EDGAR 2.0: an enhanced software platform for comparative gene content analyses

Blom, Jochen; Kreis, Julian; Spänig, Sebastian; Juhre, Tobias; Bertelli, Claire; Ernst, Corinna; Goesmann, Alexander

doi:10.1093/nar/gkw255

Cited by 334 publications

(351 citation statements)

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“…This pipeline uses Prodigal [26], RNAMMER [27] and ARAGORN [28] for the prediction of coding sequences, rRNAs, and tRNAs. Functional annotation is realized by a comparison of predicted coding sequences against a database of conserved orthologous groups of the genus Xanthomonas identified by the EDGAR software [29]. Genes that could not be annotated by this approach were compared to a collection of sequence databases comprising Swissprot, Refseq, and Pfam-A [30–32].…”

Section: Methodsmentioning

confidence: 99%

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Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

et al. 2017

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Background Xanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.), X. translucens pv. graminis (Xtg) is one of the most important bacterial pathogens in temperate grassland regions. The genomes of six Xtg strains from Switzerland, Norway, and New Zealand were sequenced in order to gain insight into conserved genomic traits from organisms covering a wide geographical range. Subsequent comparative analysis with previously published genome data of seven non-graminis X. translucens strains including the pathovars arrhenatheri, poae, phlei, cerealis, undulosa, and translucens was conducted to identify candidate genes linked to the host adaptation of Xtg to Italian ryegrass.ResultsPhylogenetic analysis revealed a tight clustering of Xtg strains, which were found to share a large core genome. Conserved genomic traits included a non-canonical type III secretion system (T3SS) and a type IV pilus (T4P), which both revealed distinct primary structures of the pilins when compared to the non-graminis X. translucens strains. Xtg-specific traits that had no homologues in the other X. translucens strains were further found to comprise several hypothetical proteins, a TonB-dependent receptor, transporters, and effector proteins as well as toxin-antitoxin systems and DNA methyltransferases. While a nearly complete flagellar gene cluster was identified in one of the sequenced Xtg strains, phenotypic analysis pointed to swimming-deficiency as a common trait of the pathovar graminis.ConclusionOur study suggests that host adaptation of X. translucens pv. graminis may be conferred by a combination of pathovar-specific effector proteins, regulatory mechanisms, and adapted nutrient acquisition. Sequence deviations of pathogen-associated molecular patterns (PAMPs), as observed for the pilins of the T4P and T3SS, are moreover likely to impede perception by the plant defense machinery and thus facilitate successful host colonization of Italian ryegrass.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3422-7) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

“…Comparative genome analysis was performed using EDGAR 2.0 [29]. The platform employs a bit score related cutoff value, which is generated based on BLAST score ratio values (SRVs) to identify orthologous genes.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

et al. 2017

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“…1, b) [102]. A new version of EDGAR was published recently [103]. The main focus of the analysis of Xanthomonas genomes is usually on virulence factors [66].…”

Section: Genomic Basicsmentioning

confidence: 99%

“…It is particularly useful for RNA-Seq experiments. (b) Comparative genomics is facilitated by EDGAR software [102,103]. Despite being a stand-alone application, it is able to communicate with the well-established genome annotation software GenDB (c) [77], which can be complemented with SAMS for the analysis of shorter DNA sequence data [269].…”

Section: Genomic Basicsmentioning

confidence: 99%

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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“…BLAST ring images were generated using BRIG (Alikhan et al 2011). Genome comparisons were performed in EDGAR (Blom et al 2009;Blom et al 2016). This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JZLL00000000 (Glaeser et al 2016).…”

Section: Analysis Of the Rrf4 Genomementioning

confidence: 99%

Detection and Characterization of Endobacteria in the Fungal Endophyte Piriformospora indica

Glaeser

Alabid

Guo

et al. 2017

Modern Tools and Techniques to Understand Microbes

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The nonpathogenic Alphaproteobacterium Rhizobium radiobacter (syn. Agrobacterium tumefaciens) (RrF4) is a subculture of the endobacterium R. radiobacter, which is intricately associated with its host, the beneficial plantcolonizing fungal basidiomycete Piriformospora indica. RrF4 is genetically very similar to the well-studied plant pathogenic R. radiobacter biovar I strain C58 (genomovar G8). Highly similar genetic content of RrF4 and C58 denotes the high potential for RrF4 to directly interact with plants. The failure to cure P. indica from its endobacterium still hampers a conclusive prediction of the bacterium's extended role in the interaction of the fungus with a broad spectrum of host plants. However, beneficial activities shown in cereals and the Brassicaceae Arabidopsis thaliana were hardly distinguishable when induced either by RrF4 or P. indica. We discuss here the various strategies employed to detect, characterize, and eventually elucidate the endobacterium's role in the tripartite symbiosis with its fungal host and a plant.

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EDGAR 2.0: an enhanced software platform for comparative gene content analyses

Cited by 334 publications

References 33 publications

Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Detection and Characterization of Endobacteria in the Fungal Endophyte Piriformospora indica

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