DNA variation in the phenotypically-diverse brown alga Saccharina japonica

BACKGROUND

Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica.

RESULTS

The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events.

CONCLUSION

Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.

DNA polymorphism in recombining and non-recombining mating-type-specific loci of the smut fungus Microbotryum

The population-genetic processes leading to the genetic degeneration of non-recombining regions have mainly been studied in animal and plant sex chromosomes. Here, we report population genetic analysis of the processes in the non-recombining mating-type-specific regions of the smut fungus Microbotryum violaceum. M. violaceum has A1 and A2 mating types, determined by mating-type-specific 'sex chromosomes' that contain 1-2 Mb long non-recombining regions. If genetic degeneration were occurring, then one would expect reduced DNA polymorphism in the non-recombining regions of this fungus. The analysis of DNA diversity among 19 M. violaceum strains, collected across Europe from Silene latifolia flowers, revealed that (i) DNA polymorphism is relatively low in all 20 studied loci (π∼0.15%), (ii) it is not significantly different between the two mating-type-specific chromosomes nor between the non-recombining and recombining regions, (iii) there is substantial population structure in M. violaceum populations, which resembles that of its host species, S. latifolia, and (iv) there is significant linkage disequilibrium, suggesting that widespread selfing in this species results in a reduction of the effective recombination rate across the genome. We hypothesise that selfing-related reduction of recombination across the M. violaceum genome negates the difference in the level of DNA polymorphism between the recombining and non-recombining regions, and may possibly lead to similar levels of genetic degeneration in the mating-type-specific regions of the non-recombining 'sex chromosomes' and elsewhere in the genome.

A microsatellite study in the Łęgucki Młyn/Popielno hybrid zone reveals no genetic differentiation between two chromosome races of the common shrew (Sorex araneus)

This study investigated a chromosome hybrid zone between two chromosomal races of the common shrew (Sorex araneus). Gene flow and genetic structure of the hybrid zone, located in the northeast of Poland, were studied using seven polymorphic autosomal microsatellite loci (L9, L14, L33, L45, L67, L68, L97) and a Y-linked microsatellite locus (L8Y). Seventy-five animals (46 of the Łęgucki Młyn race and 29 of the Popielno race) from nine different localities were examined and the data were analyzed using hierarchical AMOVA and F-statistic. The studied microsatellite loci and races (divided into nine geographical populations) were characterized by observed heterozygosity (H(O)), expected heterozygosities within (H(S)), and between (H(T)) populations, inbreeding coefficient (F(IS)), fixation index (F(ST)), and average allelic richness (A). We found that genetic structuring within and between the two chromosome races were weak and non-significant. This finding and unconstrained gene flow between the races indicates a high level of migration within the Łęgucki Młyn/Popielno hybrid zone, suggesting that evolutionarily important genetic structuring does not occur in interracial zones where races which are not genetically distinct come into contact.

Genotyping Parkinson disease-associated mitochondrial polymorphisms

OBJECTIVE

The purpose of this study was to establish a system for rapidly detecting single nucleotide polymorphisms (SNPs) in mitochondrial DNA (mtDNA) using hybridization probes and melting temperature (T(m)) analysis. This technology should prove useful for population-based studies on the interaction between genetic factors and environmental exposures and the risk of Parkinson disease (PD).

METHODS

Mitochondrial DNA (mtDNA) was extracted from whole blood. Rapid polymerase chain reaction (PCR) and melting curve analyses were performed with primers and fluorochrome-labeled probes on a LightCycler (Roche Molecular Biochemical, Mannheim, Germany). Genotyping of 10 SNPs in 15 subjects was based on the analysis of allele-specific T(m) of detection probes. The results of melting curve analyses were verified by sequencing all 150 PCR products.

RESULTS

Real-time monitoring showed optimal PCR amplification of each mtDNA fragment. The nucleotide changes at positions 1719, 4580, 7028, 8251, 9055, 10398, 12308, 13368, 13708, and 16391 from wild-type to mutant genotype resulted in 6.51, 8.29, 3.26, 7.82, 4.79, 2.84, 2.73, 9.04, 8.53, and 9.52 degrees C declines in T(m) of the detection probes, respectively. Genotyping of all 150 samples was verified by 100% correspondence with the results of sequencing. Fourteen subjects were haplogrouped by combining results for all 10 SNPs.

CONCLUSION

A rapid and reliable detection system for identifying mitochondrial polymorphisms and haplotypes was developed based on hybridization probe technology. This method may be suitable for mitochondrial genotyping of samples from large-scale epidemiology studies, and may prove useful for exploring the molecular etiopathogenesis of PD, identifying markers of genetic susceptibility, and protecting susceptible individuals from PD.

Rapid detection of 3500Q and 3531 mutations and MspI polymorphism in exon 26 at the apolipoprotein B gene

Several environmental and genetic factors are associated with high levels of cholesterol. Hypercholesterolemia is the main phenotype of Familial Defective Apolipoprotein B and Familial Hypercholesterolemia that are caused by mutations at the apolipoprotein (apo) B and LDL receptor genes, respectively. Identification of the specific genetic alteration associated with hypercholesterolemia is an important issue in clinical diagnosis of high risk for CAD. Apo B gene mutations and polymorphisms are usually screened by SSCP, DGGE, and heteroduplex, which must be confirmed by DNA sequencing or by direct detection using PCR techniques. In this study, we have optimized a PCR-RFLP procedure for identification of 3500Q and 3531 mutations and MspI polymorphism at the apo B gene. The technique can be performed in a single reaction, using the restriction endonuclease MspI for simultaneous detection of 3500Q mutation and MspI polymorphism, and NsiI for detection of 3531 mutation. The procedure was validated by analysis of control DNA samples from individuals carrying these mutations. Screening of 186 Brazilian hypercholesterolemic individuals showed that the frequency of the M-allele (7.8%) of MspI polymorphism was similar to that found in other individuals with CAD. However, neither 3500Q nor 3531 mutations were detected in this group. In conclusion, this procedure is simple and rapid, being easily introduced in clinical laboratories for direct detection of the more frequent mutations at the apo B gene associated with hypercholesterolemia.

Aging affects the association between endothelial nitric oxide synthase gene polymorphism and acute myocardial infarction in the Korean male population

OBJECTIVES

The aging process affects responsiveness and other functions of endothelium and vascular smooth muscle cells, predisposing the old vessels to the development of atherosclerotic lesions. Endothelial nitric oxide synthase (ecNOS) gene polymorphisms were shown to affect the occurrence of acute myocardial infarction (AMI). We hypothesized that aging may affect the association between the ecNOS gene polymorphism and AMI.

METHODS

We investigated the age-related distribution of the ecNOS gene a/b polymorphism in 121 male AMI patients and 206 age-matched healthy male controls.

RESULTS

The aa, ab and bb genotypes were found in 1, 49 and 156 cases among the control subjects and 5, 23 and 93 cases among the AMI patients, respectively. There was a significant correlation between the ecNOS polymorphism and AMI (p = 0.045). When the correlation was analyzed by age, the significance remained only in the group below the age of 51 (p = 0.009). The proportion of smokers was increased in the young patients when compared to the old patients (p = 0.033), indicating that smoking also has greater effect on the younger population. The incidences of hypertension and diabetes mellitus, however, were similar in both populations.

CONCLUSION

Our work provides the first evidence that links ecNOS polymorphism to the risk of AMI in relation to age. Young persons who smoke or have ecNOSaa genotype may have an increased risk of developing AMI. The functional as well as structural changes associated with aging in the vascular endothelium may mask the effect of the ecNOS polymorphism in the development of AMI in old persons.

Effects of Ava II and Hinc II polymorphisms at the LDL receptor gene on serum lipid levels of Brazilian individuals with high risk for coronary heart disease

Coronary heart disease (CHD) has presented high prevalence in the Brazilian population. Nevertheless, studies of genetic risk factors for CHD in our country are insufficiently carried out. We have investigated the effects of Ava II (exon 13) and Hinc II (exon 12) polymorphisms at the low-density lipoprotein receptor (LDLR) gene on circulating lipids of 170 white unrelated individuals presenting a lipid profile with high risk for CHD (HRG) and 130 controls (CG) from São Paulo City, Brazil. Ava II and Hinc II polymorphic regions at the LDLR gene were amplified by PCR and analyzed by enzymatic isotyping. The frequency of the genotypes A+A+ (Ava II) and H+H+ (Hinc II) was greater in HRG group compared to that of the controls (32 vs. 16% and 32 vs. 18%, respectively). Moreover, in the HRG group, A+A+ and H+H+ genotypes were associated with high concentrations of total cholesterol and LDL-C in serum (P = 0.0001). Our results indicate that Ava II and Hinc II polymorphisms at the LDLR locus contribute to the variability of total cholesterol and LDL-C levels in HRG individuals. These data suggest that the LDLR polymorphism remains a useful genetic marker for predicting CHD risk.

DNA flow cytometric quantification and DNA polymorphism analysis in the case of a complete mole with a coexisting fetus

PURPOSE

Our purpose was to investigate whether DNA flow cytometric quantification and DNA polymorphism analysis are useful for cytogenetic diagnosis in the case of a complete hydatidiform mole that coexists with a living fetus.

METHODS

Flow cytometric analysis of the nuclear DNA content and polymerase chain reaction (PCR) amplification of the minisatellite locus with the MCT118 probe were performed on the tissues (fetus, placenta and mole) obtained at the initial evacuation.

RESULTS

DNA histograms of placental, fetal, and molar tissues showed diploid peaks. PCR products demonstrated that the allele of the mole was homozygous and inherited solely from the husband and that the mole differed genetically from the fetus and the placenta.

CONCLUSIONS

These results suggested that DNA flow cytometry and DNA polymorphism analysis may be useful for the cytogenetic diagnosis of a complete hydatidiform mole and a coexisting fetus.

Highly polymorphic DNA site D14S1 maps to the region of Burkitt lymphoma translocation and is closely linked to the heavy chain gamma 1 immunoglobulin locus

Using a phage lambda Charon 4A recombinant DNA clone (lambdaCH4A-rHs18) from a human genomic library, Wyman and White detected a multiallelic common polymorphism at an EcoRI site (D14S1) flanking the DNA region homologous to the probe [Wyman, A. R. & White, R. (1980) Proc. Natl. Acad. Sci. USA 77, 6754-6758]. Subsequent studies, carried out with the cell hybrid approach and the use of a subclonal derivative (pAW101) from lambdaCH4A-rHs18 have assigned this locus to autosome 14 between 14q21 and 14qter [De Martinville, B., Wyman, A. R., White, R. & Franke, U. (1982) Am. J. Hum. Gen. 34, 216-226]. The data presented here permit the precise mapping of this locus to the subtelomeric region of autosome 14, below band 14q32, in close proximity to the heavy chain gamma1 immunoglobulin locus. These conclusions are supported by three independent lines of evidence, including studies on gene dosage, somatic cell hybrids, and pedigree analysis. Our results are in agreement with the recent assignment of the heavy chain gamma1 immunoglobulin locus to band 14q32 [Kirsch, I. R., Morton, C. C., Nakahara, K. & Leder, P. (1982) Science 216, 301-303] and are consistent with the generally held contention that one unit of meiotic recombination corresponds approximately to one million base pairs. It is to be expected that the location of the highly polymorphic D14S1 site at a measurable distance from the cluster of the heavy chain genes will provide new opportunities for a genetic approach to the question of the specific gene order within the cluster, its possible individual variation, and its biological significance in normal development and disease. It is worthwhile to point out that such a highly polymorphic DNA sequence is located in the same chromosomal region where so much somatic rearrangement goes on normally (i.e., switch region between classes of heavy chain constant region genes) and which is involved with de novo translocations associated with malignancies.

Nonrandom association of polymorphic restriction sites in the beta-globin gene cluster

By using probes for epsilon-, Psibeta(1)-, and beta-globin genes, we found four additional polymorphic restriction sites that have frequencies >0.1 in persons of Mediterranean area origin, Asian Indians, and American Blacks. Three of these (HincII sites) and the two previously described polymorphic HindIII sites [one in intervening sequence (IVS) II of each gamma-globin gene] are distributed over 32 kilobases (kb) of DNA located 5' to the delta-globin gene. This region of DNA comprises two-thirds of the beta-globin gene cluster. Since each of these five polymorphic sites can be present (+) or absent (-), in theory there exist 32 possible combinations of sites (haplotypes). However, in Italians, Greeks, Indians, and Turks, 3 of the 32 haplotypes, (+----), (-+-++), and (-++-+), account for 92% of 89 beta(A) chromosomes examined. The observed frequencies for these haplotypes are 0.64, 0.15, and 0.13 in the populations studied, in contrast to expected frequencies (based on the observed gene frequencies at each of the five sites) of 0.20, 0.006, and 0.005, respectively. In American Blacks, a fourth haplotype, (----+), which is rare in non-Black populations, has a frequency of 0.37 in contrast to its expected frequency of 0.05. These results suggest a nonrandom association of DNA sequences over 32 kb 5' to the delta-globin gene in all populations studied. Two other polymorphic sites 3' to the delta gene (the newly discovered Ava II site in IVS II of the beta-globin gene and the BamHI site 3' to it) are nonrandomly associated with each other but randomly distributed with respect to the above haplotypes. This suggests that randomization of sequences has occurred within 12 kb of DNA between these two nonrandomly associated sequence clusters. Nonrandom association of polymorphic restriction sites has practical consequences in that it limits the usefulness of these additional HincII sites for prenatal diagnosis of hemoglobinopathies by linkage analysis. These sites provide little additional information for detection of beta-thalassemia, while the polymorphic Ava II site, which lies outside the nonrandomly associated sequences 5' to the delta gene, improves the test applicability from 52% to 70% of couples at risk.