Livestock trade history, geography, and parasite strains: the mitochondrial genetic structure of Echinococcus granulosus in Argentina

A sample of 114 isolates of Echinococcus granulosus (Cestoda: Taeniidae) collected from different host species and sites in Argentina has been sequenced for 391 bp from the mitochondrial cytochrome c oxidase subunit I gene to analyze genetic variability and population structure. Nine different haplotypes were identified, 5 of which correspond to already characterized strains. Analysis of molecular variance and nested clade analysis of the distribution of haplotypes among localities within 3 main geographic regions indicate that geographic differentiation accounts for the overall pattern of genetic variability in E. granulosus populations. Significant geographic differentiation is also present when the sheep strain alone is considered. Our results suggest that geographic patterns are not due to actual restricted gene flow between regions but are rather a consequence of past history, probably related to the time and origin of livestock introduction in Argentina.     

Differentiation and Genetic Structure of Sclerophoma pythiophila Strains on Pinus sylvestris in Poland

Between 1996 and 2006, 97 strains of Sclerophoma pythiophila were isolated from 3 to 10-year-old trees of Pinus sylvestris from three regions of Poland differing by climatic conditions and geographic location. On the basis of 56 random amplified microsatellites (RAMS) markers obtained with the use of five primers, very high level of genetic variability of strains (mean Jaccard's coefficient 0.56) was ascertained. Among the analysed markers only one was completely monomorphic, whereas six were monomorphic in 90%. Greater genetic similarity was ascertained for strains in southern Poland (0.58) in comparison with strains deriving from northern Poland (0.52). Correlation between the percentage share of polymorphic loci and the average annual temperature of places of strain isolation ( r  = 0.62) were shown, as well as the number of days with snow cover ( r  = 0.79). On the basis of the amova analysis, it was ascertained that 11.6% of genetic variability was located between regions of the strains origin and 88.4% within the regions.     

粉拟青霉种内RAPD多态性分析

对来自不同地理来源和不同寄主的 １３株粉拟青霉Ｐａｅｃｉｌｏｍｙｃｅｓ ｆａｎｉｎｏｓｕｓ和其他３种拟青霉及１株球孢白僵菌进行ＲＡＰＤ分析,从ＲＡＰＤ扩增结果可知粉拟青霉种内具丰富的遗传多样型。ＲＡＰＤ扩增指纹图谱能有效地分辨不同菌株的基因型,可用于监测生防效果的菌株示踪。聚类分析结果表明种间的遗传差异要明显大于种内的差异。菌株间差异是和地理来源相关,而和寄主不相关。     

粉拟青霉种内RAPD多态性分析*

对来自不同地理来源和不同寄主的 １３株粉拟青霉Ｐａｅｃｉｌｏｍｙｃｅｓ ｆａｎｉｎｏｓｕｓ和其他３种拟青霉及１株球孢白僵菌进行ＲＡＰＤ分析,从ＲＡＰＤ扩增结果可知粉拟青霉种内具丰富的遗传多样型。ＲＡＰＤ扩增指纹图谱能有效地分辨不同菌株的基因型,可用于监测生防效果的菌株示踪。聚类分析结果表明种间的遗传差异要明显大于种内的差异。菌株间差异是和地理来源相关,而和寄主不相关。     

Evidence for coadaptation in geographic populations of Drosophila bipectinata

In order to test whether there is genetic coadaptation in geographic populations of Drosophila bipectinata with respect to body size, reciprocal crosses were made among five strains derived from ecogeographically different localities in India. Wing length was used as an index of body size, and was measured in all the five strains, and their crosses in F and F₂ generations. The statistical analysis of the data show that there is significant interpopulation variation in body size and in all the crosses, there is an increase in body size in F₁ generation when compared with mid-parent value. Further, there is a decrease in body size in F₂ generation as compared to F₁ in most of the crosses with increased variability. These results provide evidence for genetic coadaptation in geographic populations of D. bipectinata .     

Comparison of genetic variability between Czech and foreign isolates of phytopathogenic bacteria Clavibacter michiganensis subsp. sepedonicus by Rep-PCR technique

Repetitive-sequence-based polymerase chain reaction (Rep-PCR) method was used for analysis of genetic variability among bacterial populations from different world locations. Collection of 26 Czech and 13 foreign strains ofClavibacter michiganensis subsp.sepedonicus was amplified using BOX primer targeting to repetitive motif occurring in eubacterial genomes. Genetic fingerprints were visually compared and statistically evaluated by cluster analysis. Genetic similarity was estimated to be approximately 80% among all tested strains. Populations of these bacteria seem to be highly homogeneous; potential influence of geographic origin was not confirmed.     

Genetic study on indole-3-acetic acid production by ectomycorrhizal Hebeloma species: inter- and intraspecific variability in homo- and dikaryotic mycelia

Summary Interspecific variability of indole-3-acetic acid (IAA)-synthesizing activity was examined within 12 wild strains of different Hebeloma species. Interstrain variability was studied within 11 wild strains of Hebeloma cylindrosporum (Romagnési) and intrastrain variability was considered by using 20 homokaryotic and 50 controlled dikaryotic mycelia belonging to the progeny of one laboratory fruiting strain of this species.The range of variation of IAA-synthesizing activity was of the same order of magnitude within the four groups considered. No correlation was detected between, on one hand, the IAA-synthesizing activity of the mycelia and, on the other hand, their taxonomic position, their geographic origin, or their host plant.Within the progeny of one H. cylindrosporum fruiting strain, 15 of the 50 controlled dikaryons presented an activity higher than that of the original dikaryon. The variation among dikaryons could not be strictly related to the variation in parental homokaryons, indicating that genetic control of this activity probably involves a nonadditive component. Significant additive and nonadditive components of the genetic variation were detected, each of them representing about 50% of the total variation. The nonadditive heritable component could not be explained by a model involving only dominance.     

Comparative analysis of the rhythm of cercariae emergence in three strains of Schistosoma bovis (trematoda: Schistosomatidae)

A comparative experimental study of the rhythmic shedding of three geographic strains of Schistosoma bovis cercariae (Sardinian, Sudanese and Spanish) by Bulinus truncatus showed a significant difference in the emergence patterns. The results support the existence of a genetic variability of the emergence rhythms. The origin of the variability is discussed and could be found in the pastoral practice and the ecological characteristics of the different transmission foci.     

Genetic variability of proteins from mitochondria and mitochondrial fractions of mouse organs

Proteins of whole mitochondria from mouse liver and brain and proteins of liver mitochondrial fractions (plasma and rough membrane fraction) were separated by two-dimensional electrophoresis. Protein patterns of two inbred strains of mouse, C57BL/6J and DBA/2J, and of F₁ mice of these two strains were studied. The protein patterns obtained from the different mitochondrial materials were analyzed with regard to their protein composition and the genetic variability of proteins (qualitative and quantitative protein variants). Included in this analysis are data previously obtained from the cytosols and plasma membranes of the same organs and mouse strains. The results showed the following. (1) Mitochondria and organelle-free cell components (cytosol and plasma membranes) have only a few percent of their proteins in common, while two organs, liver and brain, reveal up to approximately 50% organ-nonspecific proteins. The frequency of proteins common to solubilized and structure-bound proteins ranges below 20%. (2) Genetic variability in protein amount occurs much more frequently than genetic variability in protein structure. Liver proteins reveal more genetic variants than brain proteins. Proteins solubilized in the cell show more genetic variation than structure-bound proteins. Furthermore, the results show that with regard to the composition and the genetic variability of proteins, liver and brain differ more in their mitochondria than in their cytosol and plasma membranes.This work was supported by grants from the Deutsche Forschungsgemeinschaft awarded to Sonderforschungsbereich 29.     

Differentiation of Xylella fastidiosa strains via multilocus sequence analysis of environmentally mediated genes (MLSA-E)

Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigate X. fastidiosa relationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identified a priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54 X. fastidiosa isolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with known X. fastidiosa subspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity. dN/dS ratios of environmentally mediated genes, though <1 due to high sequence similarity, are significantly greater than housekeeping gene dN/dS ratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such as X. fastidiosa isolates. Discovering the genetic relationships between X. fastidiosa isolates will provide new insights into the epidemiology of populations of X. fastidiosa, allowing improved disease management in economically important crops.     

Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in China

The genetic variability among 32 Chinese Acidithiobacillus spp. environmental isolates and four reference strains representing three recognized species of the genus Acidithiobacillus was characterized by using a combination of molecular methods, namely restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers, repetitive element PCR, arbitrarily primed PCR and 16S rRNA gene sequence analyses. 16S rRNA gene sequences revealed that all Acidithiobacillus spp. strains could be assigned to seven groups, three of which encompassed the Acidithiobacillus ferrooxidans strains from various parts of the world. A comparative analysis of the phylogenetic Group 1 and 2 was undertaken. Restriction fragment length polymorphism results allowed us to separate the 35 Acidithiobacillus strains into 15 different genotypes. An integrated phenotypic and genotypic analysis indicated that the distribution of A. ferrooxidans strains among the physiological groups were in agreement with their distribution among the genomic groups, and that no clear correlation was found between the genetic polymorphism of the Acidithiobacillus spp. strains and either the geographic location or type of habitats from which the strains were isolated. In addition, five unidentified sulfur-oxidizing isolates may represent one or two novel species of the genus Acidithiobacillus. The results showed that the Chinese Acidithiobacillus spp. isolates exhibited a high degree of genomic and phenotypic heterogeneity.     

Genetic variation among European strains of Saccharomyces paradoxus: results from DNA fingerprinting

We used microsatellite fingerprinting and RAPD analysis to characterize 28 wild European strains of Saccharomyces paradoxus. In contrast to our results from a previous allozyme survey [Naumov et al. Int. J. Syst. Bacteriol. 47: 341-344 (1997a)], these methods revealed extensive genetic variation. The RAPD primers 5'AATCGGGCTG and 5'GGGTAACGCC and the microsatellite primer (GTG)5 yielded reproducible amplification patterns of sufficient clarity and variability to distinguish individual strains from the wild. UPGMA analysis tended to group the strains according to climatic and geographic origin. A comparative study of Ty1 sequence having multiple chromosomal location was also done. Each wild S. paradoxus isolate shows a unique hybridization pattern allowing discrimination to the strain level.     

The growth,toxicity and genetic characterization of seven strains of Alexandrium catenella (Whedon and Kofoid) Balech 1985 (Dinophyceae) isolated during the 2009 summer outbreak in southern Chile

The dinoflagellate Alexandrium catenella causes recurrent harmful algal blooms in southern Chile. This species belongs to the “Alexandrium tamarense/catenella/fundyense species complex” (the “tamarensis complex”), defined by morphological attributes. Ribosomal sequences serve to differentiate five evolutionary lineages (clades) in this species complex. These distinctions reflect the geographic distribution and toxicity of the populations rather than their morphological designations. Despite the social and economic impact that harmful blooms produce in Chile, few strains of A. catenella have been isolated. Moreover, physiological and/or genetic studies of the group are scarce. The aim of this work was to examine possible physiological and genetic variability among populations of A. catenella having different geographical origins but isolated from the same toxic event. Seven strains of A. catenella were isolated and established from phytoplankton samples collected in the Aysén and Los Lagos regions of southern Chile during a recent outbreak (February–March 2009). Growth, toxicity, and ITS sequences were compared among these strains. All the strains included in this study were grouped with strains belonging to the previously described “North America” clade. The genetic diversity detected among Chilean strains was 3%, a much higher value than those reported for comparisons among strains from other parts of the world. In addition, a remarkable variability of growth parameters and toxicity was detected among strains. Strain PFB45 showed the highest PSP toxin content, whereas strain PFB41 had the lowest value of this parameter but had the highest maximum cell density. In strains PFB38, PFB42, and PFB37, more than 98% of the total PSP toxin content occurred in the form of gonyautoxins (primarily GTX-4,1 and GTX-3,2). In strains PFB39, PFB36, and PFB45, neoSTX, and STX toxins were detected. These results demonstrated remarkable variability at the genetic and physiological level among strains of A. catenella isolated from the same outbreak. No correlations were found between the phenotypic traits (growth and toxicity) and the genetic affiliation of the strains studied.     

Genetic diversity and geographical distribution of wild Saccharomyces cerevisiae strains from the wine-producing area of Charentes, France.

Electrophoretic karyotyping, mitochondrial DNA restriction fragment length polymorphism analysis, and PCR amplification of interspersed repeats were used to study the variability, phylogenetic affinities, and biogeographic distribution of wild Saccharomyces cerevisiae enological yeasts. The survey concentrated on 42 individual wine cellars in the Charentes area (Cognac region, France). A limited number (35) of predominant S. cerevisiae strains responsible for the fermentation process have been identified by the above molecular methods of differentiation. One strain (ACI) was found to be distributed over the entire area surveyed. There seemed to be little correlation between geographic location and genetic affinity.     

Analysis of genetic variability and phylogenetic analysis of selected Czech and French strains of rabbit haemorrhagic disease virus (RHDV)

The objective of this study was to analyse the genetic variability and phylogenetic analysis of six strains of rabbit haemorrhagic disease virus (RHDV), including four Czech strains (CAMPV-351, CAMPV-561, CAMPV-562, CAMPV-558) and two French strains (Fr-1, Fr-2), on the basis of a fragment of the VP60 capsid structural protein-coding gene N-terminal region. The results of our own studies were compared to 26 RHDV strains obtained from GenBank. The analysis of the genetic variability of six RHDV strains indicated that the CAMPV-561 strain is the most genetically variable. Less variable were the Fr-1 and Fr-2 strains, while the least variable was CAMPV-351. In turn, the genetic distance among the six analysed strains and 26 strains obtained from GenBank was the greatest for CAMPV-351 and Whn/China [11.3 % according to the observed divergence (OD) method and 12.2 % according to the maximum likelihood (ML) method], while it was the lowest for CAMPV-351 and FRG (0.8 % in both the OD and ML methods). In turn, the scale of the genetic distances among the six analysed strains and five RHDVa strains (99-05, NY-01, Whn/China, Triptis, Iowa2000) ranged from 9.3–10.3 % in the OD method to 10.3–13.7 % in the ML method. The image of phylogenetic dependencies generated for the strains analysed and those obtained from GenBank revealed their distribution to be in five genetic groups (G1–G5), whereas the analysed strains were included in genetic groups 2 and 3.     

The molecular diversity of different isolates of <Emphasis Type="Italic">Beauveria bassiana</Emphasis> (Bals.) Vuill. as assessed using intermicrosatellites (ISSR<Subscript>s</Subscript>)

Inter-microsatellite PCR (ISSR-PCR) markers were used to identify and to examine the genetic diversity of eleven Beauveria bassiana isolates with different geographic origins. The variability and the phylogenetic relationships between the eleven strains were analyzed using 172 ISSR-PCR markers. A high level of polymorphism (near 80%) was found using these molecular markers. Seven different isolates showed exclusive bands, and ISSR primer 873 was able to distinguish between all the strains. The dendrogram obtained with these markers is robust and in agreement with the geographical origins of the strains. All the isolates from the Caribbean region were grouped together in a cluster, while the other isolates grouped in the other cluster. The similarity exhibited between the two clusters was less than 50%. This value of homology shows the high genetic variability detected between the isolates from the Caribbean region and the other isolates. ISSR-PCR markers provide a quick, reliable and highly informative system for DNA fingerprinting, and allowed the identification of the different B. bassiana isolates studied.     

Genetic variability associated with photosynthetic pigment concentration, and photochemical and nonphotochemical quenching, in strains of the cyanobacterium Microcystis aeruginosa

Although populations of cyanobacteria are usually considered to be clonal, their capacity to survive environmental changes suggests intrapopulation genetic variation. We therefore estimated the genetic variability on the basis of two processes important for any photoautotroph - photochemical and nonphotochemical quenching - as well as photosynthetic pigment concentrations. For this purpose, two parameters related to photochemical and nonphotochemical quenching were measured using specific experimental and statistical procedures, in 25 strains of the cyanobacterium Microcystis aeruginosa, along with their contents of chlorophyll a, total carotenoids and phycocyanin. The experimental procedure allowed discrimination between genetic and nongenetic (or residual) variability among strains. The high genetic variability found in photosynthetic pigments and both photosynthetic parameters denotes large differences even among strains isolated from the same community. The high genetic diversity within a population could be important for the evolutionary success of cyanobacteria.     

Genetic variability in geographic populations of the natterjack toad (Bufo calamita)

Across altitudinal and latitudinal gradients, the proportion of suitable habitats varies, influencing the individual dispersal that ultimately can produce differentiation among populations. The natterjack toad (Bufo calamita) is distributed across a wide geographic range that qualifies the species as interesting for a geographic analysis of its genetic variability. Five populations of B. calamita in the Sierra de Gredos (Spain) were studied in an altitudinal gradient ranging from 750 to 2270 m using microsatellite markers. In addition, we analyzed the latitudinal genetic variation in B. calamita within a global European distribution using genetic diversity parameters (mean number of alleles per locus [M(a)] and expected heterozygosity [H(E)]) obtained from our results and those published in the literature. The low level of genetic differentiation found between populations of B. calamita (F(st) ranging from 0.0115 to 0.1018) and the decreases in genetic diversity with altitude (M(a) from 13.6 to 8.3, H(E) from 0.82 to 0.74) can be interpreted by the combined effects of discontinuous habitat, produced mainly by the high slopes barriers and geographic distance. In the latitudinal gradient, genetic diversity decreases from south to north as a consequence of the colonization of the species from the Pleistocene refugium. We conclude that the genetic variability in B. calamita along its wide altitudinal and latitudinal geographic distribution mainly reflects the colonization history of the species after the last glacial period.     

球孢白僵菌营养亲和型多样性与生态背景的关系

本文将来源不同的球孢白僵菌菌株分别按相同地理来源和相同分离奇主进行配对培养,发现相同地理来源菌株的营养亲和型多样性要明显小于相同分离寄主的菌株,前者的P及Shannon-Wiener多样性指数分别为0.4286及0.8708,后者分别为0.7500及1.3321。这说明来源于同一地区的菌株属于同一VCG的概率要大于相同分离寄主的菌株,同时也说明相同地理来源菌株的遗传相似性要高于相同分离寄主菌株的遗传相似性。     

Genetic diversity and population structure of Chinese <Emphasis Type="Italic">Lentinula edodes</Emphasis> revealed by InDel and SSR markers

Genetic diversity and population structure of 88 Chinese Lentinula edodes strains belonging to four geographic populations were inferred from 68 Insertion-Deletion (InDel) and two simple sequence repeat (SSR) markers. The overall values of Shannon’s information index and gene diversity were 0.836 and 0.435, respectively, demonstrating a high genetic diversity in Chinese L. edodes strains. Among the four geographic populations, the Central China population displayed a lower genetic diversity. Multiple analyses resolved two unambiguous genetic groups that corresponded to two regions from which the samples were collected—one was a high-altitude region (region 1) and the other was a low-altitude region (region 2). Results from analysis of molecular variance suggested that the majority of genetic variation was contained within populations (74.8 %). Although there was a strong genetic differentiation between populations (F _ST ?=?0.252), the variability of ITS sequences from representative strains of the two regions (<3 %) could not support the existence of cryptic species. Pairwise F _ST values and Nei’s genetic distances showed that there were relatively lower genetic differentiations and genetic distances between populations from the same region. Geographic distribution could play a vital role in the formation of the observed population structure. Mycelium growth rate and precocity of L. edodes strains displayed significant differences between the two regions. Strains from region 2 grew faster and fructified earlier, which could be a result of adaptation to local environmental factors. To the best of our knowledge, this was the first study on the genetic structure and differentiation between populations, as well as the relationship between genetic structure and phenotypic traits in L. edodes.