnut (Vigna subterranea L. Verdc.) is legume of African origin overlooked in Indonesia. It has underdeveloped in Indonesia; for example, in East Java, it is only cultivated in Gresik, Lamongan, and Bangkalan of Madura. This plant can potentially be developed in dry lands, such as Madura as it has the ability to grow and develop well in a dry environment with low nutrient level. At present, there are sparse researches on the selection and determination of the drought-tolerant character descriptors of bambara groundnut in Indonesia. The present study used the expected lines of bambara groundnut selected from local lines of various regions in Indonesia using the nested design. The results showed that the drought stress treatment led to stunted growth of 12 bambara groundnut genotypes, including the number of leaves, plant height, canopy diameter, leaf thickness, number of flowers, number of stems or branches, number of internodes, length of leaf stems, root length, root wet weight, canopy wet weight, canopy dry weight, root dry weight, and leaf chlorophyll content. However, drought leads to a slight increase in the width and length of the stomata opening and leaf proline contents. The cluster analysis based on stress index and sensitivity index can classify 3 expected lines originating from Gresik Regency (G1, G2, G3), falling into the drought stress-tolerant category. Accumulated proline contents cannot be used as a descriptor of tolerance to drought stresses in bambara groundnut since the expected lines with an increase in proline contents in leaves during drought stresses based on the cluster analysis do not fall into the genotypic cluster tolerant to drought stresses.

Alternative views of biological species: reproductively isolated units or genotypic clusters?

Wang et al. in this journal argue that it may be time to abandon a classic idea about species, the biological species concept (BSC), given recent findings with genomic data on closely related taxa. Furthermore, they propose a set of tests on genetic or genomic data that might lead to acceptance or rejection of the biological species concept. Wang et al. are not the first to critique the biological species concept (BSC), which has survived an onslaught of attacks from many fronts. What is the biological species concept? And what is the new critique about? In this commentary, I briefly cover the history of ideas about biological species, then discuss current work that depends on rich, genome-scale sequence data, before attempting to resolve issues.