Extent Of Genetic Polymorphism Research Articles

Genome skimming identifies polymorphism in tern populations and species

BackgroundTerns (Charadriiformes: Sterninae) are a lineage of cosmopolitan shorebirds with a disputed evolutionary history that comprises several species of conservation concern. As a non-model system in genetics, previous study has left most of the nuclear genome unexplored, and population-level studies are limited to only 15% of the world's species of terns and noddies. Screening of polymorphic nuclear sequence markers is needed to enhance genetic resolution because of supposed low mitochondrial mutation rate, documentation of nuclear insertion of hypervariable mitochondrial regions, and limited success of microsatellite enrichment in terns. Here, we investigated the phylogenetic and population genetic utility for terns and relatives of a variety of nuclear markers previously developed for other birds and spanning the nuclear genome. Markers displaying a variety of mutation rates from both the nuclear and mitochondrial genome were tested and prioritized according to optimal cross-species amplification and extent of genetic polymorphism between (1) the main tern clades and (2) individual Royal Terns (Thalasseus maxima) breeding on the US East Coast.ResultsResults from this genome skimming effort yielded four new nuclear sequence-based markers for tern phylogenetics and 11 intra-specific polymorphic markers. Further, comparison between the two genomes indicated a phylogenetic conflict at the base of terns, involving the inclusion (mitochondrial) or exclusion (nuclear) of the Angel Tern (Gygis alba). Although limited mitochondrial variation was confirmed, both nuclear markers and a short tandem repeat in the mitochondrial control region indicated the presence of considerable genetic variation in Royal Terns at a regional scale.ConclusionsThese data document the value of intronic markers to the study of terns and allies. We expect that these and additional markers attained through next-generation sequencing methods will accurately map the genetic origin and species history of this group of birds.

Genetic polymorphism at the C-terminal domain (region III) of knob-associated histidine-rich protein (KAHRP) of Plasmodium falciparum in isolates from Iran

The knob-associated histidine-rich protein (KAHRP) plays a major role in the virulence of Plasmodium falciparum and is one of the targets for molecular therapy. The primary structure of KAHRP of P. falciparum consists of three domains (regions I-III), of which the C-terminal domain (region III) is the most polymorphic segment of this protein. One of the main obstacles is genetic diversity in designing and developing of malaria control strategies such as molecular therapy and vaccines. The primary objective of the present study was to investigate and analyze the extent of genetic polymorphism at the region III of KAHRP of P. falciparum in isolates from Iran. A fragment of the kahrp gene spanning the C-terminal domain was amplified by nested PCR from 50 P. falciparum isolates collected from two malaria endemic areas of Iran during 2009 to August 2010 and sequenced. In this study, three allelic types were observed at the C-terminal domain of KAHRP on the basis of the molecular weight of nested PCR products and the obtained sequencing data. The presence of multiple alleles of the kahrp gene indicates that several P. falciparum strains exist in the malaria endemic areas of Iran. Our findings will be valuable in the design and the development of the molecular therapeutic reagents for falciparum malaria.

Polymorphisms in the promoter region of bovine PRKAB1 gene

The AMP-activated protein kinase (AMPK) is an evolutionarily conserved sensor of cellular and systemic energy balance. PRKAB1, the gene that encodes the beta1 regulatory subunit of AMPK, has been shown to be highly involved in the glycogen metabolism. To date, several mutations affecting function of human PRKAB1 have been identified, but few studies have shown a complete description of variability of the promoter region of PRKAB1. Therefore, the extent of genetic polymorphisms in the promoter region of PRKAB1 gene was investigated in a sample of 811 Chinese indigenous bovine individuals using a PCR-SSCP (single strand conformation polymorphism) strategy. Sequence analysis revealed 12 single nucleotide polymorphisms and one 10 bp insertion and one 4 bp deletion variations, which are within some important transcription factor binding sites: GC-Box factors SP1/GC, PAX-3 binding sites, zinc binding protein factors, nuclear respiratory factor 1, and serum response element binding factor. It is expected that these polymorphisms regulate PRKAB1 gene transcription and might have consequences at a regulatory level.

Molecular Genetic Characterization of the Merozoite Surface Protein 1 Gene of Plasmodium vivax from Reemerging Korean Isolates

Plasmodium vivax merozoite surface protein 1 (PvMSP-1) has been considered a major candidate for the development of an antimalaria vaccine, but the molecule exhibits antigenic diversity among isolates. The extent of genetic polymorphism in the region between interspecies conserved blocks 4 and 5 (ICB4 and ICB5) of the PvMSP-1 gene was analyzed for 30 Korean isolates. Two genotypes, SK-A and SK-B, were identified on the basis of amino acid substitution. Almost all the amino acid sequences of the Korean isolates were nearly identical to those of the Solomon Island isolate Solo-83 (97.8 to 99.9% similarity) and Philippine isolates Ph-79, Ph-52-2, and Ph-49 (97.3 to 99.8% similarity). Also, we report two sequences in the isolates that were characterized on the basis of restriction fragment length polymorphism (RFLP). The RFLP profiles following digestion with the DraI restriction enzyme produced two distinguishable patterns. This study might be the first report of the region between ICB4 and ICB5 of the MSP-1 gene of P. vivax in South Korea.

Differential evolution of repetitive sequences in Cryptosporidium parvum and Cryptosporidium hominis

Cryptosporidium parvum and Cryptosporidium hominis are two morphologically identical species of Apicomplexan protozoa infecting humans. Although the genomes of these species are 97% identical, their host range is strikingly different. C. parvum infects humans and animals and is primarily a zoonotic infection, whereas C. hominis is typically not detected in animals. The extent of genetic polymorphism in both species has been surveyed locally, but not on a larger geographical scale. Herein, a collection of unrelated C. parvum and C. hominis isolates was genotyped using multiple, randomly distributed micro- and minisatellites. In average, minisatellites, consisting of tandemly repeated sequence motifs of 6–24 basepair, were more polymorphic than microsatellites. When the average number of micro- and minisatellite alleles per locus was used as a measure of heterogeneity, no difference between C. parvum and C. hominis was found. However, the frequency distribution of alleles in both species was significantly different and in 6 of the 14 loci the size of the C. parvum and C. hominis repeats did not overlap. Assuming that C. parvum and C. hominis evolved from a common ancestor, these observations suggest a differential evolution of repeat length at these loci.

Plasmodium vivax: Polymorphism in the Merozoite Surface Protein 1 Gene from Wild Colombian Isolates

Gutierrez, A., Vicini, J., Patarroyo, M. E., Murillo, L. A., and Patarroyo, M. A. 2000. Plasmodium vivax: Polymorphism in the merozoite surface protein 1 gene from wild colombian isolates. Experimental Parasitology95, 215–219. The Plasmodium vivax merozoite surface protein-1 (PvMSP-1) has been considered a candidate for a malaria vaccine against erythrocytic stages. PvMSP-1 is immunogenic during natural infections and exhibits antigenic polymorphism. The extent of genetic polymorphism in a region between the so-called interspecies conserved blocks (ICBs) 2 and 4 of the PvMSP-1 was analyzed in 20 isolates taken from patients from two different areas in Colombia. Variation is unevenly distributed along this gene segment among the isolates. Comparative analysis of these sequences led to the definition of five sequence types (ST1 to 5). ST1 to ST4 exhibit a variation pattern associated with sequences present in the Salvador or Belem sequences. However, ST5 has clusters of sequence that have not been previously described. The changes found along the five variants confirm the important role of recombinational and/or gene conversion events in generating allelic diversity.

Analysis of Natural Intraspecific Variation in Rhododendron nilagiricum Zenk of Nilgiris using RAPD

Rhododendron nilagiricum Zenk is the only paleoendemic species of Rhododendron found at Nilgiris. Random amplified polymorphic DNA (RAPD) analysis was carried out to study the extent of genetic polymorphism in trees collected from five locations at Nilgiris. Of the 15 primers tested, 10 revealed polymorphism. The percentage polymorphism ranged from 40 to 92 with an average of 61.5 polymorphism per primer. Pair wise comparisons were made for the RAPD profiles obtained through the use of 10 primers in the representative samples. Data analysis was done by using the POPGENE statistical package. The similarity matrix and the dendrogram obtained showed that there was close similarity between trees collected from different regions of Nilgiris. The cluster analysis showed positive correspondence between genetic diversity and geographic distance. Primer OPZ 13 generated the highest number of bands among the primers, revealed maximum polymorphism and had the greatest capacity for discriminating individuals of R. nilagiricum collected from different regions of Nilgiris.

Prevalence and Genetic Variability of Arcobacter Species in Mechanically Separated Turkey

A survey for Arcobacter spp. and Arcobacter butzleri in mechanically separated turkey was conducted during the winter of 1995 and summer and fall of 1996. Arcobacter spp. and A. butzleri were identified by polymerase chain reaction and species-specific oligonucleotide probes. Arcobacter spp. were isolated from 77% (303 out of 395) of the mechanically separated turkey samples with 74% (223 out of 303) of these samples positive for A. butzleri. Of the 121 A. butzleri isolates tested, 86 different pattems were evident following amplification of enterobacterial repetitive intergenic consensus sequences. The extent of genetic polymorphism indicated multiple sources of contamination.

Genetic polymorphism and fertility parameters in the Aymara of Chile and Bolivia.

To determine whether increased fitness in natural populations is associated with heterozygosity, several studies have attempted to correlate heterozygosity at one or a few genetic loci with fitness-related quantitative traits. The results have been equivocal at best. Furthermore, data on fertility-related parameters and the extent of genetic polymorphism at a large number of loci in man are quite scanty. This report examines the association of four fertility-related parameters (number of pregnancies, number of livebirths, number of children surviving at least one year and number of children alive at the time of the survey) with heterozygosity at 17 polymorphic immunological and biochemical systems in the Aymara of Chile and Bolivia. Women 45 years of age and above, on whom complete fertility histories and phenotype data are available, were included in the study (n = 190). None of the fertility parameters seem to be correlated with heterozygosity, as measured by the proportion of polymorphic loci. For some individual loci, however, an association between heterozygous state and fertility parameters exists. Even in these cases, heterozygosity did not always confer higher fertility. To see whether these negative results are due to heterogeneity in the data, the total sample was divided according to altitude of residence and ethnicity. The conclusions remained the same, indicating that the lack of association of these fertility parameters with genetic polymorphism is not due to population heterogeneity alone. Reproductive fitness differentials, therefore, were not detectable in the Aymara by heterozygosity determined by the polymorphic genetic systems scored by serological and electrophoretic techniques.