High Genetic Similarity Research Articles

Recent Update of COVID-19 Vaccines.

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has been recently identified as a novel member of beta coronaviruses (CoVs) and the cause of coronavirus disease 2019 (COVID-19). It has been first discovered in China and soon has spread across continents with an escalating number of mortalities. There is an urgent need for developing a COVID-19 vaccine to control the rapid transmission and the deleterious impact of the virus. The potent vaccine should have a good tolerable and efficacious profile to induce target-specific humoral and cellular immune responses. It should also exhibit no or minimal detrimental effects in children, young adults, and elderly people with or without co-morbidities from different racial backgrounds. Previously published findings of SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV) played vital role in the characterization of surface spike proteins as the tool of entry of the SARS-CoV-2 into host cells. It has become evident that SARS-CoVs have high genetic similarity and this implies antecedent vaccination strategies could be implicated in the production of COVID-19 vaccines. Although several vaccines have been approved and rolled out, only a handful of them have passed the three phases of clinical studies. This review highlights the completed, and ongoing clinical trials of COVID-19 vaccines and efforts are being made globally to avert the pandemic.

Assessment of Insulin, GLUT2 and inflammatory cytokines genes expression in pancreatic β-Cells in zebrafish (Danio rario) with overfeeding diabetes induction w/o glucose.

In recent years, zebrafish have been proposed as a model for rapid analysis of gene function and biological activity due to high genetic similarities with humans. The aim of this study was to determine the effects of overfeeding-induced diabetes w/o glucose on inflammatory cytokine as well as insulin and glucose transporter-2 genes (GLUT2) genes expression in the pancreas in zebrafish. The experiment was performed on 120 zebrafish (duplicated sample) with a specific genetic mapping (AB-Wild type). A total of 8 tanks, each containing 15 fish per 2-liter water, were used and divided into four groups: (1) Control group, (2) regular diet with glucose,3) Only Artemia overfeeding and 4) Combined Artemia with glucose. We induced T2DM zebrafish using glucose monohydrate solution in water and repeated daily Artemia feeding. In this model, fasting blood glucose increase is preceded by obesity and glucose intolerance. The experiment lasted for two months. Blood glucose and fish biometrics were measured in two steps. The expression of TNFα, IFNγ, GLUT2 and Insulin genes were quantified by a Real-Time qPCR System (Applied Biosystems, USA) using a set of specific primers. The highest mortality rate was observed in combined Artemia and glucose (p < 0.05). We showed significantly higher expression of IL-1B and TNF-α as well as inhibitory cytokines such as IFNγ genes in overfeeding induced diabetes(OID) which was highest in the combined Artemia and glucose group.(p < 0.05)The GLUT2 gene expression was higher in the pure artemia group which decreased to a lower level by adding glucose to Artemia in the diet. (p < 0.05). Also, the lowest insulin gene expression was observed in the combined group (p < 0.05). In zebrafish, diabetes induction with overfeeding and supraphysiological glucose in diet accompanied with higher expression of inflammatory cytokines genes in the pancreas as well as lower insulin and GLU2 genes. These epigenetic factors appeared to initiate pancreatic beta dysfunction alongside insulin resistance and could have a crucial role in the pathogenesis of overfeeding-induced diabetes using primitive animal models.

Effects of the Probiotic Activity of Bacillus subtilis DSM 29784 in Cultures and Feeding Stuff.

The European Union banned the usage of antibiotic growth promoters in animal production. The probiotic microorganism of the genus Bacillus appeared to be an attractive candidate to replace antibiotics. The Bacillus subtilis DSM 29784 is one of these strains. To date, the probiotic effect has not been completely understood, but it is supposed that the effect depends on metabolites of the microorganism. Imaging high-performance thin-layer chromatography (HPTLC) is a powerful tool to visualize differences in the metabolite profile of bacteria with high genetic similarity to allow a better understanding of the probiotic effect. In comparison to other bacteria, especially these bacterial cells were more robust to harsh cultivation conditions and produced a higher level of antioxidants or bioactive substances such as surfactin. HPTLC enabled the comparison of pure cell cultures to the spore cultivation in the feed, and the results explain and support the probiotic effect.

Genetic diversity analysis of Linseed (Linum usitatissimum L.) accessions using RAPD Markers

It is important to analyse the degree of genetic variation existing within the genome to extend the genetic base of linseed/flaxseed accessions in order to preserve, evaluate and use genetic resources accurately and successfully. The main aim of the current investigation was to evaluate the scope and spread of genomic variation across different linseed accessions by employing molecular markers (RAPD). The genomic DNA of 12 linseed accessions was amplified with 16 decamer RAPD primers that generated 81 total bands, among which 75 bands were polymorphic and 6 bands were monomorphic. Polymorphic band numbers varied from least 2 (OPS-11) to highest 10 (OPS-07). The magnitude of polymorphism ranged from 75% to 100% among all accessions with a mean of 93.15 % across all the accessions. The value of Polymorphic Information Content (PIC) varied from 0.133% to 0.708% with a mean of 0.45% for each primer. The maximum PIC value (0.708) was found with the primer OPS-07 and (0.702) with OPM-13. The primer OPS-03 showed the minimum PIC value (0.133). Two main different clusters -I and -II were seen in the cluster analysis depending on RAPD data. Cluster-II comprises one accession (IC 564585) that was the highly varied accession, whereas Cluster-I comprises of some sub clusters with all the remaining accessions. The Jaccard's similarity coefficient varied from 8.2 to 96.3%. The accessions BHU-A and BHU-B had the highest genetic similarity (96.3%), followed by BHU-B and IC 564605 (96.2%). More divergent accessions were discovered to be IC 564585, IC 564616, IC 564631, IC 564622, and IC 564630. The current investigation provides innovative knowledge to breeders on the germplasm of linseed that would be employed in subsequent research to improve linseed genotypes.

First linkage maps and a pilot QTL analysis for early growth performance in common dentex (Dentex dentex) and sharpsnout seabream (Diplodus puntazzo)

Two potential candidate species for the Mediterranean aquaculture–the common dentex (Dentex dentex) and the sharpsnout seabream (Diplodus puntazzo)-are used in the present study in order to depict their genetic architecture for the first time. We have constructed the first linkage maps for both species using SNP markers derived from ddRAD sequencing. The quality of the maps produced was verified from comparative analysis with the most studied and phylogenetically related sparid species, the gilthead sea bream (Sparus aurata). A high genetic similarity was detected, based on the high number of alignments of the two new species against the reference genome of the gilthead seabream. Furthermore, a pilot study for QTL analysis per species was performed using phenotypic measurements at the juvenile stage (approximately 2 g) and revealed putative genomic areas which affect juvenile growth performance. One of those areas was located close to a candidate gene (ANGPTL6 gene) which affects growth performance. The present study improves our knowledge on the genetic architecture of those two species by presenting not only the first linkage maps, but also by providing some indications for growth performance QTL. The results can be used as a starting point to initiate further research for the genetic improvement of these two new species.

Genotoxicity evaluation using primary hepatocytes isolated from rhesus macaque (Macaca mulatta)

Non-human primates (NHPs) have played a vital role in fundamental, pre-clinical, and translational studies because of their high physiological and genetic similarity to humans. Here, we report a method to isolate primary hepatocytes from the livers of rhesus macaques (Macaca mulatta) after in situ whole liver perfusion. Isolated primary macaque hepatocytes (PMHs) were treated with various compounds known to have different pathways of genotoxicity/carcinogenicity and the resulting DNA damage was evaluated using the high-throughput CometChip assay. The comet data were quantified using benchmark dose (BMD) modeling and the BMD50 values for treatments of PMHs were compared with those generated from primary human hepatocytes (PHHs) in our previous study (Seo et al. Arch Toxicol 2020, 2207–2224). The results showed that despite varying CYP450 enzyme activities, PMHs had the same sensitivity and specificity as PHHs in detecting four indirect-acting (i.e., requiring metabolic activation) and seven direct-acting genotoxicants/carcinogens, as well as five non-carcinogens that are negative or equivocal for genotoxicity in vivo. The BMD50 estimates and their confidence intervals revealed species differences for DNA damage potency, especially for direct-acting compounds. The present study provides a practical method for maximizing the use of animal tissues by isolating primary hepatocytes from NHPs. Our data support the use of PMHs as a reliable surrogate of PHHs for evaluating the genotoxic hazards of chemical substances for humans.

Antibiotic resistance and random amplified polymorphic DNA typing of Klebsiella pneumoniae isolated from clinical and water samples.

The study aimed to screen for the presence of multidrug-resistant Klebsiella pneumoniae from diarrheal stool and environmental water samples and to check the epidemiological link between the two categories. Isolates obtained after culturing on different media were tested for antibiotic resistance and extended-spectrum beta-lactamase (ESBL) production. Polymerase chain reaction (PCR) analysis was done for important β-lactamase encoding genes. Random amplified polymorphic DNA (RAPD) typing was done using two primers. Results showed a high prevalence of K.pneumoniae from fish market effluents compared with stool and well water. Stool isolates showed high resistance to ceftazidime (80.0%) and cefepime (80.0%), fish market effluent isolates to cefoperazone-sulbactam (92.1%), and erythromycin (78.9%), while well water isolates to erythromycin (72.7%) and cefuroxime (54.4%). The ESBL genes blaCTX , blaSHV , and blaTEM were detected in 22.85%, 14.28%, and 42.85% of K.pneumoniae isolates, respectively. The results of RAPD-PCR showed high genetic similarities between the isolates from different sources. PRACTITIONER POINTS: Detection of multi-drug resistant Klebsiella strains in hospital wastewater and drinking water sources has progressively increased since its emerging resistance to third-generation cephalosporins and carbapenems. Detection of beta-lactamase encoding genes by molecular techniques and typing by random amplified polymorphic DNA (RAPD) can be useful in identifying the genetic fingerprints for epidemiological study. Implementation of effective antimicrobial stewardship program and infection control policy thereby helps assess the risk factors associated with infections.

Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto.

Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.

Proximity to Industrial Poultry and Hog Production and Emergency Department Visits for Urinary Tract Infection in North Carolina, USA

BACKGROUND AND AIM: An increasing share of urinary tract infections (UTIs) are caused by uropathogenic {Escherichia coli} lineages that have also been identified in poultry and hogs with high genetic similarity to human clinical isolates. We investigated industrial food animal production as a potential source of community uropathogen exposure by examining relationships of poultry and hog density with emergency department (ED) visits for suspected UTI in North Carolina (NC). METHODS: ED visits for UTI in 2016-2019 were identified by ICD-10 code from NC's ZIP Code-level syndromic surveillance system and livestock counts were obtained from permit and agricultural census data. We calculated separate poultry and hog densities (animals/km²) by census block with a 5km buffer on the block perimeter and weighted by block population to estimate mean ZIP Code densities. Associations between livestock density and UTI incidence were estimated using a reparametrized Besag-York-Mollié (BYM2) model with Poisson likelihood and ZIP Code population offset to account for spatial autocorrelation. We assessed effect measure modification by ZIP Code rurality and patient sex, age, and race/ethnicity. RESULTS:Complete covariate data were available for 726 contiguous NC ZIP Codes; 233 had zero density of both poultry and hogs. UTI incidence was positively associated with a log10 density increase of both poultry (rate ratio [RR]: 1.05, 95% confidence interval [CI]: 0.99-1.11) and hogs (RR: 1.05, 95%CI: 0.98-1.14). Compared with hog-free ZIP Codes, all hog density tertiles were associated with increased UTI incidence (highest-density tertile RR: 1.21, 95%CI: 1.06-1.40); associations with poultry density tertiles were similar but weaker. The strongest associations were observed for ZIP Codes with hogs but no poultry (n=39) or with the highest-density tertiles of both animals (n=52; RR: 1.35, 95%CI: 1.11-1.62). Estimates were consistently elevated among females, young adults, and American Indian and Asian individuals. CONCLUSIONS:Industrial livestock production may be associated with increased UTI incidence in neighboring communities. KEYWORDS: Confined animal feeding operation (CAFO), syndromic surveillance, areal data, Bayesian hierarchical spatial model, intrinsic conditional autoregressive (ICAR) prior

Cluster of Symptomatic Graft-to-Host Transmission of Herpes Simplex Virus Type 1 in an Endothelial Keratoplasty Setting

PurposeDescemet's membrane endothelial keratoplasty (DMEK) is becoming the gold standard to treat corneal endothelial dysfunctions worldwide. Compared with conventional penetrating keratoplasty, infectious complications after DMEK are ill defined. We describe the clinical picture of 2 DMEK recipients, operated on the same day and in the same clinic, who developed atypical herpes simplex virus type 1 (HSV-1) infection in the transplant recipient eye within days post-DMEK. Because recipients received cornea tissue from 2 different donors prepared by the same eye bank, the likelihood of a common HSV-1 source was determined.DesignCase series.ParticipantsTwo DMEK recipients who developed atypical intraocular HSV-1 disease shortly after surgery and surplus cornea specimens of 6 donors.MethodsSurplus cornea donor (pre-DMEK cornea remnants and conditioned cornea storage and transport media) and recipient samples (post-DMEK aqueous humor) were assayed for HSV-1 DNA and infectious virus by real-time polymerase chain reaction (RT-PCR) and cell culture, respectively. Target-enriched whole viral genome sequencing was performed on HSV-1 DNA–positive ocular specimens.Main Outcome MeasuresClinical picture of atypical intraocular HSV-1 infection post-DMEK and presence and homology of HSV-1 genomes between ocular specimens of DMEK donors and recipients.ResultsHerpes simplex virus type 1 DNA was detected in aqueous humor and donor cornea specimens of both DMEK cases, but not in the cornea remnants of 6 randomly selected donors processed by the same eye bank. Infectious HSV-1 was isolated from the cornea remnant and corresponding culture medium of 1 cornea donor. Notably, whole-genome sequencing of virus DNA-positive specimens demonstrated exceptionally high genetic similarity between HSV-1 strains in recipient and donor specimens of both DMEK cases.ConclusionsData indicate cross-contamination of cornea grafts during DMEK preparation with subsequent graft-to-host HSV-1 transmission that caused atypical sight-threatening herpetic eye disease shortly after DMEK. Ophthalmologists should be aware that HSV-1 transmission by DMEK is possible and can lead to atypical ocular disease, a condition that can easily be prevented by taking appropriate technical and clinical measures at both eye bank and surgical levels.

Comparative mitochondrial genome analysis of the Mongolian redfin, Chanodichthys mongolicus (Xenocyprididae) from China reveals heteroplasmy

This study determined the mitochondrial genome (mitogenome) of Chanodichthys mongolicus from China's Qiantang River and analyzed its phylogenetic history in the Subfamily Cultrinae. Next-generation sequencing was used to obtain the mitogenome of C. mongolicus, GenBank Accession Number MZ032228. The mitochondrial genome length of C. mongolicus from China's Qiantang River is 16,622 bp. The genome contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two central noncoding regions (the control region and the origin of light strand replication). Based on BLAST comparisons, the sequence identity of C. mongolicus MZ032228 from China's Qiantang River was 99.84% to that of Ancherythroculter wangi MG783573 from China's Nei River, 99.75% to C. mongolicus AP009060 from Russia's Black River. The phylogenetic analysis is consistent with BLAST comparisons in confirming that A. wangi MG783573 and C. mongolicus MZ032228 show a high genetic similarity. This study also confirms mitochondrial DNA heteroplasmy in C. mongolicus for the first time and documents 35 heterogeneous loci that were detected.

Sequence Analysis and Structure Prediction of Malaysia SARS-CoV-2 Strain’s Structural and Accessory Proteins

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that transmitted from animal to human became a life-threatening pandemic in 2020. Scientists are currently testing several drugs to eradicate the COVID-19 outbreak. However, there is no 100 % effective drug or vaccine against SARS-CoV-2 has been discovered so far. In this study, we explored the structure prediction and functional analysis of 75 Malaysia SARS-CoV-2 strain’s structural and accessory proteins without the presence of experimental models. Physiochemical analysis, secondary structure analysis, structure prediction, functional characterization, active site identification, and evolutionary analysis based on the amino acid sequences retrieved from National Centre for Biotechnology Information (NCBI). Three-dimensional (3-D) protein structures were built using the Swiss model. The quality of protein models was verified by ERRAT, PROCHECK, and Verify 3D tools. Active prediction analysis revealed the high potential active sites of proteins where the anti-viral drug or vaccine may bind and inhibit the viral activities. Molecular phylogenetic analysis of ORF10, ORF8, and ORF6 proteins from five different species was analyzed. The results from this analysis proved that Homo sapiens SARS-CoV-2 had high genetic similarity with the bat coronavirus. These analyses may help in designing structure-based anti-viral drugs or to develop potential vaccines for SARS-CoV-2.

Study of Genetic Diversity of Glycyrrizha glabra L. Populations Using ISSR Molecular Markers

Twenty-two G. glabra populations were used to study the genetic diversity of ISSR molecular markers. 12 primers were used to amplification of genomic DNA fragments of G. glabra populations. High genetic diversity based on ISSR markers was observed among individuals. A total of 130 bands were formed and 105 bands were polymorphic. The mean polymorphism percentage among studied populations was 80.47. The highest polymorphic percentages were assigned to IS23, IS21, IS9, IS13 and IS15 primers. The mean of PIC and MI were 0.347 and 2.47, respectively. The Shannon index (I) varied between 0.207-0.393 and the Nei genetic variation index (h) from 0.140 to 0.026. Darab and Solataniyeh populations showed the lowest and highest genetic diversity, respectively. The percentage of polymorphic loci was varied between 35.224 to 65.71%. The observe allele number and effective alleles number was 1.46 and 1.34, respectively. Based on the genetic distance Nei, populations Bardsir and Baft had the highest genetic similarity (0.888) and populations Bardsir and Solataniyeh had the least genetic similarity (0.132). The studied populations were grouped into three main groups by cluster analysis using UPGAM and Jaccard's similarity coefficient. The results showed that the ISSR marker is a reliable marker system for revealing a high level of polymorphism and can be used to study genetic diversity and further examinations as a subset of breeding programs in G. glabra.

CRISPR/Cas9 in zebrafish: An attractive model for FBN1 genetic defects in humans.

BackgroundMutations in the fibrillin‐1 gene (FBN1) are associated with various heritable connective tissue disorders (HCTD). The most studied HCTD is Marfan syndrome. Ninety percent of Marfan syndrome is caused by mutations in the FBN1 gene. The zebrafish share high genetic similarity to humans, representing an ideal model for genetic research of human diseases. This study aimed to generate and characterize fbn1 +/− mutant zebrafish using the CRISPR/Cas9 gene‐editing technology.MethodsCRISPR/Cas9 was applied to generate an fbn1 frameshift mutation (fbn1 +/−) in zebrafish. F1 fbn1 +/− heterozygotes were crossed with transgenic fluorescent zebrafish to obtain F2 fbn1 +/− zebrafish. Morphological abnormalities were assessed in F2 fbn1 +/− zebrafish by comparing with the Tuebingen (TU) wild‐type controls at different development stages.ResultsWe successfully generated a transgenic line of fbn1 +/− zebrafish. Compared with TU wild‐type zebrafish, F2 fbn1 +/− zebrafish exhibited noticeably decreased pigmentation, increased lengths, slender body shape, and abnormal cardiac blood flow from atrium to ventricle.ConclusionWe generated the first fbn1 +/− zebrafish model using CRISPR/Cas9 gene‐editing approach to mimic FBN1 genetic defects in humans, providing an attractive model of Marfan syndrome and a method to determine the pathogenicity of gene mutation sites.

Morphological diversity in growth characteristics of Jatropha curcas l. accessions from South- West Nigeria

Jatropha curcas is a multi-purpose tree with significant economic importance that has not been fully exploited due to lack of adequate breeding programme in Nigeria. Consequently upon this, 31 accessions collected from 4 states in Southwestern Nigeria were assessed for their morphological diversity in order to establish this as a bed rock for further breeding programmes. Data were collected on plant height, numbers of leaves and collar diameter; these were subjected to analysis of variance, principal component analysis and cluster analysis using Minitab version 17. The results showed significant differences (p≤0.05) among the 31 accessions assessed. Principal component analysis indicated that the first three axes contributed 97.8% of the total variation observed. The first axis accounted for 68% of the total variation while the second and third axes accounted for 24.7% and 5.1%, respectively, of the total variation recorded. Cluster analysis as well as the dendrogram revealed three distinct clusters of genetic similarities and differences. High genetic similarities were observed among accessions collected from the different states whereas some accessions collected from similar regions had low genetic similarities. Cluster 1 consisted of 21 genotypes with their characters falli ng below the grand mean. Cluster 2 had nine genotypes, they produced the highest values for all the characters assessed. Cluster 3 with only one genotype has its values below the ground mean. Members of cluster 2 have proven to be superior. The existence of morphological diversity offers potential for selection among the accessions in the breeding of J. curcas from southwestern Nigeria.

Genetic diversity and mating‐type frequency of Exserohilum turcicum in Turkey

AbstractNorthern corn leaf blight caused by Exserohilum turcicum is one of the most significant diseases in maize‐growing fields, resulting in yield reduction worldwide. Genetic diversity and mating‐type of E. turcicum were determined using isolates collected from 7 important maize cultivation provinces in 4 different geographic regions of Turkey during 2014–2015. Multilocus haplotypes of E. turcicum isolates were characterized using 13 simple sequence repeats (SSR) primer pairs, which were amplified in PCR multiplex reactions. The evaluation of mating‐type ratio generated from the E. turcicum population was by χ2 significance test. MAT‐1 and MAT‐2 mating‐type were shown in the population; however, the χ2 significance test did not support the sexual reproduction hypothesis in any region. The E. turcicum population was found to produce predominantly asexual reproduction in Turkey. Numerous E. turcicum isolates showed very high genetic similarity and did not show a distinct cluster dependent on region or mating‐type on a dendrogram of genetic diversity. This result showed that one‐hundred per cent similarity in most of the collected isolates from different regions might also support long‐distance migration.

Mycotoxin Profile and Phylogeny of Pathogenic Alternaria Species Isolated from Symptomatic Tomato Plants in Lebanon.

The tomato is one of the most consumed agri-food products in Lebanon. Several fungal pathogens, including Alternaria species, can infect tomato plants during the whole growing cycle. Alternaria infections cause severe production and economic losses in field and during storage. In addition, Alternaria species represent a serious toxicological risk since they are able to produce a wide range of mycotoxins, associated with different toxic activities on human and animal health. Several Alternaria species were detected on tomatoes, among which the most important are A. solani, A. alternata, and A. arborescens. A set of 49 Alternaria strains isolated from leaves and stems of diseased tomato plants were characterised by using a polyphasic approach. All strains were included in the recently defined phylogenetic Alternaria section and grouped in three well-separated sub-clades, namely A. alternata (24 out of 49), A. arborescens (12 out of 49), and A. mali morpho-species (12 out of 49). One strain showed high genetic similarity with an A. limoniasperae reference strain. Chemical analyses showed that most of the Alternaria strains, cultured on rice, were able to produce alternariol (AOH), alternariol methyl ether (AME), altenuene (ALT) and tenuazonic acid (TA), with values up to 5634, 16,006, 5156, and 4507 mg kg−1, respectively. In addition, 66% of the strains were able to co-produce simultaneously the four mycotoxins investigated. The pathogenicity test carried out on 10 Alternaria strains, representative of phylogenetic sub-clades, revealed that they were all pathogenic on tomato fruits. No significant difference among strains was observed, although A. alternata and A. arborescens strains were slightly more aggressive than A. mali morpho-species strains. This paper reports new insights on mycotoxin profiles, genetic variability, and pathogenicity of Alternaria species on tomatoes.

Phenotypic characterization and inheritance of enzymatic browning on cut surfaces of stems and leaf ribs of romaine lettuce

Enzymatic browning is a major postharvest quality defect of romaine lettuce (Lactuca sativa L.). This study provides the first analysis of the relationship between the browning of leaf ribs and stems across twelve lettuce genotypes (ten cultivars, a breeding line, and a plant introduction). While all samples showed a progressive increase in browning index (BI) and decline in lightness (L*) and hue (h°) during 5 °C storage, differences in the rate of browning development were observed among genotypes. The most intensive browning was observed mainly around the vascular bundles dispersed along the rim area of the stems. Browning on the cut surfaces of the stems was correlated with browning on the cut leaf ribs, with Pearson correlation coefficients of 0.886 for BI, 0.891 for L* and 0.866 for h°. These results showed that the degree of browning in leaf ribs can be predicted by the browning degree of the stems. High genetic similarity was found among four cultivars with limited browning (Darkland, Parris Island Cos, Green Towers, and Hearts Delight) and also between cultivars with severe browning (King Henry and Tall Guzmaine). The highest broad-sense heritability (H2) in both trials (July and November 2018) was 0.88 and 0.92 for stem and rib browning, respectively. The method based on stem browning can be used to simplify postharvest phenotypic evaluation of lettuce and to decipher the genetics of browning to accelerate the breeding of browning-resistant cultivars.

Genetic Similarity of Avena sativa L. Varieties as an Example of a Narrow Genetic Pool of Contemporary Cereal Species.

The assessment of the genetic diversity of cultivated varieties is a very important element of breeding programs. This allows the determination of the level of genetic differentiation of cultivated varieties, their genetic distinctiveness, and is also of great importance in the selection of parental components for crossbreeding. The aim of the present study was to determine the level of genetic diversity of oat varieties currently grown in Central Europe based on two marker systems: ISSR and SCoT. The research conducted showed that both these types of markers were suitable for conducting analyses relating to the assessment of genetic diversity. The calculated coefficients showed that the analyzed cultivars were characterized by a high genetic similarity. However, the UPGMA and PCoA analyses clearly indicated the distinctiveness of the breeding programs conducted in Central European countries. The high genetic similarity of the analyzed forms allow us to conclude that it is necessary to expand the genetic pool of oat varieties. Numerous studies show that landraces may be the donor of genetic variation.

Comparative genetic analyses provide clues about capsule switching in Streptococcus suis 2 strains with different virulence levels and genetic backgrounds

Streptococcus suis (S. suis) is a major bacterial pathogen in the swine industry and an emerging zoonotic agent. S. suis produces an important extracellular component, capsular polysaccharide (CPS), based on which dozens of serotypes have been identified. Through virulence genotyping, we revealed the relatedness between subpopulations of S. suis serotype 2 (SS2), S. suis serotype 3 (SS3) and S. suis serotype 7 (SS7) strains despite their serotype differences. Multilocus sequence typing (MLST) was used to characterize the whole S. suis population and revealed capsule switching between S. suis strains. Importantly, capsule switching occurred in the SS2, SS3 and SS7 strains belonging to CC28 and CC29, which are phylogenetically distinct from the main CC1 SS2 lineage. To further explore capsule switching in S. suis, comparative genomic analyses were performed using available complete S. suis genomes. Phylogenetic analyses suggested that the SS2 strains could be divided into two clades (1 and 2), and those classified into clade 2 colocalized with SS3 and SS7 strains, in accordance with the above virulence genotyping and MLST analyses. Clade 2 SS2 strains presented high genetic similarity to SS3 and SS7 and shared common competence and defensive elements with them but were significantly different from Clade 1 SS2 strains. Notably, although the cps loci shared by Clade 1 and 2 SS2 strains were almost identical, a specific region of the cps locus of strain NSUI002 (Clade 2 SS2) could be found in the SS3 cps locus but not in the Clade 1 SS2 strain. These data indicated that the SS2 strains in CC28 and CC29 might have acquired the cps locus through capsule switching, which could explain the distinct genetic lineages within the SS2 population.