Nejvíce citovaný článek - PubMed ID 11411692
Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites
Genetic variability of Phoma sorghina, a ubiquitous facultative phytopathogen, was investigated on 41 isolates cultivated from surface-sterilized sorghum grains originating from South Africa and Texas; pearl millet isolates from Namibia were also included. Most of the isolates from Texas produced intense red pigments, especially on Czapek-Dox agar plates. Many African isolates formed conspicuous dark radial substrate hyphae with intercalated chlamydospores on oatmeal plates. Conidial dimensions and shape were very variable (mean lengths 4.5-5.7 microm). Haplotypes were defined based on 53 markers from banding patterns obtained with rep-PCR (primers: M13core, ERIC IR). The shared geographic origin was partially reflected in the clades of the haplotype phylogram. The values of G(ST) were intermediate; 16-37 % of the variation was found between the populations. Nm values of gene flow were 0.84-1.15. Average gene diversity H(E) was moderate (0.256). Sequences of ITS-rDNA were obtained from 21 isolates. Allele 1 was found in 9 isolates scattered throughout the clades, allele 2 occurred in 6 isolates (5 of them from the same clade), alleles 3 and 4 were shared by two isolates each and two isolates were unique. Alleles 1 and 2 were also found among highly related sequences from GenBank. All shared an 8-bp deletion near the 5' end of ITS2 that was not found in any other Phoma/Didymella species and which may be a typical marker for P. sorghina. Among related species, members of legume-associated Ascochyta/Didymella complex, Epicoccum spp., D. applanata and P. glomerata were found.
- MeSH
- alely MeSH
- Ascomycota klasifikace genetika izolace a purifikace MeSH
- DNA fungální genetika MeSH
- fylogeneze MeSH
- genetická variace MeSH
- jedlá semena mikrobiologie MeSH
- mezerníky ribozomální DNA genetika MeSH
- molekulární sekvence - údaje MeSH
- ribozomální DNA genetika MeSH
- Sorghum mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Jihoafrická republika MeSH
- Texas MeSH
- Názvy látek
- DNA fungální MeSH
- mezerníky ribozomální DNA MeSH
- ribozomální DNA MeSH
Leishmaniasis is a geographically widespread severe disease, with an increasing incidence of two million cases per year and 350 million people from 88 countries at risk. The causative agents are species of Leishmania, a protozoan flagellate. Visceral leishmaniasis, the most severe form of the disease, lethal if untreated, is caused by species of the Leishmania donovani complex. These species are morphologically indistinguishable but have been identified by molecular methods, predominantly multilocus enzyme electrophoresis. We have conducted a multifactorial genetic analysis that includes DNA sequences of protein-coding genes as well as noncoding segments, microsatellites, restriction-fragment length polymorphisms, and randomly amplified polymorphic DNAs, for a total of approximately 18,000 characters for each of 25 geographically representative strains. Genotype is strongly correlated with geographical (continental) origin, but not with current taxonomy or clinical outcome. We propose a new taxonomy, in which Leishmania infantum and L. donovani are the only recognized species of the L. donovani complex, and we present an evolutionary hypothesis for the origin and dispersal of the species. The genus Leishmania may have originated in South America, but diversified after migration into Asia. L. donovani and L. infantum diverged approximately 1 Mya, with further divergence of infraspecific genetic groups between 0.4 and 0.8 Mya. The prevailing mode of reproduction is clonal, but there is evidence of genetic exchange between strains, particularly in Africa.
- MeSH
- biologická evoluce * MeSH
- časové faktory MeSH
- genetické markery MeSH
- Leishmania donovani klasifikace genetika MeSH
- vznik druhů (genetika) MeSH
- zeměpis * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- genetické markery MeSH
BACKGROUND: Despite the medical importance of trichomoniasis, little is known about the genetic relatedness of Trichomonas vaginalis strains with similar biological characteristics. Furthermore, the distribution of endobionts such as mycoplasmas or Trichomonas vaginalis virus (TVV) in the T. vaginalis metapopulation is poorly characterised. RESULTS: We assayed the relationship between 20 strains of T. vaginalis from 8 countries using the Random Amplified Polymorphic DNA (RAPD) analysis with 27 random primers. The genealogical tree was constructed and its bootstrap values were computed using the program FreeTree. Using the permutation tail probability tests we found that the topology of the tree reflected both the pattern of resistance to metronidazole (the major anti-trichomonal drug) (p < 0.01) and the pattern of infection of strains by mycoplasmas (p < 0.05). However, the tree did not reflect pattern of virulence, geographic origin or infection by TVV. Despite low bootstrap support for many branches, the significant clustering of strains with similar drug susceptibility suggests that the tree approaches the true genealogy of strains. The clustering of mycoplasma positive strains may be an experimental artifact, caused by shared RAPD characters which are dependent on the presence of mycoplasma DNA. CONCLUSIONS: Our results confirmed both the suitability of the RAPD technique for genealogical studies in T. vaginalis and previous conclusions on the relatedness of metronidazol resistant strains. However, our studies indicate that testing analysed strains for the presence of endobionts and assessment of the robustness of tree topologies by bootstrap analysis seem to be obligatory steps in such analyses.
- MeSH
- druhová specificita MeSH
- fenotyp MeSH
- fylogeneze MeSH
- lidé MeSH
- Mycoplasma genetika izolace a purifikace MeSH
- mykoplazmové infekce genetika MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- polymorfismus genetický genetika MeSH
- protozoální DNA genetika MeSH
- RNA-viry genetika izolace a purifikace MeSH
- technika náhodné amplifikace polymorfní DNA metody MeSH
- trichomonádová vaginitida genetika MeSH
- Trichomonas vaginalis genetika mikrobiologie patogenita virologie MeSH
- virulence genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- protozoální DNA MeSH