We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively.The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists. .
- MeSH
- Databases, Genetic MeSH
- Species Specificity MeSH
- Karyotype MeSH
- Karyotyping MeSH
- Evolution, Molecular MeSH
- DNA, Ribosomal genetics MeSH
- RNA, Ribosomal, 5S genetics MeSH
- RNA, Ribosomal genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
BACKGROUND: Loaches of the family Nemacheilidae are one of the most speciose elements of Palearctic freshwater ichthyofauna and have undergone rapid ecological adaptations and colonizations. Their cytotaxonomy is largely unexplored; with the impact of cytogenetical changes on this evolutionary diversification still unknown. An extensive cytogenetical survey was performed in 19 nemacheilid species using both conventional (Giemsa staining, C- banding, Ag- and Chromomycin A3/DAPI stainings) and molecular (fluorescence in situ hybridization with 5S rDNA, 45S rDNA, and telomeric (TTAGGG)n probes) methods. A phylogenetic tree of the analysed specimens was constructed based on one mitochondrial (cytochrome b) and two nuclear (RAG1, IRBP) genes. RESULTS: Seventeen species showed karyotypes composed of 2n = 50 chromosomes but differentiated by fundamental chromosome number (NF = 68-90). Nemachilichthys ruppelli (2n = 38) and Schistura notostigma (2n = 44-48) displayed reduced 2n with an elevated number of large metacentric chromosomes. Only Schistura fasciolata showed morphologically differentiated sex chromosomes with a multiple system of the XY1Y2 type. Chromomycin A3 (CMA3)- fluorescence revealed interspecific heterogeneity in the distribution of GC-rich heterochromatin including its otherwise very rare association with 5S rDNA sites. The 45S rDNA sites were mostly located on a single chromosome pair contrasting markedly with a pattern of two (Barbatula barbatula, Nemacheilus binotatus, N. ruppelli) to 20 sites (Physoschistura sp.) of 5S rDNA. The cytogenetic changes did not follow the phylogenetic relationships between the samples. A high number of 5S rDNA sites was present in species with small effective population sizes. CONCLUSION: Despite a prevailing conservatism of 2n, Nemacheilidae exhibited a remarkable cytogenetic variability on microstructural level. We suggest an important role for pericentric inversions, tandem and centric fusions in nemacheilid karyotype differentiation. Short repetitive sequences, genetic drift, founder effect, as well as the involvement of transposable elements in the dispersion of ribosomal DNA sites, might also have played a role in evolutionary processes such as reproductive isolation. These remarkable dynamics of their genomes qualify river loaches as a model for the study of the cytogenetic background of major evolutionary processes such as radiation, endemism and colonization of a wide range of habitats.
- MeSH
- Phylogeny MeSH
- Heterochromatin * MeSH
- In Situ Hybridization, Fluorescence MeSH
- Karyotyping veterinary MeSH
- Cypriniformes classification genetics MeSH
- Rivers MeSH
- DNA, Ribosomal genetics MeSH
- DNA Transposable Elements MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Cílem práce bylo zhodnotit molekulárně genetickými metodami (MGM) spektrum původců dermatofytóz na území České republiky s rozdělením podle hlavních klinických forem. Během dvou let (červenec 2011 až červen 2013) bylo na šesti regionálních pracovištích zachyceno 3235 kultivačně pozitivních vzorků s dermatofyty. Nejvyšší počet izolátů pocházel z případů tinea unguium (55,5 %), dále t. corporis (29,2 %), t. pedis (14,6 %) a t. capitis (0,7 %). Druhová identifikace izolátů všech druhů (n = 672) s výjimkou Trichophyton rubrum (n = 2 563) byla provedena MGM (PCR-fingerprinting nebo sekvenace ITS oblasti rDNA). Pro T. rubrum byla molekulárně ověřena jen identifikace morfologicky nejednoznačných izolátů (n = 189). Celkem bylo identifikováno 14 druhů dermatofytů, přičemž nejvýznamnější změnou oproti minulosti bylo vysoké zastoupení zoofilního druhu Arthroderma benhamiae, který působil velkou část případů t. corporis (22,9 %) a t. capitis (29,2 %). Geofilní druhy působily jen 1,3 % všech infekcí, přestože se jednalo o druhově nejpočetnější skupinu, ve které byly odhaleny dva nepopsané druhy a také přehlížené druhy Microsporum persicolor a M. fulvum. Klíčová slova: Arthroderma benhamiae – DNA sekvenace – geofilní dermatofyty – ITS oblast rDNA – PCR-fingerprinting – tinea capitis – tinea corporis – tinea pedis – tinea unguium – zoofilní dermatofyty
The aim of the study was to evaluate the spectrum of causative agents of the main clinical forms of dermatophytoses in the Czech Republic by molecular genetic methods (MGM). During two years (from July 2011 to June 2013), 3255 cultivation specimens were positive for dermatophytes. The highest number of specimens was isolated from tinea unguinum (55,5%), then tinea corporis (29,2%), tinea pedis (14,6%) and tinea capitis (0,7%). The identification of isolated species (n = 672) except for Trichophytom rubrum (n = 2563) was performed by MGM (PCR fingerprinting or sequencing of ITS segments of rDNA). For T. rubrum only morphologically non-clear isolates were identified (n = 189). In total, 14 species of dermatophytes were identified. The most important change noticed compared to previous results was an increased detection of Arthroderma benhamiae in the cases of tinea corporis (22,9%) and tinea capitis (29,2%). Geophilic species caused only 1,3% of all infections even if this group comprised the highest number of species with two newly described ones and also Microsporum persicolor and M. fulvum wich are usually overlooked in the morphological examination. Key words: Arthroderma benhamiae – DNA sequencing – geophilic dermatopytes – ITS region of rDNA – PCR-fingerprinting – tinea capitis – tinea corporis – tinea pedis – tinea unguinum – zoophilic dermatophytes
- Keywords
- Arthroderma benhamiae, zoofilní dermatofyty, tinea unguium, tinea corporis, PCR-fingerprinting, ITS oblast rDNA, geofilní dermatofyty, Trichophyton rubrum,
- MeSH
- Arthrodermataceae genetics isolation & purification classification MeSH
- Dermatomycoses * epidemiology genetics microbiology MeSH
- DNA Fingerprinting MeSH
- DNA, Fungal analysis MeSH
- DNA Primers diagnostic use MeSH
- Species Specificity MeSH
- Fungi * genetics isolation & purification classification MeSH
- Humans MeSH
- Microsporum genetics isolation & purification classification MeSH
- Mycological Typing Techniques methods MeSH
- Polymerase Chain Reaction MeSH
- DNA, Ribosomal MeSH
- Sequence Analysis, DNA MeSH
- Tinea Capitis epidemiology genetics microbiology MeSH
- Tinea Pedis epidemiology genetics microbiology MeSH
- Tinea * epidemiology genetics microbiology MeSH
- Trichophyton genetics isolation & purification classification MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Female MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
Sekvenování genů 16S, 18S a ITS regionů se stalo jedním z nejdůležitějších nástrojů v molekulární diagnostice, zejména v oblasti mikrobiologie, patologie a soudního lékařství. Výše zmíněné geny, obsahující konzervované i variabilní oblasti, jsou hojně využívány pro taxonomické zařazení bakterií a eukaryot. Sekvenování 16S rDNA umožňuje detekci bakteriálních infekcí, zatímco sekvenace ITS regionů a 18S rDNA je využívána při identifikaci mykotických, případně parazitárních infekcí, a to především v případech, kdy tradiční metody selhávají. Tento článek se zaměřuje na rozšířené možnosti těchto metod, jejich uplatnění v klinické diagnostice a výzkumu, zkoumá výhody a nevýhody, a diskutuje potenciální budoucí vývoj v oblasti technologie sekvenování nové generace (NGS).
Gene sequencing of 16S, 18S, and ITS regions is a crucial tool in molecular diagnostics, especially in microbiology, pathology and forensic medicine. These genes contain conserved and variable regions and are widely used for the taxonomic classification of bacteria and eukaryotes. Sequencing of 16S rDNA helps detect bacterial infections, while sequencing of ITS regions and 18S rDNA is used to identify fungal or parasitic infections, especially when traditional methods are ineffective. This article focuses on the expanded possibilities of these methods, their application in clinical diagnostics and research, their advantages and disadvantages, and discusses potential future developments in the field of next-generation sequencing (NGS) technology.
- Keywords
- Internal Transcribed Spacers, 16S rDNA, 18S rDNA,
- MeSH
- Molecular Diagnostic Techniques classification methods MeSH
- DNA, Bacterial analysis genetics classification MeSH
- DNA analysis genetics classification ultrastructure MeSH
- Communicable Diseases * diagnosis genetics MeSH
- Humans MeSH
- High-Throughput Nucleotide Sequencing * classification methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Review MeSH
Uvádíme kazuistiku kožní mykotické infekce typu tinea corporis u čtyřicetileté ženy. Ložisko infekce bylo lokalizované na hřbetu levé ruky a nereagovalo na úvodní lokální léčbu ciklopiroxolaminem. Změna léčby na systémovou terapii terbinafinem byla spojena s výskytem nežádoucích účinků a musela být ukončena. Ložisko bylo úspěšně vyléčeno kombinací lokálních antimykotik naftifinu a natamycinu. Jako původce infekce byl izolován zástupce geofilních dermatofytů Microsporum incurvatum, který je poměrně vzácně izolován z klinického materiálu a pravděpodobně žádný případ infekce zatím nebyl popsán v České republice. Identifikace izolátu byla ověřena sekvenací oblasti ITS rDNA. Vzhledem k morfologické podobnosti s druhy M. gypseum a M. fulvum je možné, že část infekcí přisuzovaných těmto druhům je ve skutečnosti působena právě M. incurvatum. Dále se v článku diskutuje o kontroverzní taxonomii druhu spolu s možnostmi, jak je možné ho rozlišit od příbuzných druhů. Klíčová slova: Arthroderma – ciklopiroxolamin – dermatofytózy – naftifin – natamycin – terbinafin
We present a case of mycotic infection of tinea corporis type in a forty-year old woman. The lesion was localised on the dorsal aspect of the left hand and did not react to ciclopirox olamine. The systemic therapy by terbinafine was stopped because of its side effects. The lesion was treated successfully with local antimycotics naftifine and natamycin. The geophillic dermatophyte Microsporum incurvatum was isolated and verified by the sequencing of ITS rDNA. This dermatophyte is rarely isolated from clinical material and probably no case was described in the Czech Republic. It is possible that some infections caused by M. incurvatum are attributed to M. gypseum and M. fulvum due to morphologic similarity of these species. The controversial taxonomy of this species and possibility of its differentiation from other species is discussed as well. Key words: Arthroderma – ciclopirox olamine– dermatophytoses – naftifine – natamycin – terbinafine
- Keywords
- ciklopiroxolamin, naftifin, dermatofytózy,
- MeSH
- Allylamine analogs & derivatives therapeutic use MeSH
- Anti-Bacterial Agents therapeutic use MeSH
- Antifungal Agents * therapeutic use MeSH
- Anti-Infective Agents, Local therapeutic use MeSH
- Arthrodermataceae genetics isolation & purification classification MeSH
- DNA, Fungal MeSH
- Adult MeSH
- Enzyme Inhibitors adverse effects therapeutic use MeSH
- Drug Therapy, Combination MeSH
- Humans MeSH
- Microsporum * genetics isolation & purification classification MeSH
- Naphthalenes adverse effects therapeutic use MeSH
- Natamycin therapeutic use MeSH
- Pyridones adverse effects therapeutic use MeSH
- DNA, Ribosomal MeSH
- Hand MeSH
- Sequence Analysis, DNA MeSH
- Terbinafine MeSH
- Terminology as Topic MeSH
- Tinea * diagnosis drug therapy MeSH
- Check Tag
- Adult MeSH
- Humans MeSH
- Female MeSH
- Publication type
- Case Reports MeSH
- Research Support, Non-U.S. Gov't MeSH
