Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites.

Hampl, Vladimı́r; Pavlı́ček, Adam; Flegr, Jaroslav

doi:10.1099/00207713-51-3-731

Cited by 306 publications

(201 citation statements)

References 15 publications

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“…The matrices were created with the help of PyElph 1.4 software [15] and were assembled in Microsoft Excel. An UPGMA (Unweighted Pair Group Method with Arithmetic Mean [21]) dendrogram was constructed based on a Jaccard's similarity coefficient into FreeTree 0.9.1.50 [6]. Statistical analyses were conducted in FAMD 1.3 (Fingerprint Analysis with Missing Data) software [19].…”

Section: Discussionmentioning

confidence: 99%

RAPD-inferred genetic variability of some indigenousRhizobium leguminosarumisolates from red clover (Trifolium pratenseL.) nodules

Stefan

Roșu

Stedel

et al. 2015

Acta Biologica Hungarica

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The application of commercial rhizobial inoculants to legume crops is proving to be an alternative to synthetic fertilizer use. The challenge for sustainable agriculture resides in the compatibility between crop, inoculants and environmental conditions. The evaluation of symbiotic efficiency and genetic diversity of indigenous rhizobial strains could lead to the development of better inoculants and increased crop production. The genetic variability of 32 wild indigenous rhizobial isolates was assessed by RAPD (Random Amplified Polymorphic DNA). The strains were isolated from red clover (Trifolium pratense L.) nodules from two distinct geographical regions of Northern and Eastern Romania. Three decamer primers were used to resolve the phylogenetic relationships between the investigated isolates. Cluster analysis revealed a high diversity; most strains clustered together based on their geographical location.

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Section: Discussionmentioning

confidence: 99%

RAPD-inferred genetic variability of some indigenousRhizobium leguminosarumisolates from red clover (Trifolium pratenseL.) nodules

Stefan

Roșu

Stedel

et al. 2015

Acta Biologica Hungarica

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“…Program POPGENE 1.32 (Yeh et al, 1999) was used to calculate the percentage of polymorphic loci. Pairwise genetic distance matrix between individuals was obtained by the Jaccard similarity index, and used to construct the Neighborjoining dendrogram with the program FreeTree (Hampl et al, 2001) and MEGA 6.0 (Tamura et al, 2013). Scatter plot of principal coordinates was constructed using the programs DistPCOA (Legendre &Anderson, 1998) andStatistica 7.1 (StatSoft, 2005).…”

mentioning

confidence: 99%

Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker

et al. 2015

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The genetic diversity of the specimens of four natural populations of Arapaima from Araguaia-Tocantins basin was assessed within and among these stocks, using five primers for ISSR. COI (cytochrome c oxidase subunit I) partial sequences confirmed that the specimens belongs to Arapaima gigas. The ISSR provided 168 loci, of which 165 were polymorphic. However, the number of loci for each population and expected heterozygosity values were low. AMOVA showed 52.63% intra-population variation and 47.37% inter-population variation. The F ST was high among all populations (F ST ≥ 0.25), however, the cluster analysis (PCoA) and Bayesian inference showed three major groups: Araguaiana-MT + São Félix do Araguaia-MT, Novo Santo Antônio-MT and Itupiranga-PA. The genetic distance was not correlated with geographical distance. The ISSR marker revealed that the populations of the Araguaia-Tocantins are structured and have a low genetic diversity. These are the first data from a population analysis using molecular markers for A. gigas of Araguaia-Tocantins basins and may be used to define the best management strategies and conservation projects for this species.A diversidade genética dos espécimes de quatro populações naturais de Arapaima coletados na bacia do Araguaia-Tocantins foi avaliada com base em cinco primers para marcadores moleculares ISSR. A sequência parcial do COI (cytochrome c oxidase subunit I) confirmou que os espécimes pertencem à espécie Arapaima gigas. Os ISSR forneceram 168 loci, dos quais 165 polimórficos. No entanto, para cada população, os valores de heterozigosidade esperada foram baixos. A AMOVA mostrou 52,63% de variação intrapopulacional e 47,37% interpopulacional. O F ST foi alto entre todas as populações (F ST ≥ 0,25); entretanto, a análise de agrupamento e a inferência Bayesiana mostraram três grandes grupos: Araguaiana-MT + São Félix do Araguaia-MT, Novo Santo Antônio-MT e Itupiranga-PA. A distância genética não teve correlação com a distância geográfica. Os ISSRs se mostraram eficientes para determinar a diversidade genética para a A. gigas, revelando que as populações da bacia Araguaia-Tocantins estão estruturadas e com baixa diversidade genética. Estes são os primeiros dados de análise populacional utilizando ISSR para A. gigas da bacia Araguaia-Tocantins e poderão ser utilizados para definir as melhores estratégias de manejo e projetos de conservação dessa espécie.

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“…Isolates for which satisfactory amplification was not obtained with all primers were removed from the data matrix. This binary data matrix was then used for phenetic analysis (NJ and UPGMA) on FreeTree (Pavlicek et al 1999;Hampl et al 2001) and for analyses of molecular variance (AMOVA). The robustness of the phenetic trees was tested with bootstrapping and jackknifing methods.…”

Section: Rapd Amplification and Fingerprinting Analysismentioning

confidence: 99%

Genetic diversity of sterile culturedTrebouxiaphotobionts associated with the lichen-forming fungusXanthoria parietinavisualized with RAPD-PCR fingerprinting techniques

Nyati

Werth

Honegger³

2013

The Lichenologist

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Photobiont diversity within populations of Xanthoria parietina was studied at the species level by means of ITS analyses and at the subspecific level with fingerprinting techniques (RAPD-PCR) applied to sterile cultured algal isolates. Populations from coastal, rural and urban sites from NW, SW and central France and from NE Switzerland were investigated. Between 8 and 63 samples per population, altogether 150 isolates, were subjected to phenetic and ordination analyses. Epiphytic samples of X. parietina associated with different genotypes of Trebouxia decolorans but saxicolous samples contained T. arboricola. For comparison the T. gelatinosa photobiont of a small population of Teloschistes chrysophthalmus (4 samples) was investigated. ITS sequences of T. decolorans isolates from different geographic locations were largely similar. In all populations a surprisingly high diversity of genotypes was observed in Trebouxia isolated from lichen thalli growing side by side. As Trebouxia spp. are assumed to be asexually reproducing haplonts, the genetic background of this diversity is discussed. Fingerprinting techniques are a powerful tool for obtaining valuable insights into the genetic diversity within the algal partner of lichen-forming fungi at the population level, provided that sterile cultured isolates are available.

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Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites.

Cited by 306 publications

References 15 publications

RAPD-inferred genetic variability of some indigenousRhizobium leguminosarumisolates from red clover (Trifolium pratenseL.) nodules

RAPD-inferred genetic variability of some indigenousRhizobium leguminosarumisolates from red clover (Trifolium pratenseL.) nodules

Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker

Genetic diversity of sterile culturedTrebouxiaphotobionts associated with the lichen-forming fungusXanthoria parietinavisualized with RAPD-PCR fingerprinting techniques

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