Enterococcus faecium is emerging as an important cause of multidrug resistance and hospital acquired infections, special attention being paid to the vancomycin resistant species. Therefore, the ...characterization of pathogenic strains/isolates plays an important role in the epidemiology of infectious diseases. The enterococcal rate was determined from wastewaters in Cluj-Napoca area. As presence of E. faecium was detected, a number of isolates from wastewater, birds and humans were epidemiologically analyzed according to the MLST website. Comparisons were performed against a collection of available isolates, with multiple origins, contained in the MLST database. Out of the Enterococcus isolates collected from wastewater, 11 were identified as E. faecalis (40.74%); 8 as E. casseliflavus (29.62%); 5 as E. faecium (18.50%); 2 as E. gallinarum (7.40%) and one isolate as E. durans. Based on the MLST data and using the eBURST algorithm, the isolates of E. faecium sampled from Romania were split in three groups: one group comprised isolates from human hosts and wastewater (Cj316, 106/6, Cj197, Cj22, 129/6, Cj117, Cj24, 284/7, and 43/7), while the second (G9, G10-2, G7, G3-2, and G9-1) and the third group (G8, G6, and 40/7) originated from bird hosts. The rest of the isolates were not joined in a particular group, assuming the lack of a phylogenetic bond between these isolates. The obtained data suggested the existence of at least two phylogenetic lines of E. faecium in Romania: a line that had mainly human host prevalence, while in the other line the animal hosts dominated.
Onobrychis montana DC. Subsp. transsilvanica (Simonk.) Jáv. (Fabaceae) is a plant taxon, endemic to the South-Eastern Carpathians, whose taxonomic status is treated inconsistently by the classic ...taxonomy based on morphological traits. In a previous study, by sequencing several chloroplast DNA regions and AFLP genotyping, we tried to elucidate the controversy concerning its taxonomic status in relation to the more widespread O. montana DC., and determined its phylogeographic structure within the Carpathians. The present study, based on DNA fingerprinting by seven SSR markers, brings more insights on this problematic taxon by conferring higher resolution and sub-clustering previously identified phylogeographic groups. However, the newly SSR genetic data are in agreement with molecular evidence revealed by AFLP and chloroplastic SNPs and do not support O. montana DC. Subsp. transsilvanica (Simonk.) Jáv. As a distinct species from O. montana DC.
Microsatellite markers previously developed for other leguminous species were tested for cross-genus transferability and evaluated for their potential usefulness in providing an improved assessment ...of the genetic relationships between two closely related taxa belonging to Onobrychis genus (Fabaceae). Candidate microsatellite markers were tested for polymorphism and replicability in sixteen populations of O. montana DC. subsp. transsilvanica (Simonk.) Jáv. and O. montana. Out of the 23 SSRs, there were identified seven polymorphic loci. In total 32 alleles were detected and the number of alleles per locus varied from two to six. PIC values ranged from 0.375 to 0.6454, and four SSRs displayed a PIC > 0.5. Relative uniform rates of genetic diversity were obtained. In case of O. montana DC. subsp. transsilvanica (Simonk.) Jáv. the observed and expected heterozygosity ranged from 0.100 to 0.952 and from 0.219 to 0.525, respectively, while for O. montana ranged from 0.166 to 0.750 and from 0.083 to 0.375, respectively. Seven polymorphic SSRs with clear and reproducible amplification were identified. These markers proved to be very efficient for unambiguous population discrimination based on both geographic and taxonomic criteria. Hereafter, these SSR markers can be used as tools for evolutionary studies in Onobrychis genus, as well in providing knowledge on patterns of the species phylogeography.
Although the Carpathians represent one of the main elements of the European Alpine System and an important area of endemism, only a few phylogeographic studies concerning this region have focused on ...the detailed intraspecific variation in alpine plant species. Using two molecular marker systems, we (1) aimed to elucidate the controversy concerning the status of the endemic Carpathian taxon Onobrychis transsilvanica Simonk. in relation to the more widespread Onobrychis montana DC. and (2) determined the phylogeographic structure of O.transsilvanica within the Carpathians. For O.transsilvanica, our data suggest either a recent postglacial speciation with incomplete lineage sorting or genetic divergence followed by subsequent continuous gene flow during the glacial period. The genetic structure of the complex does not support O.transsilvanica as a distinct species from O.montana. Within the Carpathians, the extant populations of O.transsilvanica comprise two major allopatric lineages, which have been isolated from each other for a long period of time. Unexpectedly, the major genetic break was not in line with a classical biogeographical boundary in the Carpathians but rather separated a group from the southwestern edge of the mountains. We also discovered an additional divergent haplotype lineage, with weaker genetic support, within the O.transsilvanica populations.
Maize has always been under constant human selection ever since it had been domesticated. Intensive breeding programs that resulted in the massive use of hybrids nowadays have started in the 60s. ...That brought significant yield increases but reduced the genetic diversity at the same time. Consequently, breeders and researchers alike turned their attention to national germplasm collections established decades ago in many countries, as they may hold allelic variations that could prove useful for future improvements. These collections are mainly composed of inbred lines originating from well-adapted local open pollinated varieties. However, there is an overall lack of data in the literature about the genetic diversity of maize in SE Europe, and its potential for future breeding efforts. There are no data, whatsoever, on the nutritional quality of the grain, primarily dictated by the zein proteins. We therefore sought to use the Romanian maize germplasm as an entry point in understanding the molecular make-up of maize in this part of Europe. By using 80 SSR markers, evenly spread throughout the genome, on 82 inbred lines from various parts of the country, we were able to decipher population structure and the existing relationships between those and the eight international standards used, including the reference sequenced genome B73. Corroborating molecular data with a standardized morphological, physiological, and biochemical characterization of all 90 inbred lines, this is the first comprehensive such study on the existing SE European maize germplasm. The inbred lines we present here are an important addition to the ever-shrinking gene pool that the breeding programs are faced-with, because of the allelic richness they hold. They may serve as parental lines in crosses that will lead to new hybrids, characterized by a high level of heterosis, nationwide and beyond, due to their existing relationship with the international germplasm.
Microsatellites are codominant markers that, due to their high polymorphism, are a common choice for detecting genetic variability in various organisms, including fungi, plants, and animals. However, ...the process of developing these markers is both costly and time-consuming. As a result, the cross-species amplification has become a more rapid and more affordable alternative in biological studies. The objective of this study was to assess the applicability of 13 SSR markers, originally designed for Carex curvula, in other 14 species belonging to different sections of the genus. All the markers were successfully transferred with a mean of 90.76%, and 100% transferability was reached in two species (C. baldensis and C. rupestris). The lowest transferability was registered in the G165 marker, which did not produce amplification in six species. Together, the microsatellites amplified a total of 183 alleles, ranging from 10 to 19 alleles per locus, with an average of 14.07. The mean number of different alleles ranged from 0.846 to a maximum of 2.077 per locus. No significant departures from the Hardy–Weinberg equilibrium were detected in polymorphic loci. The transferability of the 13 SSR markers proved highly successful in various Carex species, across different clades and sections of the genus.
Background
Microsatellite primers were developed and tested to genotype several populations of
Carex curvula
s. l. (Cyperaceae), in order to infer the phylogeographic relationships of the populations ...within species and the boundaries between the two described subspecies:
C. curvula
subsp.
curvula
and
C. curvula
subsp.
rosae
.
Methods and results
Candidate microsatellite loci were isolated based on next-generation sequencing. We tested 18 markers for polymorphism and replicability in seven
C. curvula
s. l. populations and identified 13 polymorphic loci with dinucleotide repeats. Genotyping results showed the total number of alleles per locus varied from four to 23 (including both infrataxa), and the observed and expected heterozygosity ranged between 0.1 to 0.82 and 0.219 to 0.711, respectively. Furthermore, the NJ tree showed a clear separation between
C. curvula
subsp.
curvula
and
C. curvula
subsp.
rosae
.
Conclusion
The development of these highly polymorphic markers proved to be very efficient not only in delineating between the two subspecies, but also in genetic discriminating at population level within each infrataxon. They are promising tools for evolutionary studies in Cariceae section, as well as in providing knowledge on patterns of the species phylogeography.
The Carpathians represent not only a European hotspot of plant diversity for both species richness and endemism, but also an important stepping-stone area in historical migrations between the flora ...of the Asian and European mountain systems and a starting point of postglacial recolonizations for many species. Yet, until recent years, phylogeographical studies for alpine or arctic-alpine plants were focused on the Alps, whereas peripheral mountain ranges, including the Carpathians, were either neglected or insufficiently sampled. In this study, we aimed to complement the Alpine phylogeographic structure of an emblematic high-alpine European endemic taxon, Eritrichium nanum, by focusing on the Carpathian range of the species. We sampled nine populations from the South-Eastern Carpathians and performed ITS1 sequencing and AFLP fingerprinting. In case of ITS1 region, all the populations, no matter of their geographic origin, presented the same ribotype. The AFLP analysis indicated that, within the Carpathians, the extant populations of E. nanum comprised two major allopatric lineages. One important result of the research was the discovery that the species’ sole important genetic break was located in the Southern Carpathians, separating populations of the Retezat Mountains from all the others in the Carpathians.