Article

Letunic I, Bork P.. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
Bioinformatics (Impact Factor: 4.98). 02/2007; 23(1):127-8. DOI: 10.1093/bioinformatics/btl529
Source: PubMed

ABSTRACT

Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees
can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be
mapped onto the tree. Export to several bitmap and vector graphics formats is supported.

Availability: iTOL is available at http://itol.embl.de

Contact: bork{at}embl.de

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    • "Then, the phylogenetic trees of aligned AP2-ERF proteins were constructed using CLC Genomics Workbench via the Neighbor-Joining (NJ) method with the following parameters: WAG protein substitution model, gamma distribution, and bootstrap (1,000). The constructed phylogenetic trees were visualized with ITOL (Letunic and Bork, 2007). Amino acid composition of the AP2-ERF proteins was calculated by using MEGA 6.0.1. "
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    ABSTRACT: Apetala2-ethylene-responsive element binding factor (AP2-ERF) superfamily with common AP2-DNA binding domain have developmentally and physiologically important roles in plants. Since common bean genome project has been completed recently, it is possible to identify all of the AP2-ERF genes in the common bean genome. In this study, a comprehensive genome-wide in silico analysis identified 180 AP2-ERF superfamily genes in common bean (Phaseolus vulgaris). Based on the amino acid alignment and phylogenetic analyses, superfamily members were classified into four subfamilies: DREB (54), ERF (95), AP2 (27) and RAV (3), as well as one soloist. The physical and chemical characteristics of amino acids, interaction between AP2-ERF proteins, cis elements of promoter region of AP2-ERF genes and phylogenetic trees were predicted and analyzed. Additionally, expression levels of AP2-ERF genes were evaluated by in silico and qRT-PCR analyses. In silico micro-RNA target transcript analyses identified nearly all PvAP2-ERF genes as targets of by 44 different plant species’ miRNAs were identified in this study. The most abundant target genes were PvAP2/ERF-20-25-62-78-113-173. miR156, miR172 and miR838 were the most important miRNAs found in targeting and BLAST analyses. Interactome analysis revealed that the transcription factor PvAP2-ERF78, an ortholog of Arabidopsis At2G28550, was potentially interacted with at least 15 proteins, indicating that it was very important in transcriptional regulation. Here we present the first study to identify and characterize the AP2-ERF transcription factors in common bean using whole-genome analysis, and the findings may serve as a references for future functional research on the transcription factors in common bean. © 2015, Leibniz Research Centre for Working Environment and Human Factors. All rights reserved.
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    • "The alignment was filtered using the greengenes lanemask. Phylogenetic analysis was performed using FastTree (Price, Dehal and Arkin 2010), and the online tool iTOL was used for tree visualization (Letunic and Bork 2007). The OTU map generated in QIIME using the result of usearch qf was used for further diversity analyses. "
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    ABSTRACT: The springtail Folsomia candida is an important model organism for soil ecology, ecotoxicology and ecogenomics. The decomposer activities of soil invertebrates like Folsomia depend on their relationship with microbial communities including gut symbionts. In this paper, we apply high-throughput sequencing to provide a detailed characterization of the bacterial community associated with parthenogenetic F. candida. First, we evaluated a method to suppress the amplification of DNA from the endosymbiont Wolbachia, to prevent it from interfering with the identification of less abundant Operational Taxonomic Units (OTUs). The suppression treatment applied was effective against Wolbachia and did not interfere with the detection of the most abundant OTUs (59 OTUs, contributing over 87% of the reads). However, this method did affect the inferred community composition. Significant differences were subsequently observed in the composition of bacterial communities associated with two different strains of F. candida. A total of 832 OTUs were found, of which 45% were only present in one strain and 17% only in the other. Among the 20 most abundant OTUs 16 were shared between strains. Denaturing Gradient Gel Electrophoresis (DGGE) and clone libraries, although unable to capture the full diversity of the bacterial community, provided results that supported the NGS data.
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    • ", 2014 ) . The dendrograms were created in Mega6 and edited in iTOL ( Letunic and Bork , 2007 ; Tamura et al . , 2013 ) . "
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    ABSTRACT: Multiple studies confirm laccase role in fungal pathogenicity and lignocellulose degradation. In spite of broad genomic research, laccases from plant wilt pathogen Fusarium oxysporum are still not characterized. The study aimed to identify F. oxysporum genes that may encode laccases sensu stricto and to characterize the proteins in silico in order to facilitate further research on their impact on the mentioned processes. Twelve sequenced F. oxysporum genomes available on Broad Institute of Harvard and MIT (2015) website were analyzed and three genes that may encode laccases sensu stricto were found. Their amino acid sequences possess all features essential for their catalytic activity, moreover, the homology models proved the characteristic 3D laccase structures. The study shades light on F. oxysporum as a new source of multicopper oxidases, enzymes with possible high redox potential and broad perspective in biotechnological applications.
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