Echinococcus granulosus (Batsch, 1786), a cestode of the Teniidae family, causes human cystic echinococcosis (CE) also known as hydatid disease. Echinococcus granulosus sensu lato includes the G1, G3, G4, G5, G6/7 and G8/10 genotypes which are known to cause human CE. This study aimed to differentiate genotypes of E. granulosus s.l. complex by employing EmsB, a tandemly repeated multilocus microsatellite, using next-generation sequencing (MIC-NGS). Human and animal histopathology-confirmed hydatid cyst tissue samples and reference DNA samples of E. granulosus G1, G3, G4, G5, G6/7 and G10 underwent MIC-NGS assay with custom primers amplifying a 151 bp EmsB DNA fragment. NGS data were analysed using online Galaxy analysis pipeline, a phylogenetic tree was constructed by MEGA software, and haplotype networking was performed with PopArt 1.7. All sixty samples (49 from animals and 11 from humans) included were successfully identified and genotyped with a 100 % success rate. The study showed improved discrimination power to distinguish all study samples including closely related E. granulosus s.s. genotypes G1-G3. The maximum likelihood tree reaffirmed the monophyly of E. granulosus s.l. The median-joining haplotype networking revealed 12 distinct haplotypes. In conclusion, MIC-NGS assay was shown to be sensitive, specific and simple to apply to clinical samples offering a powerful discriminatory tool for the genotyping of E. granulosus s.l.

• MeSH
• Echinococcus granulosus * genetics   MeSH
• Echinococcosis * veterinary   parasitology   MeSH
• Phylogeny MeSH
• Genotype * MeSH
• Genotyping Techniques veterinary   MeSH
• Humans MeSH
• Microsatellite Repeats * MeSH
• High-Throughput Nucleotide Sequencing * MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH

"Genetics and Genomics in Medicine is a new textbook written for undergraduate and graduate students, as well as medical researchers, which explains the science behind the uses of genetics and genomics in medicine today. It is not just about rare inherited and chromosomal disorders, but how genetics affects the whole spectrum of human health and disease. DNA technologies are explained, with emphasis on the modern techniques that have revolutionized the use of genetic information in medicine and are indicating the role of genetics in common complex diseases. The detailed, integrative coverage of genetic approaches to treatment and prevention includes pharmacogenomics and the prospects for personalized medicine. Cancers are essentially genetic diseases and are given a dedicated chapter that includes new insights from cancer genome sequencing. Clinical disorders are covered throughout and there are extensive end-of-chapter questions and problems"--Provided by publisher.

Wilt (Fusarium oxysporum f. sp. lentis; Fol) is one of the major diseases of lentil worldwide. Two hundred and thirty-five isolates of the pathogen collected from 8 states of India showed substantial variations in morphological characters such as colony texture and pattern, pigmentation and growth rate. The isolates were grouped as slow (47 isolates), medium (118 isolates) and fast (70 isolates) growing. The macroconidia and microconidia (3.0-77.5 × 1.3-8.8 μm for macroconidia and 1.8-22.5 × 0.8-8.0 μm for microconidia for length × width) were variable in size and considering the morphological features, the populations were grouped into 12 categories. Seventy representative isolates based on their morphological variability and place of origin were selected for further study. A set of 10 differential genotypes was identified for virulence analysis and based on virulence patterns on these 10 genotypes, 70 Fol isolates were grouped into 7 races. Random amplified polymorphic DNA (RAPD), universal rice primers (URPs), inter simple sequence repeats (ISSR) and sequence-related amplified polymorphism (SRAP) were used for genetic diversity analysis. URPs, ISSR and SRAP markers gave 100% polymorphism while RAPD gave 98.9% polymorphism. The isolates were grouped into seven clusters at genetic similarities ranging from 21 to 80% using unweighted paired group method with arithmetic average analysis. The major clusters include the populations from northern and central regions of India in distinct groups. All these three markers proved suitable for diversity analysis, but their combined use was better to resolve the area specific grouping of the isolates. The sequences of rDNA ITS and TEF-1α genes of the representative isolates were analysed. Phylogenetic analysis of ITS region grouped the isolates into two major clades representing various races. In TEF-1α analysis, the isolates were grouped into two major clades with 28 isolates into one clade and 4 remaining isolates in another clade. The molecular groups partially correspond to the lentil growing regions of the isolates and races of the pathogen.

• MeSH
• Biological Variation, Population MeSH
• Cicer * MeSH
• Lens Plant * genetics   MeSH
• DNA Primers MeSH
• Fusarium * genetics   MeSH
• Phylogeny MeSH
• Genetic Variation MeSH
• Plant Diseases MeSH
• DNA, Ribosomal MeSH
• Random Amplified Polymorphic DNA Technique MeSH
• Publication type
• Journal Article MeSH

Cieľ: Cieľom práce bola genetická charakterizácia súboru prípadov suspektných z parciálnej moly hydatidózy na základe nejednoznačného morfologického obrazu placentárneho tkaniva. Súbor a metodika: Práca predkladá výsledky genetickej analýzy súboru 10 pacientok s rôznymi klinickými prejavmi reprodukčných strát, u ktorých bola na základe histopatologického vyšetrenia suponovaná parciálna mola hydatidóza. Kompozícia genómu produktu koncepcie bola určená genotypizáciou krátkych tandemových opakovaní (STR – short tandem repeats) použitím komerčnej súpravy „Devyser Compact v3“ (Devyser). Výsledky a závery: Z 10 vyšetrených prípadov bol v piatich zistený diandrický monogynický triploidný genóm charakteristický pre parciálnu molu. V štyroch prípadoch boli vylúčené aneuploidie chromozómov 13, 18, 21, X a Y, v jednom prípade bol diagnostikovaný Patauov syndróm. Pri nejednoznačnom histopatologickom obraze môže patológom v diferenciálnej diagnostike parciálnej moly významne pomôcť konzultačná DNA analýza (ideálne STR genotypizácia). Histopatologický obraz parciálnej moly hydatidózy môže byť v skorých štádiách gravidity v niektorých prípadoch neúplný a nejednoznačný, čo môže viesť k falošne negatívnemu výsledku vyšetrenia. Na druhej strane, mnohé iné patológie, napr. aneuploidie alebo digynická triploidia, môžu mať histopatologický obraz podobný parciálnej mole, čo naopak vedie k falošnej pozitivite vyšetrenia. Presná diagnostika parciálnej moly hydatidózy použitím molekulárnych genetických metód prispeje k stanoveniu adekvátnej dispenzárnej starostlivosti.

Objective: The aim of the study was the genetic characterization of a set of cases with an unclear morphological profile of the placental tissue suspected of a partial hydatidiform mole. Patients and methods: This work presents the results of a genetic analysis of a group of 10 patients with various clinical manifestations of reproductive loss, where a partial hydatidiform mole was suspected on the basis of a histopathological examination. The composition of the genome of the products of conception was determined by short tandem repeats (STR) genotyping using a commercial kit “Devyser Compact v3 (Devyser) “. Results and conclusions: Out of 10 analyzed cases, five had diandric monogynic triploid genome, characteristic for a partial mole. Aneuploidies of chromosomes 13, 18, 21, X and Y were excluded in four cases and Patau‘s syndrome was diagnosed in one case. In the case of an unclear histopathological profile, consultative DNA analysis (ideally STR genotyping) can significantly help the pathologist in the differential diagnosis of a partial mole. The histopathological profile of a partial hydatidiform mole may be in some cases incomplete and unclear, especially in the early weeks of gestation, which can lead to false negativity of the examination. On the other hand, other pathologies, for example aneuploides or digynic triploidy, may produce a histopathological profile similar to a partial mole, which leads to false positivity. Accurate diagnosis of a partial hydatidiform mole using molecular genetic methods contributes to the determination of adequate dispensary care for patients.

• MeSH
• Aneuploidy MeSH
• Genotyping Techniques methods   MeSH
• Clinical Studies as Topic MeSH
• Humans MeSH
• Microsatellite Repeats MeSH
• Hydatidiform Mole * diagnosis   genetics   MeSH
• Placenta MeSH
• Pregnancy MeSH
• Check Tag
• Humans MeSH
• Pregnancy MeSH
• Female MeSH

In pathogenic fungi and oomycetes, interspecific hybridization may lead to the formation of new species having a greater impact on natural ecosystems than the parental species. From the early 1990s, a severe alder (Alnus spp.) decline due to an unknown Phytophthora species was observed in several European countries. Genetic analyses revealed that the disease was caused by the triploid hybrid P. × alni, which originated in Europe from the hybridization of P. uniformis and P. × multiformis. Here, we investigated the population structure of P. × alni (158 isolates) and P. uniformis (85 isolates) in several European countries using microsatellite markers. Our analyses confirmed the genetic structure previously observed in other European populations, with P. uniformis populations consisting of at most two multilocus genotypes (MLGs) and P. × alni populations dominated by MLG Pxa-1. The genetic structure of P. × alni populations in the Czech Republic, Hungary and Sweden seemed to reflect the physical isolation of river systems. Most rare P. × alni MLGs showed a loss of heterozygosity (LOH) at one or a few microsatellite loci compared with other MLGs. This LOH may allow a stabilization within the P. × alni genome or a rapid adaptation to stress situations. Alternatively, alleles may be lost because of random genetic drift in small, isolated populations, with no effect on fitness of P. × alni. Additional studies would be necessary to confirm these patterns of population diversification and to better understand the factors driving it.

• MeSH
• Ecosystem MeSH
• Genetic Variation MeSH
• Genotype MeSH
• Microsatellite Repeats genetics   MeSH
• Plant Diseases MeSH
• Phytophthora * genetics   MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Europe MeSH
• Sweden MeSH

Genetic diversity and population structure studies of local olive germplasm are important to safeguard biodiversity, for genetic resources management and to improve the knowledge on the distribution and evolution patterns of this species. In the present study Algerian olive germplasm was characterized using 16 nuclear (nuSSR) and six chloroplast (cpSSR) microsatellites. Algerian varieties, collected from the National Olive Germplasm Repository (ITAFV), 10 of which had never been genotyped before, were analyzed. Our results highlighted the presence of an exclusive genetic core represented by 13 cultivars located in a mountainous area in the North-East of Algeria, named Little Kabylie. Comparison with published datasets, representative of the Mediterranean genetic background, revealed that the most Algerian varieties showed affinity with Central and Eastern Mediterranean cultivars. Interestingly, cpSSR phylogenetic analysis supported results from nuSSRs, highlighting similarities between Algerian germplasm and wild olives from Greece, Italy, Spain and Morocco. This study sheds light on the genetic relationship of Algerian and Mediterranean olive germplasm suggesting possible events of secondary domestication and/or crossing and hybridization across the Mediterranean area. Our findings revealed a distinctive genetic background for cultivars from Little Kabylie and support the increasing awareness that North Africa represents a hotspot of diversity for crop varieties and crop wild relative species.

• MeSH
• Chloroplasts genetics   MeSH
• Phylogeny * MeSH
• Genetic Variation * MeSH
• Humans MeSH
• Microsatellite Repeats genetics   MeSH
• Olea classification   genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Algeria MeSH
• Italy MeSH
• Morocco MeSH
• Greece MeSH
• Africa, Northern MeSH
• Spain MeSH

Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

• MeSH
• Chromosomes, Plant genetics   MeSH
• Diploidy MeSH
• Polymorphism, Single Nucleotide MeSH
• Quantitative Trait Loci * MeSH
• Chromosome Mapping methods   MeSH
• Microsatellite Repeats MeSH
• Polyploidy MeSH
• Triticum genetics   MeSH
• Sequence Analysis, DNA MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Publication type
• Journal Article MeSH
• Comparative Study MeSH

BACKGROUND: African annual killifishes (Nothobranchius spp.) are adapted to seasonally desiccating habitats (ephemeral pools), surviving dry periods as dormant eggs. Given their peculiar life history, geographic aspects of their diversity uniquely combine patterns typical for freshwater taxa (river basin structure and elevation gradient) and terrestrial animals (rivers acting as major dispersal barriers). However, our current knowledge on fine-scale inter-specific and intra-specific genetic diversity of African annual fish is limited to a single, particularly dry region of their distribution (subtropical Mozambique). Using a widespread annual killifish from coastal Tanzania and Kenya, we tested whether the same pattern of genetic divergence pertains to a wet equatorial region in the centre of Nothobranchius distribution. RESULTS: In populations of Nothobranchius melanospilus species group across its range, we genotyped a part of mitochondrial cytochrome oxidase subunit 1 (COI) gene (83 individuals from 22 populations) and 10 nuclear microsatellite markers (251 individuals from 16 populations). We found five lineages with a clear phylogeographic structure but frequent secondary contact. Mitochondrial lineages were largely congruent with main population genetic clusters identified on microsatellite markers. In the upper Wami basin, populations are isolated as a putative Nothobranchius prognathus, but include also a population from a periphery of the middle Ruvu basin. Other four lineages (including putative Nothobranchius kwalensis) coexisted in secondary contact zones, but possessed clear spatial pattern. Main river channels did not form apparent barriers to dispersal. The most widespread lineage had strong signal of recent population expansion. CONCLUSIONS: We conclude that dispersal of a Nothobranchius species from a wet part of the genus distribution (tropical lowland) is not constrained by main river channels and closely related lineages frequently coexist in secondary contact zones. We also demonstrate contemporary connection between the Ruvu and Rufiji river basins. Our data do not provide genetic support for existence of recently described cryptic species from N. melanospilus complex, but cannot resolve this issue.

• MeSH
• Killifishes genetics   MeSH
• Ecosystem * MeSH
• Phylogeny MeSH
• Phylogeography MeSH
• Genetic Variation * MeSH
• Genetic Drift MeSH
• Microsatellite Repeats MeSH
• DNA, Mitochondrial genetics   MeSH
• Genetics, Population MeSH
• Rivers MeSH
• Electron Transport Complex IV genetics   MeSH
• Fresh Water MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Tanzania MeSH

South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").

• MeSH
• Biodiversity MeSH
• Cyprinidae classification   genetics   MeSH
• Cytochromes b genetics   MeSH
• Demography MeSH
• Phylogeny MeSH
• Genetic Variation MeSH
• Genetic Drift MeSH
• Genotype MeSH
• Microsatellite Repeats MeSH
• DNA, Mitochondrial chemistry   MeSH
• Mitochondria genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Europe MeSH
• Asia, Western MeSH

Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. Its highly polyploid, complex genome has hindered progress in understanding its molecular structure. Flow cytometric sorting and analysis has been used in other important crops with large genomes to dissect the genome into component chromosomes. Here we present for the first time a method to prepare suspensions of intact sugarcane chromosomes for flow cytometric analysis and sorting. Flow karyotypes were generated for two S. officinarum and three hybrid cultivars. Five main peaks were identified and each genotype had a distinct flow karyotype profile. The flow karyotypes of S. officinarum were sharper and with more discrete peaks than the hybrids, this difference is probably due to the double genome structure of the hybrids. Simple Sequence Repeat (SSR) markers were used to determine that at least one allelic copy of each of the 10 basic chromosomes could be found in each peak for every genotype, except R570, suggesting that the peaks may represent ancestral Saccharum sub genomes. The ability to flow sort Saccharum chromosomes will allow us to isolate and analyse chromosomes of interest and further examine the structure and evolution of the sugarcane genome.

• MeSH
• Alleles MeSH
• Cell Cycle drug effects   genetics   MeSH
• Chromosomes, Plant genetics   MeSH
• DNA, Plant metabolism   MeSH
• Fluorescence MeSH
• Genome, Plant * MeSH
• Hydroxyurea pharmacology   MeSH
• Karyotype MeSH
• Kinetics MeSH
• Plant Roots drug effects   MeSH
• Polyploidy * MeSH
• Flow Cytometry methods   MeSH
• Saccharum drug effects   genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH