TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers

Slabbinck, Bram; Dawyndt, Peter; Martens, Miet; Vos, Paul De; Baets, Bernard De

doi:10.1093/bioinformatics/btn031

Cited by 55 publications

(59 citation statements)

References 2 publications

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“…In addition, this gene combination recognised all 34 Russula species. This conclusion was also supported by the analysis using TaxonGap (Slabbinck et al 2008) and SpeciesIdentifier in TaxonDNA (Meier et al 2006), as shown in Table 2. Second, the PCR amplification and sequencing success rates were relatively higher in ITS and rpb2 (88.1% in Table 3).…”

Section: Discussionsupporting

confidence: 62%

“…Similarity matrices were calculated using the MegAlign program in DNAStar v7.1 (Lasergene, WI, USA) and the resulting output was analysed and visualised in TaxonGap 2.4.1 (Slabbinck et al 2008). The intra-and inter-specific pairwise distances were analysed in MEGA 7.0.26 with Kimura's two-parameter (K2P) model (Kumar et al 2016) and SpeciesIdentifier 1.8 in TaxonDNA (Meier et al 2006).…”

Section: Comparison Of Intra-and Inter-specific Divergencementioning

confidence: 99%

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A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

Zhao

Zhang

et al. 2018

Mycology

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Russula is a worldwid genus which has a high species diversity . Aiming accurate and rapid species identification, candidate genes nLSU (28S), ITS, tef-1α, mtSSU, rpb1, and rpb2, were analysed as potential DNA barcodes. This analysis included 433 sequences from 38 well-circumscribed Russula species of eight subgenera. Two vital standards were analysed for success species identification using DNA barcodes, specifically inter-and intra-specific variations together with the success rates of PCR amplification and sequencing. Although the gap between inter-and intra-specific variations was narrow, ITS met the qualification standards for a target DNA barcode. Overlapping inter-and intra-specific pairwise distances were observed in nLSU, tef-1α, mtSSU, and rpb2. The success rates of PCR amplification and sequencing in mtSSU and rpb1 were lower than those of others. Gene combinations were also investigated for resolution of species recognition. ITS-rpb2 was suggested as the likely target DNA barcode for Russula, owing to the two viatal standards above. Since nLSU has the lowest minimum of inter-specific variation, and tef-1α has the highest overlap between intra-and inter-species variations among the candidate genes, they are disqualified from the selection for DNA barcode of Russula. ARTICLE HISTORY

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Section: Discussionsupporting

confidence: 62%

Section: Comparison Of Intra-and Inter-specific Divergencementioning

confidence: 99%

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

Zhao

Zhang

et al. 2018

Mycology

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“…A partition homogeneity test (PHT) was performed with 1000 replicates in PAUP 4.0b10 [41] to evaluate statistical congruence between sequence data from EF-1α and RPB2 gene regions. The aligned sequences of each gene and the combined EF-1α and RPB2 genes were analyzed using DNAstar 7.1.0 (Lasergene, USA) to calculate the similarity matrices and then illustrate the intra-and inter-specific variations of the candidate barcode loci for each of the 19 species tested in this study, using a visualization analysis tool, TaxonGap 2.4.1 [42]. As suggested by Martens et al [43], Nectria pseudotrichia was designated as the outgroup in the analysis.…”

Section: Comparison Of Intra-and Inter-specific Divergencesmentioning

confidence: 99%

“…The successful species identification of a DNA barcode requires a clear distinction between intra-and inter-specific divergences [47]. The intraand inter-specific variations of the candidate DNA barcode regions for each of the 19 Neonectria species generated using TaxonGap [42] indicated that the EF-1α gene provided a somewhat better resolution compared with the ITS, β-tubulin, and RPB2 genes (Figure 1). For the EF-1α gene, the smallest inter-specific variation was 1.7%, which is shown as a thin and black line in Figure 1.…”

Section: Selection Of Dna Barcode Markers For Neonectriamentioning

confidence: 99%

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Zhao

Luo

Zhuang

et al. 2011

Sci. China Life Sci.

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To determine a suitable DNA barcode for the genus Neonectria, the internal transcribed spacer rDNA, β-tubulin, EF-1α, and RPB2 genes were selected as candidate markers. A total of 205 sequences from 19 species of the genus were analyzed. Intraand inter-specific divergences and the ease of nucleotide sequence acquisition were treated as criteria to evaluate the feasibility of a DNA barcode. Our results indicated that any single gene among the candidate markers failed to serve as a successful barcode, while the combination of the partial EF-1α and RPB2 genes recognized all species tested. We tentatively propose the combined partial EF-1α and RPB2 genes as a DNA barcode for the genus. During this study, two cryptic species were discovered, based on the combined data of morphology and DNA barcode information. We described and named these two new species N. ditissimopsis and N. microconidia. intra-specific variation, inter-specific variation, morphology, DNA barcode, sequence analysis Citation:Zhao P, Luo J, Zhuang W Y, et al. DNA barcoding of the fungal genus Neonectria and the discovery of two new species . Sci China Life Sci, 2011, 54: 664 -674,

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“…TaxonGap analysis (Slabbinck et al, 2008) was performed on type strains representing the different subgroups of the Pseudomonas fluorescens group. TaxonGap allows visual comparison of the discriminatory power of different biomarkers to differentiate a set of operational taxonomic units (OTUs), but also for their abilities to differentiate members constituting an OTU.…”

Section: Selection Of the Rpod Gene To Differentiate Pseudomonasmentioning

confidence: 99%

An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media

et al. 2013

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The last decade has shown an increased interest in the utilization of bacteria for applications ranging from bioremediation to wastewater purification and promotion of plant growth. In order to extend the current number of micro-organism mediated applications, a continued quest for new agents is required. This study focused on the genus Pseudomonas, which is known to harbour strains with a very diverse set of interesting properties. The aim was to identify growth media that allow retrieval of a high Pseudomonas diversity, as such increasing the chance of isolating isolates with beneficial properties. Three cultivation media: trypticase soy agar (TSA), potato dextrose agar (PDA) and Pseudomonas isolation agar (PIA) were evaluated for their abilities to grow Pseudomonas strains. TSA and PDA were found to generate the largest Pseudomonas diversity. However, communities obtained with both media overlapped. Communities obtained with PIA, on the other hand, were unique. This indicated that the largest diversity is obtained by sampling from either PDA or TSA and from PIA in parallel. To evaluate biodiversity of the isolated Pseudomonas members on the media, an appropriate biomarker had to be identified. Hence, an introductory investigation of the taxonomic resolution of the 16S rRNA, rpoD, gyrB and rpoB genes was performed. The rpoD gene sequences not only had a high phylogenetic content and the highest taxonomic resolution amongst the genes investigated, it also had a gene phylogeny that related well with that of the 16S rRNA gene.

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TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers

Abstract: Graphical User Interface; Executable JAVA archive file, source code, supplementary information and sample files can be downloaded from the website: http://www.kermit.ugent.be/taxongap

Cited by 55 publications

References 2 publications

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

An rpoD gene sequence based evaluation of cultured Pseudomonas diversity on different growth media

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