The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Ostrovsky, Alexander; Mahmoud, Alexandru; Lonie, Andrew; Syme, Anna; Fouilloux, Anne; Bretaudeau, Anthony; Nekrutenko, Anton; Kumar, Anup; Eschenlauer, Arthur C.; DeSanto, Assunta D; Guerler, Aysam; Serrano-Solano, Beatriz; Batut, Bérénice; Grüning, Björn; Langhorst, Bradley W.; Carr, Bridget; Raubenolt, Bryan; Hyde, Cameron J.; Bromhead, Catherine J; Barnett, Christopher B.; Royaux, Coline; Gallardo, Cristóbal; Blankenberg, Daniel; Fornika, Daniel J; Baker, Dannon; Bouvier, Dave; Clements, D. L.; Morais, David Anderson de Lima; Tabernero, David Lopez; Larivière, Delphine; Nasr, Engy; Afgan, Enis; Zambelli, Federico; Heyl, Florian; Psomopoulos, Fotis; Coppens, Frederik; Price, Gareth; Cuccuru, Gianmauro; Corguillé, Gildas Le; Kuster, Greg Von; Akbulut, Gulsum Gudukbay; Rasche, Helena; Hotz, Hans-Rudolf; Eguinoa, Ignacio; Makunin, Igor V.; Ranawaka, Isuru; Taylor, James; Joshi, Jayadev; Hillman-Jackson, Jennifer; Goecks, Jeremy; Chilton, John; Kamali, Kaivan; Suderman, Keith; Poterlowicz, Krzysztof; Yvan, Le Bras; Lopez-Delisle, Lucille; Sargent, Luke; Bassetti, Madeline E.; Tangaro, M. A.; Beek, Marius van den; Čech, Martin; Bernt, Matthias; Fahrner, Matthias; Tekman, Mehmet; Föll, Melanie Christine; Schatz, Michael C.; Crusoe, Michael R.; Roncoroni, Miguel; Kucher, Natalie; Coraor, Nate; Stoler, Nicholas; Rhodes, Nick; Soranzo, Nicola; Pinter, Niko; Goonasekera, Nuwan; Moreno, Pablo; Videm, Pavankumar; Petera, Mélanie; Mandreoli, Pietro; Jagtap, Pratik; Gu, Qiang; Weber, Ralf; Lazarus, Ross; Vorderman, Ruben H P; Hiltemann, Saskia; Golitsynskiy, Sergey; Garg, Shilpa; Bray, Simon; Gladman, Simon; Leo, Simone; Mehta, Subina; Griffin, Timothy J.; Jalili, Vahid; Vandenbrouck, Yves; Wen, Victor; Nagampalli, Vijay K; Bacon, Wendi; Koning, Willem de; Maier, Wolfgang; Briggs, Peter

doi:10.1093/nar/gkac247

Cited by 669 publications

(302 citation statements)

References 21 publications

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“…Quality control was performed with FastQC and Kraken2 software, within the Galaxy Europe Server [ 22 ]. The draft genomes were de novo assembled in the software CLC Genomics Workbench (Qiagen, Venlo, The Netherlands) and submitted to PathogenWatch ( , accessed on 15 February 2022) [ 23 ] for species identification, determination of sequence type (ST), and detection of antimicrobial resistance and virulence genes.…”

Section: Methodsmentioning

confidence: 99%

Genomic Diversity of NDM-Producing Klebsiella Species from Brazil, 2013–2022

et al. 2022

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Background: Since its first report in the country in 2013, NDM-producing Enterobacterales have been identified in all the Brazilian administrative regions. In this study, we characterized by antimicrobial susceptibility testing and by molecular typing a large collection of NDM-producing Klebsiella isolates from different hospitals in Brazil, mainly from the state of Sao Paulo, over the last decade. Methods: Bacterial isolates positive for blaNDM-genes were identified by MALDI-TOF MS and submitted to antimicrobial susceptibility testing by disk diffusion or broth microdilution (for polymyxin B). All isolates were submitted to pulsed-field gel electrophoresis, and isolates belonging to different clusters were submitted to whole genome sequencing by Illumina technology and downstream analysis. Mating out assays were performed by conjugation, plasmid sizes were determined by S1-PFGE, and plasmid content was investigated by hybrid assembly after MinIon long reads sequencing. Results: A total of 135 NDM-producing Klebsiella were identified, distributed into 107 different pulsotypes; polymyxin B was the only antimicrobial with high activity against 88.9% of the isolates. Fifty-four isolates presenting diversified pulsotypes were distributed in the species K. pneumoniae (70%), K. quasipneumoniae (20%), K. variicola (6%), K. michiganensis (a K. oxytoca Complex species, 2%), and K. aerogenes (2%); blaNDM-1 was the most frequent allele (43/54, 80%). There was a predominance of Clonal Group 258 (ST11 and ST340) encompassing 35% of K. pneumoniae isolates, but another thirty-one different sequence types (ST) were identified, including three described in this study (ST6244 and ST6245 for K. pneumoniae, and ST418 for K. michiganensis). The blaNDM-1 and blaNDM-7 were found to be located into IncF and IncX3 type transferable plasmids, respectively. Conclusions: Both clonal (mainly driven by CG258) and non-clonal expansion of NDM-producing Klebsiella have been occurring in Brazil in different species and clones, associated with different plasmids, since 2013.

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Section: Methodsmentioning

confidence: 99%

Genomic Diversity of NDM-Producing Klebsiella Species from Brazil, 2013–2022

et al. 2022

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“…These and other analyses were performed on the UC-Riverside High Performance Computing Cluster, the Galaxy Platform [93], or dedicated local workstations. To identify markers for linkage analysis, Illumina reads were trimmed using Sickle (github.com/najoshi/sickle) using default settings.…”

Section: Chromosome-scale Assemblymentioning

confidence: 99%

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly

Matson

Liang²,

Lonardi³

et al. 2022

PLoS Pathog

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Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.

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“…For ChIP-sequencing, the analysis was performed using the Galaxy tool (v 22.05) ( ) ( Galaxy Community, 2022 ). Briefly, after the FastQC quality check, the paired-end reads were aligned to the reference Candida albicans SC5314 genome (assembly GCA_000182965.3) using Bowtie 2 (Galaxy Version 2.4.4), and the generated BAM files were filtered with Filter BAM (-q=20) (Galaxy Version SAMTOOLS: 1.8).…”

Section: Methodsmentioning

confidence: 99%

Effects of Hst3p inhibition in Candida albicans: a genome-wide H3K56 acetylation analysis

Conte

Eletto

Pannetta

et al. 2022

Front. Cell. Infect. Microbiol.

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Candida spp. represent the third most frequent worldwide cause of infection in Intensive Care Units with a mortality rate of almost 40%. The classes of antifungals currently available include azoles, polyenes, echinocandins, pyrimidine derivatives, and allylamines. However, the therapeutical options for the treatment of candidiasis are drastically reduced by the increasing antifungal resistance. The growing need for a more targeted antifungal therapy is limited by the concern of finding molecules that specifically recognize the microbial cell without damaging the host. Epigenetic writers and erasers have emerged as promising targets in different contexts, including the treatment of fungal infections. In C. albicans, Hst3p, a sirtuin that deacetylates H3K56ac, represents an attractive antifungal target as it is essential for the fungus viability and virulence. Although the relevance of such epigenetic regulator is documented for the development of new antifungal therapies, the molecular mechanism behind Hst3p-mediated epigenetic regulation remains unrevealed. Here, we provide the first genome-wide profiling of H3K56ac in C. albicans resulting in H3K56ac enriched regions associated with Candida sp. pathogenicity. Upon Hst3p inhibition, 447 regions gain H3K56ac. Importantly, these genomic areas contain genes encoding for adhesin proteins, degradative enzymes, and white-opaque switching. Moreover, our RNA-seq analysis revealed 1330 upregulated and 1081 downregulated transcripts upon Hst3p inhibition, and among them, we identified 87 genes whose transcriptional increase well correlates with the enrichment of H3K56 acetylation on their promoters, including some well-known regulators of phenotypic switching and virulence. Based on our evidence, Hst3p is an appealing target for the development of new potential antifungal drugs.

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Cited by 669 publications

References 21 publications

Genomic Diversity of NDM-Producing Klebsiella Species from Brazil, 2013–2022

Genomic Diversity of NDM-Producing Klebsiella Species from Brazil, 2013–2022

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly

Effects of Hst3p inhibition in Candida albicans: a genome-wide H3K56 acetylation analysis

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