scholarly journals Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli

2005 ◽  
Vol 187 (21) ◽  
pp. 7185-7192 ◽  
Author(s):  
Margarita Flores ◽  
Lucia Morales ◽  
Agustín Avila ◽  
Víctor González ◽  
Patricia Bustos ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nucleotide Polymorphisms ◽  
Rhizobium Etli ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Genetic Elements ◽  
Hypervariable Regions ◽  
The Common ◽  
Different Strains ◽  
Model Strain

ABSTRACT Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification.

scholarly journals Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus

2021 ◽  
Vol 22 (4) ◽  
pp. 1832
Author(s):  
Eugene Metakovsky ◽  
Laura Pascual ◽  
Patrizia Vaccino ◽  
Viktor Melnik ◽  
Marta Rodriguez-Quijano ◽  
...  
Keyword(s):  
Common Wheat ◽  
Dna Sequences ◽  
Fragment Length Polymorphism ◽  
Snp Markers ◽  
Group Iv ◽  
Nucleotide Polymorphisms ◽  
High Genetic Diversity ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
B Genome

The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.

scholarly journals A NOTE ON PHASING LONG GENOMIC REGIONS USING LOCAL HAPLOTYPE PREDICTIONS

2006 ◽  
Vol 04 (03) ◽  
pp. 639-647 ◽  
Author(s):  
ELEAZAR ESKIN ◽  
RODED SHARAN ◽  
ERAN HALPERIN
Keyword(s):  
Large Scale ◽  
Computational Cost ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Novel Approach ◽  
Maximum Likelihood Criterion ◽  
The Common ◽  
Genomic Regions ◽  
High Computational Cost ◽  
Combining Information

The common approaches for haplotype inference from genotype data are targeted toward phasing short genomic regions. Longer regions are often tackled in a heuristic manner, due to the high computational cost. Here, we describe a novel approach for phasing genotypes over long regions, which is based on combining information from local predictions on short, overlapping regions. The phasing is done in a way, which maximizes a natural maximum likelihood criterion. Among other things, this criterion takes into account the physical length between neighboring single nucleotide polymorphisms. The approach is very efficient and is applied to several large scale datasets and is shown to be successful in two recent benchmarking studies (Zaitlen et al., in press; Marchini et al., in preparation). Our method is publicly available via a webserver at .

scholarly journals An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

2021 ◽  
Author(s):  
Thomas K. F. Wong ◽  
Teng Li ◽  
Louis Ranjard ◽  
Steven Wu ◽  
Jeet Sukumaran ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Real Data ◽  
Reference Sequence ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Short Read ◽  
Pooled Samples ◽  
Haplotype Information

AbstractA current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian model of inference to estimates the phylogeny of the haplotypes and their relative frequencies, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and frequencies of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.

scholarly journals A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

2019 ◽  
pp. 1-5
Author(s):  
Svetlana Kovalchuk ◽  
Arina Tagmazyan ◽  
Eugene Klimov
Keyword(s):  
Nucleotide Substitution ◽  
Milk Proteins ◽  
Test System ◽  
Nucleotide Polymorphisms ◽  
Dna Testing ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Selection Of

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

Diagnosing genetically diverse avian malarial infections using mixed-sequence analysis and TA-cloning

Parasitology ◽  
2005 ◽  
Vol 131 (1) ◽  
pp. 15-23 ◽  
Author(s):  
J. PÉREZ-TRIS ◽  
S. BENSCH
Keyword(s):  
Dna Sequences ◽  
Accurate Method ◽  
The Other ◽  
Multiple Infections ◽  
Template Switching ◽  
Mixed Infections ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
In The Wild ◽  
Host Parasite

Birds harbouring several malarial parasites are common in the wild, and resolving such multiple infections is important for our understanding of host–parasite relationships. We propose a simple and reasonably accurate method for detecting and resolving multiple infections, based on the analysis of parasite cytochrome b DNA sequences: genetically mixed infections are first identified by double nucleotide peaks on sequence electropherograms, and later retrieved by TA-cloning. We applied this method to wild birds, and to experimentally created mixes with varying proportion of two parasites (Plasmodium spp. and Haemoproteus spp.). In general, the method was very efficient in detecting and resolving multiple infections, but some problems were encountered. Several multiple infections were erroneously scored as simple, either because one of the parasite lineages was a better target for the primers used, or because it was much more abundant in the mix. On the other hand, single nucleotide substitutions and template switching during PCR produced artificial sequences in some clones. We discuss the utility of the method, and propose a framework for its use when screening for genetically diverse avian malarial parasites.

scholarly journals Cloning and analysis of the esterase genes conferring insecticide resistance in the peach-potato aphid, Myzus persicae (Sulzer)

1993 ◽  
Vol 294 (2) ◽  
pp. 569-574 ◽  
Author(s):  
L M Field ◽  
M S Williamson ◽  
G D Moores ◽  
A L Devonshire
Keyword(s):  
Insecticide Resistance ◽  
Dna Sequences ◽  
Myzus Persicae ◽  
Amino Acid Sequences ◽  
In Vitro Translation ◽  
Cdna Clones ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Potato Aphid ◽  
Peach Potato Aphid

Full-length cDNA clones encoding the esterases (E4 and FE4) that confer insecticide resistance in the peach-potato aphid [Myzus persicae (Sulzer)] were isolated and characterized. The E4 cDNA contained an open reading frame of 1656 nucleotides, coding for a protein of 552 amino acids. The FE4 cDNA shared 99% identity with E4 over this region, the most important difference being a single nucleotide substitution resulting in the FE4 mRNA having an extra 36 nucleotides at the 3′ end. The derived amino acid sequences for the N-terminus of E4 and FE4 were identical, with the first 23 residues being characteristic of a signal peptide and the next 40 residues being an exact match to the N-terminal sequence determined by Edman degradation of both purified proteins. The predicted molecular masses of 58.8 and 60.2 kDa for the E4 and FE4 polypeptides were consistent with those previously observed by in vitro translation of mRNA. Five potential N-linked glycosylation sites were present in both polypeptides, in accordance with earlier evidence that the native esterases are glycoproteins. Comparison of the aphid esterase protein sequences with other serine hydrolases provided evidence that their activity involves a charge-relay system with a catalytic triad the same as that found in acetylcholinesterase. Restriction mapping and sequencing of cloned genomic DNA showed that the E4 gene is spread over 4.3 kb with six introns and that the previously reported differences between the 3′ ends of the E4 and FE4 genes result from single nucleotide substitutions and not gross differences in the DNA sequences.

scholarly journals POLYMORPHISMS IN THE GENES OF REPARATIONS AMONG EMPLOYEES OF THE ATOMIC INDUSTRY OF KAZAKHSTAN

2020 ◽  
Vol 1 (337) ◽  
pp. 5-10
Author(s):  
D. M. Botbаeyev ◽  
А. M. Belkozhаev ◽  
A. K. Khanseitova ◽  
A. Zh. Borbayeva ◽  
N. А. Аitkhozhinа
Keyword(s):  
Nuclear Industry ◽  
Repair System ◽  
Nucleotide Polymorphisms ◽  
Low Dose Radiation ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Variable Regions ◽  
And Control ◽  
Dose Radiation

Single nucleotide polymorphisms (SNPs) are the most convenient marker and the widespread subject of polymorphism testing. To identify the presence or absence of the effects of chronic low-dose radiation on nuclear industry personnel, the occurrence of single-nucleotide substitutions at the polymorphic sites of the genes of the repair system 3 and 6 of the introns of the APC gene P53.11 gene, in positions -2549 of the VEGF gene, XPD gene rs313181 ( Lys751Gln) and rs25487 of the XRCC gene (Аrg399Gln) were compared. Analysis of allele frequencies and distribution of genotypes in the variable regions of the tested genes was performed by the method of polymerase chain reaction (PCR), followed by determination of restriction fragment length polymorphism (RFLP). When com-paring the frequencies of alleles and the distribution of genotypes between the second group of miners (11–20 years’ experience) and control, differences in the distribution of genotypes in the rs25487 XRCC plot (χ2 = 7.11, p = 0.028) were revealed. These differences satisfy the criterion p <0.05 and, accordingly, are statistically significant. Key words: polymorphism, genes, a nuclear industry.

scholarly journals (293) Single Nucleotide Polymorphism in matK and Ribosomal ITS of Astilbe

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1081E-1082
Author(s):  
Brian W. Trader ◽  
Richard E. Veilleux ◽  
Holly L. Scoggins
Keyword(s):  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Its1 Region ◽  
Rdna Genes ◽  
Species Hybrids ◽  
Plant Specimen

The genus Astilbe (Saxifragaceae) comprises about 13 species and is ranked consistently among the top 10 landscape perennials. Through extensive hybridization, selection and marketing, the lineage of many Astilbehas been lost. Subdioecious Astilbebiternatais the only species in the genus native to North America while other members of the genus are endemic to Asia and monoecious. Due to the unusual geographic distribution of the species and the variation in floral development among them, development of genetic markers using single nucleotide polymorphisms (SNPs) would confirm phylogenetic relationships and establish lineage within the genus. Astilbespecies, hybrids, and cultivars were obtained from plant nurseries and botanical gardens across the country. To elucidate relationships among the genus, we conducted phylogenetic analysis of DNA sequences of the chloroplast gene matKand the internal transcriber spacer (ITS) of ribosomal rDNA genes. DNA was extracted, and gene primers trnK3914 and trnK2R were used to amplify matK, and primers 1406F and ITS2 were used to amplify the ITS1 region between 18S and 5.8S ribosomal DNA units. Both matKand ITS were sequenced for each plant specimen and sequences were aligned to identify nucleotide diversity and detect SNPs. Variation in nucleotide sequence for either gene yielded similar dendrograms. Nucleotide variation among the Astilbeutilized in this study has allowed the development of SNP markers that may be useful for fingerprinting unknown hybrids or cultivars in the industry, and may be used for species alignment within the genus.

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