The use of Random Amplified Polymorphic DNA (RAPD) markers for the study of taxonomical relationships among species of ASPHODELUS sect. Verinea (Asphodelaceae)

RAPD analysis was applied to the three species of Asphodelus sect. Verinea (Pomel) Boissier (Asphodelaceae): Asphodelus fistulosus L., A. ayardii Jahand. & Maire, and A. tenuifolius Cav. Fifteen populations, five per species, were used and eight primers were sampled. A total of 97 amplification products were generated, and 4–12 polymorphic products per primer were obtained. Several specific RAPD markers were detected for A. ayardii and A. tenuifolius, while only two for A. fistulosus, which shares most amplification products with the two former species. Results that reinforce the specific status of the three taxa are shown. Asphodelus tenuifolius showed the highest interpopulation variability in agreement with the high specialization of other characters in this species. In accordance with these results, an amphidiploid origin for A. fistulosus, with the participation of A. ayardii and A. tenuifolius, is suggested.     

Chloroplast and nuclear DNA studies in a few members of the <Emphasis Type="Italic">Brassica oleracea</Emphasis> L. group using PCR-RFLP and ISSR-PCR markers: a population genetic analysis

A population genetic analysis of chloroplast and nuclear DNA was performed covering nine wild populations of Brassica oleracea. Three members of the n = 9 group, all close to B. oleracea, Brassica alboglabra Bailey, Brassica bourgeaui (Webb) O. Kuntze and Brassica montana Pourret, were also studied to better understand their relationship with B. oleracea. Chloroplast DNA was analysed using the PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism) method. The ISSR-PCR (inter-simple sequence repeat - polymerase chain reaction) technique was adopted to study nuclear DNA. Twelve primer pairs of chloroplast DNA showed very good amplification. The amplified product of each primer pair, digested by three restriction enzymes, revealed no variation of cpDNA among the taxa studied. This indicates they may have the same chloroplast genotype. Seven selected ISSR primers have detected genetic variation, both within and among the populations/taxa surveyed. The information obtained on the intra- and inter-populational genetic diversity of wild populations of B. oleracea neatly defined the individual plants. It could provide important guidelines for backing management and conservation strategies in this species. The study confirms a close relationship between B. alboglabra, B. bourgeaui and B. montana, which is parallel to their morphological similitude.     

Emergence of Amoxicillin-Resistant Variants of Spain9V-ST156 Pneumococci Expressing Serotype 11A Correlates with Their Ability to Evade the Host Immune Response

Capsular switching allows pre-existing clones of Streptococcus pneumoniae expressing vaccine serotypes to escape the vaccine-induced immunity by acquisition of capsular genes from pneumococci of a non-vaccine serotype. Here, we have analysed the clonal composition of 492 clinical isolates of serotype 11A causing invasive disease in Spain (2000–2012), and their ability to evade the host immune response. Antibiograms, serotyping and molecular typing were performed. The restriction profiles of pbp2x, pbp1a and pbp2b genes were also analysed. Interaction with the complement components C1q, C3b, C4BP, and factor H was explored whereas opsonophagocytosis assays were performed using a human cell line differentiated to neutrophils. Biofilm formation and the polymorphisms of the major autolysin LytA were evaluated. The main genotypes of the 11A pneumococci were: ST62 (447 isolates, 90.6%), followed by ST6521 (35 isolates, 7.3%) and ST838 (10 isolates, 2.1%). Beta lactam resistant serotype 11A variants of genotypes ST838 and ST6521 closely related to the Spain^9V-ST156 clone were first detected in 2005. A different pattern of evasion of complement immunity and phagocytosis was observed between genotypes. The emergence of one vaccine escape variant of Spain^9V-ST156 (ST6521^11A), showing a high potential to avoid the host immune response, was observed. In addition, isolates of ST6521^11A showed higher ability to produce biofilms than ST838^11A or ST62^11A, which may have contributed to the emergence of this PEN-resistant ST6521^11A genotype in the last few years. The emergence of penicillin-resistant 11A invasive variants of the highly successful ST156 clonal complex merits close monitoring.     

The occurrence of acylated flavonol glycosides in the cruciferae

Nine acylated glycosides of kaempferol or quercetin were identified in Sisymbrium gilliesii, and in three Crambe spp. They were usually present together with the related unacylated glycosides. Acylation is a very common characteristic of the four crucifer species studied.     

Association between chloroplast DNA and mitochondrial DNA haplotypes in Prunus spinosa L. (Rosaceae) populations across Europe

Chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) were studied in 24 populations of Prunus spinosa sampled across Europe. The cpDNA and mtDNA fragments were amplified using universal primers and subsequently digested with restriction enzymes to obtain the polymorphisms. Combinations of all the polymorphisms resulted in 33 cpDNA haplotypes and two mtDNA haplotypes. Strict association between the cpDNA haplotypes and the mtDNA haplotypes was detected in most cases, indicating conjoint inheritance of the two genomes. The most frequent and abundant cpDNA haplotype (C20; frequency, 51 %) is always associated with the more frequent and abundant mtDNA haplotype (M1; frequency, 84 %). All but two of the cpDNA haplotypes associated with the less frequent mtDNA haplotype (M2) are private haplotypes. These private haplotypes are phylogenetically related but geographically unrelated. They form a separate cluster on the minimum-length spanning tree.     

Chloroplast DNA diversity within and among populations of the allotetraploid Prunus spinosa L.

High chloroplast DNA (cpDNA) diversity was found within and among populations of Prunus spinosa sampled from seven European deciduous forests. A study of 12% of the total chloroplast genome detected 44 mutations, which were distributed over 24 haplotypes; four were common to two or more populations and the rest were unique haplotypes. The most-abundant and widely distributed haplotype was H2 (frequency = 41% approximately). Six of the seven populations were polymorphic. All of the six polymorphic populations had ”private” haplotypes (frequency < 5%) in addition to common haplotypes. The UPGMA dendrogram demonstrated a correlation between populations and their geographical locations. The total diversity was high (h_T= 0.824) and a major portion of it was within populations (h_s= 0.663). The level of population subdivision for unordered alleles was low (G_ST= 19.5%) and for ordered alleles was lower (N_ST= 13.6%). No phylogeographic structure could be demonstrated in the present geographical scale. High polymorphism in the cpDNA of P. spinosa has to be considered carefully when planning phylogenetic studies involving this species. Received: 20 September 1999 / Accepted: 10 November 1999     

Chloroplast DNA study in wild populations and some cultivars of Prunus avium L.

The PCR-RFLP technique was used to detect chloroplast DNA diversity in wild populations of Prunus avium from five European deciduous forests and some cultivars. A study of 10.8% of the total chloroplast genome detected eight insertion-deletion (indel) mutations, distributed over 12 haplotypes. Six haplotypes (H1, H2, H3, H4, H5 and H6) were found in wild populations and eight (H2, H6, H7, H8, H9, H10, H11 and H12) in the cultivars. Only two haplotypes (H2 and H6) are shared by the wild populations and the cultivars. The most-abundant and frequent haplotype in wild populations is H2 (frequency=78%). The wider geographical distribution along with the high frequency reflects its ancient origin. Of the five populations, three are polymorphic. Populations GA (Scotland) and KE (Germany) have unique haplotypes. The total cpDNA diversity in wild populations is h_T=0.40, and a major portion of it is within populations (h_S=0.37). The genetic differentiation among populations was low (G_STC=0.08) and no genetic structure among wild populations was observed. A minimum-length spanning tree, demonstrating relationships among the haplotypes in wild populations, indicated two possible chloroplast lineages. The ten identified cultivars were represented by seven haplotypes; this result proposes the possible utilisation of the PCR-RFLP technique for the characterisation of sweet cherry cultivars. The cpDNA diversity in P. avium should be considered carefully for phylogenetic studies involving this species. Received: 10 July 2000 / Accepted: 19 October 2000     

Population genetic analysis of European Prunus spinosa (Rosaceae) using chloroplast DNA markers

Chloroplast DNA diversity in Prunus spinosa, a common shrub of European deciduous forests, was assessed using the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) technique. Thirty-two haplotypes were detected in 25 populations spread across the European continent. Ten haplotypes were shared by two or more populations, and 22 were private. The major proportion of the total cpDNA diversity (H(T) = 0.73) was located within the populations (H(S) = 0.49), and differentiation between populations was low (G(ST) = 0.33) compared with other forest species. Haplotype diversity was higher in southern Europe than in northern Europe, indicating probable localization of glacial refugia in southern Europe. The minimum-length spanning tree of haplotypes showed incongruency between the phylogeny of haplotypes and their geographic locations. This might be the result of intensive seed movements following recolonization, which thereby erased the phylogeographic structure in P. spinosa.     

Effects of life-history traits and species distribution on genetic structure at maternally inherited markers in European trees and shrubs

Aim To examine relationships between life‐history traits, ecological and chorological characteristics of woody plant species and patterns of genetic differentiation among populations as assessed by chloroplast DNA (cpDNA) markers, and to compare them with patterns previously described from nuclear markers. Location Europe. Methods Data on cpDNA variation were compiled for 29 temperate European broad‐leaved tree and shrub species. Six qualitative and three quantitative characters of the species were tested for their relationship with two parameters of genetic population differentiation (G_ST and N_ST). Both direct species comparisons and phylogenetically independent contrast analyses were performed. Results When the phylogeny was not taken into account, five characters were significantly related to levels of population differentiation. The relationship disappeared in all but two cases (distribution type and seed mass) when analyses controlled for phylogenetic relationships among species. Main conclusions The correlation between distribution type (boreal‐temperate or temperate) and cpDNA differentiation of temperate European woody plant species suggests that their Quaternary history, in particular the location and isolation of their glacial refugia, is an important determinant of their present‐day level of genetic structure. By contrast, the relationship between life‐history traits and genetic differentiation at maternally inherited markers is weaker, especially when phylogenetic effects are controlled for.     

Presence of Giardia cysts and Cryptosporidium oocysts in drinking water supplies in northern Spain

AIMS: To evaluate the prevalence of Cryptosporidium and Giardia in surface water supplies from the province of Alava, northern Spain, and to investigate possible associations among the presence of these pathogenic protozoa with microbiological, physicochemical and atmospheric parameters. METHODS AND RESULTS: A total of 284 samples of drinking and recreational water supplies were analysed. Cryptosporidium oocysts were found in 63.5% of river samples, 33.3% of reservoirs samples, 15.4% and 22.6% of raw water samples from conventional and small water treatment facilities (respectively), 30.8% of treated water from small treatment facilities, and 26.8% of tap water from municipalities with chlorination treatment only. Giardia cysts were found in 92.3% of river samples, 55.5% of reservoirs samples, 26.9% and 45.2% of raw water samples from conventional and small water treatment facilities (respectively), 19.2% of treated water from small treatment facilities, and 26.8% of tap water from municipalities with chlorination treatment only. The presence of Cryptosporidium and Giardia had significant Pearson's correlation coefficients (P < 0.01) with the turbidity levels of the samples, and a number of significant associations were also found with the count levels for total coliforms and Escherichia coli. The samples were positive for Cryptosporidium significantly (P < 0.05) more frequently during the autumn season than during the spring and winter seasons. No significant differences were found in the seasonal pattern of Giardia. A moderate association (r = 0.52) was found between rainfall and the presence of Cryptosporidium oocysts. CONCLUSIONS: Cryptosporidium and Giardia are consistently found at elevated concentrations in surface waters for human consumption from the province of Alava, northern Spain. SIGNIFICANCE AND IMPACT OF THE STUDY: Water treatments based on rapid filtration process and/or chlorination only are often unsatisfactory to provide safe drinking water, a situation that represents an important public health problem for the affected population because of the risk of waterborne outbreaks.