Autoři uvádějí své zkušenosti s neradioaktivní DNA-diagnostikou Duchennovy a Beckerovy muskulární dystrofie, při které využili polymorfismu krátkých tandemových repeticí ze čtyř intronových oblastí (introny 44, 45, 49, 50) a dvou oblastí 5'-konce dystrofínového genu. Oblasti s tandemovými repeticemi byly amplifikovány pomocí polymerázové řetězové reakce a po rozdělení v denaturačním polyakrylamidovém gelu byly identifikovány barvením stříbrem. Předkládané výsledky ukazují spolehlivost a jednoduchost neradioaktivní diagnostiky, kterou je možno zavést v každé DNA-laboratoři.
The authors present their experience with non-radioactive diagnostics of Duchenne and Becker muscular dystrophy using short tandem repeat polymorphism from four intron loci (introns 44, 45, 49, 50) and two 5'terminus regions of the dystrophine gene. Regions with tandem repeats were amplified by the polymerase chain reaction and after senaration in denaturin£f polvacrylamide gel identified by silver staining. The results presented show the reliability and simplicity of non-radioactive diagnostics, which could be introduced in every DNA-laboratory.
- MeSH
- Silver Staining MeSH
- Child MeSH
- DNA analysis genetics MeSH
- Adult MeSH
- Electrophoresis, Polyacrylamide Gel methods MeSH
- Genetic Testing methods standards statistics & numerical data MeSH
- Introns MeSH
- Humans MeSH
- Minisatellite Repeats genetics MeSH
- Check Tag
- Child MeSH
- Adult MeSH
- Humans MeSH
- Male MeSH
- Female MeSH
Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88-98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley.
- MeSH
- Chromosomes, Plant genetics MeSH
- Genome, Plant * MeSH
- Hordeum genetics MeSH
- Triticum genetics MeSH
- Tandem Repeat Sequences * MeSH
- Publication type
- Journal Article MeSH
Allele frequencies for 17 short tandem repeats (STRs) autosomal loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, CSF1PO, FGA, PentaD, PentaE, TH01, TPOX, vWA) were studied in an extensive sample (max. N=1411) of unrelated individuals originating from the Czech Republic. Population and forensic parameters were estimated. Except for FGA and Penta E loci, no deviations from the Hardy-Weinberg equilibrium were detected. A comparative analysis with published data revealed significant differences in allele frequencies for some loci from the Polish population and three Hungarian populations (Ashkenazim population and Romany populations from Debrecen and Baranya County, respectively). A combination of these 17 STR loci provides a powerful tool for forensic identification in the native Czech population.
- MeSH
- DNA Fingerprinting MeSH
- Gene Frequency MeSH
- Humans MeSH
- Polymerase Chain Reaction MeSH
- Genetics, Population MeSH
- Tandem Repeat Sequences MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
Pro klonální analýzu kmenů Streptococcus pneumoniae z invazivního pneumokokového onemocnění byla v NRLpro streptokokové nákazy SZÚ zavedena a ověřena metoda Multiple-Locus Variable number tandem repeat Ana-lysis (MLVA). Oproti rutinně používané metodě Multilocus Sequence Typing (MLST) je výhodou metody MLVAsnadnost a rychlost provedení i nižší nákladnost. Rozlišení klonů je u obou metod obdobné. Standardem klonálníanalýzy pro molekulární surveillance původců závažných pneumokokových infekcí je však MLST, MLVA můžebýt doplňkem pro klonální porovnání izolátů z lokálních epidemiologických situací.
The NRL for Streptococcal Infections implemented and tested Multiple-Locus Variable number tandem repeatAnalysis (MLVA) for clonal analysis of Streptococcus pneumoniae strains from invasive pneumococcal disease.As compared to the routinely used Multilocus Sequence Typing (MLST) method, MLVA has the advantage of beingeasier, faster, and less expensive to perform. Both methods have similar resolution. Nevertheless, the standardmethod for clonal analysis in molecular surveillance of causative agents of severe pneumococcal infections isMLST, and MLVA can be used as a complementary method for clonal comparison of local isolates.
- MeSH
- DNA, Bacterial genetics MeSH
- Minisatellite Repeats genetics MeSH
- Multilocus Sequence Typing * methods MeSH
- Pneumococcal Infections diagnosis epidemiology MeSH
- Streptococcus pneumoniae * genetics isolation & purification MeSH
- Bacterial Typing Techniques methods MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
Amplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities. Using the satellite DNA-rich legume plant Lathyrus sativus as a model, we demonstrated this approach by analyzing 11 major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73× genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of the L. sativus chromosomes, which suggests that these genome regions are favourable for satellite DNA accumulation.
- MeSH
- Centromere MeSH
- Chromosomes, Plant MeSH
- DNA, Plant genetics MeSH
- Gene Frequency * MeSH
- Genome, Plant MeSH
- Heterochromatin MeSH
- Lathyrus genetics MeSH
- Evolution, Molecular MeSH
- Nanopores * MeSH
- Retroelements * MeSH
- DNA, Satellite * MeSH
- Tandem Repeat Sequences * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Cíl práce: Cílem práce je Multiple-locus variable number tandem repeat analýza (MLVA) souboru kmenů B. pertussis ze sbírky Národní referenční laboratoře pro pertusi a difterii (NRL/DIPE) Státního zdravotního ústavu (SZÚ) Praha. Jedná se o kmeny získané ze vzorků klinického materiálu převážně na území ČR v téměř padesátiletém období 1967–2015 (červen). Je porovnávána genetická diverzita a zastoupení detekovaných MLVA typů (MT) ve třech obdobích lišících se vakcinační strategií a trendem výskytu pertuse. Na podkladě získaných výsledků je posouzena vhodnost použití metody MLVA pro analýzu epidemických výskytů B. pertussis v ČR. Materiál a metodiky: Vzorky DNA extrahované z kmenů B. pertussis studovaného souboru byly analyzovány metodou MLVA podle standardizovaného postupu. Data byla zpracována pomocí algoritmu eBURST, pro statistické zpracování byl zvolen výpočet Simpsonova indexu diverzity (DI). Data byla zpracována pro celý soubor a též odděleně pro skupiny kmenů z tří období: 1967–1980, 1990–2007 a 2008–2015 (červen). Výsledky: V souboru bylo detekováno 14 různých MT, z toho 3 dosud nezjištěné. Nejčetnější byly v celém souboru MT27 a MT29. MT29 převládal v období 1967–1980, MT27 v obdobích 1990–2007 a 2008–2015 (červen). Hodnota DI byla nejnižší (0,49) pro období 2008–2015 (červen), pro dvě předchozí období byly hodnoty vyšší a vzájemně srovnatelné (0,667 pro období 1967–1980 a 0,654 pro období 1990–2007). Závěr: MLVA analýzou souboru kmenů B. pertussis izolovaných z klinického materiálu na území ČR v období 1967–2015 (červen) byl prokázán pokles genetické diverzity ve studované populaci a změny v zastoupení a četnosti jednotlivých MT. Tyto změny lze charakterizovat jako postupný nárůst výskytu celosvětově rozšířených MT v České republice na úkor MT regionálně unikátních. Převažujícím MT, stejně jako ve většině geografických oblastí s dlouhodobě proočkovanou populací, je MT27. Výsledky MLVA analýzy souboru 136 kmenů B. pertussis mohou být podkladem pro účelné využití metody k molekulárně epidemiologickému zpracování souborů menšího rozsahu.
Aim: To perform multiple-locus variable number tandem repeat analysis (MLVA) of B. pertussis strains from the collection of the National Reference Laboratory for Diphtheria and Pertussis (NRL/DIPE), National Institute of Public Health (NIPH), Prague. The study strains were isolated from clinical specimens collected mostly in the Czech Republic over a nearly 50-year period from 1967 to 2015 (June). The isolates from three periods characterized by different vaccination strategies and trends in pertussis are compared for genetic diversity and distribution of MLVA types (MT). Based on the results obtained, the suitability for use of MLVA in the analysis of epidemic outbreaks of B. pertussis in the Czech Republic is considered. Material and methods: DNA samples extracted from B. pertussis strains included in the present study were examined by MLVA using the standard protocol. Data were processed by means of the eBURST algorithm and the calculation of the Simpson diversity index (DI) was used for the statistical analysis. Data were analyzed as a whole and also separately for strains from the three periods: 1967–1980, 1990–2007, and 2008–2015 (June). Results: Fourteen different MT were detected in the study strains, with three of them not being reported before. The most common MTs were MT27 and MT29. MT29 was predominant in 1967–1980 while MT27 was the most prevalent in 1990–2007 and 2008–2015 (June). The DI was the lowest (0.49) in 2008–2015 (June), and comparably higher DIs were calculated for the two previous periods (i.e. 0.667 for 1967–1980 and 0.654 for 1990–2007). Conclusion: MLVA revealed a decrease in genetic diversity and shifts in MT distribution of B. pertussis strains isolated from clinical specimens in the Czech Republic from 1967 to 2015 (June). These shifts in the Czech Republic can be characterized as a progressive increase in global MTs at the expense of the locally unique ones. The most common MT, similarly to other geographical areas with long-term high vaccination coverage, is MT27. The results of MLVA of 136 B. pertussis strains can provide a background for using this method in molecular epidemiological analysis of smaller groups of strains.
- MeSH
- Vaccines, Acellular immunology MeSH
- Genes, Bacterial genetics MeSH
- Bordetella pertussis * genetics MeSH
- Time Factors MeSH
- DNA, Bacterial genetics MeSH
- Genetic Variation genetics MeSH
- Mass Vaccination MeSH
- Humans MeSH
- Minisatellite Repeats * genetics MeSH
- Multilocus Sequence Typing * MeSH
- Whooping Cough epidemiology microbiology prevention & control MeSH
- Pertussis Vaccine immunology MeSH
- Tandem Repeat Sequences genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
- Czechoslovakia MeSH
KEY MESSAGE: Fluorescence in situ hybridization with probes for 45 cDNAs and five tandem repeats revealed homoeologous relationships of Agropyron cristatum with wheat. The results will contribute to alien gene introgression in wheat improvement. Crested wheatgrass (Agropyron cristatum L. Gaertn.) is a wild relative of wheat and a promising source of novel genes for wheat improvement. To date, identification of A. cristatum chromosomes has not been possible, and its molecular karyotype has not been available. Furthermore, homoeologous relationship between the genomes of A. cristatum and wheat has not been determined. To develop chromosome-specific landmarks, A. cristatum genomic DNA was sequenced, and new tandem repeats were discovered. Their distribution on mitotic chromosomes was studied by fluorescence in situ hybridization (FISH), which revealed specific patterns for five repeats in addition to 5S and 45S ribosomal DNA and rye subtelomeric repeats pSc119.2 and pSc200. FISH with one tandem repeat together with 45S rDNA enabled identification of all A. cristatum chromosomes. To analyze the structure and cross-species homoeology of A. cristatum chromosomes with wheat, probes for 45 mapped wheat cDNAs covering all seven chromosome groups were localized by FISH. Thirty-four cDNAs hybridized to homoeologous chromosomes of A. cristatum, nine hybridized to homoeologous and non-homoeologous chromosomes, and two hybridized to unique positions on non-homoeologous chromosomes. FISH using single-gene probes revealed that the wheat-A. cristatum collinearity was distorted, and important structural rearrangements were observed for chromosomes 2P, 4P, 5P, 6P and 7P. Chromosomal inversions were found for pericentric region of 4P and whole chromosome arm 6PL. Furthermore, reciprocal translocations between 2PS and 4PL were detected. These results provide new insights into the genome evolution within Triticeae and will facilitate the use of crested wheatgrass in alien gene introgression into wheat.
BACKGROUND: A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained. RESULTS: Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences. CONCLUSION: The large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.
- MeSH
- Gene Amplification * MeSH
- Chromosomes, Plant genetics MeSH
- Phylogeny MeSH
- Gene Library MeSH
- Heterochromatin genetics MeSH
- In Situ Hybridization, Fluorescence MeSH
- Genome Components MeSH
- Sequence Analysis, DNA MeSH
- Oligonucleotide Array Sequence Analysis MeSH
- Tandem Repeat Sequences * MeSH
- DNA Transposable Elements * MeSH
- Chromosomes, Artificial, Bacterial MeSH
- Secale genetics MeSH
- Publication type
- Journal Article MeSH
The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.
- MeSH
- Genome * MeSH
- Gorilla gorilla classification genetics MeSH
- Karyotyping methods MeSH
- Cats MeSH
- Chromosome Mapping methods statistics & numerical data MeSH
- Chromosome Banding MeSH
- Fishes classification genetics MeSH
- Software * MeSH
- Tandem Repeat Sequences MeSH
- Base Composition * MeSH
- Animals MeSH
- Check Tag
- Cats MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
