EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure

Dieckmann, Marius Alfred; Beyvers, Sebastian; Nkouamedjo-Fankep, Rudel Christian; Hanel, Patrick; Jelonek, Lukas; Blom, Jochen; Goesmann, Alexander

doi:10.1093/nar/gkab341

Cited by 97 publications

(94 citation statements)

References 33 publications

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“…The core genome of A. hydrophila strains was determined using the web server EDGAR version 3.0 (Web Server) https://edgar3.computational.bio.uni-giessen.de/ ( Dieckmann et al, 2021 ). This bioinformatics tool is based on ‘score ratio values’ (SRVs) methodology for orthology estimation.…”

Section: Methodsmentioning

confidence: 99%

Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

et al. 2021

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Aeromonas are Gram-negative rods widely distributed in the environment. They can cause severe infections in fish related to financial losses in the fish industry, and are considered opportunistic pathogens of humans causing infections ranging from diarrhea to septicemia. The objective of this study was to determine in silico the contribution of genomic islands to A. hydrophila. The complete genomes of 17 A. hydrophila isolates, which were separated into two phylogenetic groups, were analyzed using a genomic island (GI) predictor. The number of predicted GIs and their characteristics varied among strains. Strains from group 1, which contains mainly fish pathogens, generally have a higher number of predicted GIs, and with larger size, than strains from group 2 constituted by strains recovered from distinct sources. Only a few predicted GIs were shared among them and contained mostly genes from the core genome. Features related to virulence, metabolism, and resistance were found in the predicted GIs, but strains varied in relation to their gene content. In strains from group 1, O Ag biosynthesis clusters OX1 and OX6 were identified, while strains from group 2 each had unique clusters. Metabolic pathways for myo-inositol, L-fucose, sialic acid, and a cluster encoding QueDEC, tgtA5, and proteins related to DNA metabolism were identified in strains of group 1, which share a high number of predicted GIs. No distinctive features of group 2 strains were identified in their predicted GIs, which are more diverse and possibly better represent GIs in this species. However, some strains have several resistance attributes encoded by their predicted GIs. Several predicted GIs encode hypothetical proteins and phage proteins whose functions have not been identified but may contribute to Aeromonas fitness. In summary, features with functions identified on predicted GIs may confer advantages to host colonization and competitiveness in the environment.

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Section: Methodsmentioning

confidence: 99%

Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

et al. 2021

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“…Further database comparisons were implemented to improve functional interpretation of the genome sequence, e.g., PhiBase [34], CAZy [35], KAAS [36], and antiSMASH fungal version 6.0 [37]. In the last step, isolates 1/2/21 and O8/2 were compared to the highly aggressive AG1-IB isolate 7/3/14 by means of the comparative genomics tool EDGAR 3.0 [38][39][40]. To calculate the relatedness between the R. solani AG1-IB isolates, other R. solani strains and the related fungi Coprinopsis cinerea okayama 7#130 [41], Piriformospora indica DSM 11827 [42], and Cryptococcus neoformans var.…”

Section: Genome Analysis Comparative Genomics and Phylogeneticsmentioning

confidence: 99%

Genome Analyses of the Less Aggressive Rhizoctonia solani AG1-IB Isolates 1/2/21 and O8/2 Compared to the Reference AG1-IB Isolate 7/3/14

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et al. 2021

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Rhizoctonia solani AG1-IB of the phylum Basidiomycota is known as phytopathogenic fungus affecting various economically important crops, such as bean, rice, soybean, figs, cabbage and lettuce. The isolates 1/2/21 and O8/2 of the anastomosis group AG1-IB originating from lettuce plants with bottom rot symptoms represent two less aggressive R. solani isolates, as confirmed in a pathogenicity test on lettuce. They were deeply sequenced on the Illumina MiSeq system applying the mate-pair and paired-end mode to establish their genome sequences. Assemblies of obtained sequences resulted in 2092 and 1492 scaffolds, respectively, for isolate 1/2/21 and O8/2, amounting to a size of approximately 43 Mb for each isolate. Gene prediction by applying AUGUSTUS (v. 3.2.1.) yielded 12,827 and 12,973 identified genes, respectively. Based on automatic functional annotation, genes potentially encoding cellulases and enzymes involved in secondary metabolite synthesis were identified in the AG1-IB genomes. The annotated genome sequences of the less aggressive AG1-IB isolates were compared with the isolate 7/3/14, which is highly aggressive on lettuce and other vegetable crops such as bean, cabbage and carrot. This analysis revealed the first insights into core genes of AG1-IB isolates and unique determinants of each genome that may explain the different aggressiveness levels of the strains.

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“…We report here the averages of the reciprocal comparisons obtained on http://enve-omics.ce.gatech.edu/ani/ ( Rodriguez-R and Konstantinidis, 2016 ). Moreover, a phylogenomic tree of the 14 Streptomyces strains under study, as well as eight additional well characterized pathogenic Streptomyces species was built using EDGAR 3.0 ( Dieckmann et al, 2021 ). Streptomyces griseolus NRRL B-2925 T , a non-pathogenic Streptomyces species was used as an outgroup.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of Potato Common Scab-Causing Streptomyces spp. Displaying Varying Virulence

et al. 2021

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Common scab of potato causes important economic losses worldwide following the development of necrotic lesions on tubers. In this study, the genomes of 14 prevalent scab-causing Streptomyces spp. isolated from Prince Edward Island, one of the most important Canadian potato production areas, were sequenced and annotated. Their phylogenomic affiliation was determined, their pan-genome was characterized, and pathogenic determinants involved in their virulence, ranging from weak to aggressive, were compared. 13 out of 14 strains clustered with Streptomyces scabiei, while the last strain clustered with Streptomyces acidiscabies. The toxicogenic and colonization genomic regions were compared, and while some atypical gene organizations were observed, no clear correlation with virulence was observed. The production of the phytotoxin thaxtomin A was also quantified and again, contrary to previous reports in the literature, no clear correlation was found between the amount of thaxtomin A secreted, and the virulence observed. Although no significant differences were observed when comparing the presence/absence of the main virulence factors among the strains of S. scabiei, a distinct profile was observed for S. acidiscabies. Several mutations predicted to affect the functionality of some virulence factors were identified, including one in the bldA gene that correlates with the absence of thaxtomin A production despite the presence of the corresponding biosynthetic gene cluster in S. scabiei LBUM 1485. These novel findings obtained using a large number of scab-causing Streptomyces strains are challenging some assumptions made so far on Streptomyces’ virulence and suggest that other factors, yet to be characterized, are also key contributors.

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EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure

Cited by 97 publications

References 33 publications

Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

Prediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila

Genome Analyses of the Less Aggressive Rhizoctonia solani AG1-IB Isolates 1/2/21 and O8/2 Compared to the Reference AG1-IB Isolate 7/3/14

Comparative Genomics of Potato Common Scab-Causing Streptomyces spp. Displaying Varying Virulence

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