RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Li, Wenjun; O’Neill, Kathleen; Haft, Daniel H.; DiCuccio, Michael; Chetvernin, Vyacheslav; Badretdin, Azat; Coulouris, George; Chitsaz, Farideh; Derbyshire, Myra K.; Durkin, A. Scott; Gonzales, Noreen R.; Gwadz, Marc; Lanczycki, Christopher J.; Song, Jakyoung; Thanki, Narmada; Wang, Jiyao; Yamashita, Roxanne A.; Yang, Mei‐Jie; Chen, Zheng; Marchler‐Bauer, Aron; Thibaud‐Nissen, Françoise

doi:10.1093/nar/gkaa1105

Cited by 704 publications

(554 citation statements)

References 26 publications

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“…For the public projects, EDGAR has to rely on findable and accessible annotations. To ensure maximal comparability, EDGAR3.0 uses the RefSeq annotations, as all genomes in RefSeq are re-annotated using the latest version of the PGAP pipeline ( 31 ). For private projects, EDGAR has to rely on the genomes provided by the users.…”

Section: Discussionmentioning

confidence: 99%

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

Dieckmann

Beyvers

Nkouamedjo-Fankep

et al. 2021

Nucleic Acids Research

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The EDGAR platform, a web server providing databases of precomputed orthology data for thousands of microbial genomes, is one of the most established tools in the field of comparative genomics and phylogenomics. Based on precomputed gene alignments, EDGAR allows quick identification of the differential gene content, i.e. the pan genome, the core genome, or singleton genes. Furthermore, EDGAR features a wide range of analyses and visualizations like Venn diagrams, synteny plots, phylogenetic trees, as well as Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI) matrices. During the last few years, the average number of genomes analyzed in an EDGAR project increased by two orders of magnitude. To handle this massive increase, a completely new technical backend infrastructure for the EDGAR platform was designed and launched as EDGAR3.0. For the calculation of new EDGAR3.0 projects, we are now using a scalable Kubernetes cluster running in a cloud environment. A new storage infrastructure was developed using a file-based high-performance storage backend which ensures timely data handling and efficient access. The new data backend guarantees a memory efficient calculation of orthologs, and parallelization has led to drastically reduced processing times. Based on the advanced technical infrastructure new analysis features could be implemented including POCP and FastANI genomes similarity indices, UpSet intersecting set visualization, and circular genome plots. Also the public database section of EDGAR was largely updated and now offers access to 24,317 genomes in 749 free-to-use projects. In summary, EDGAR 3.0 provides a new, scalable infrastructure for comprehensive microbial comparative gene content analysis. The web server is accessible at http://edgar3.computational.bio.

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Section: Discussionmentioning

confidence: 99%

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

Dieckmann

Beyvers

Nkouamedjo-Fankep

et al. 2021

Nucleic Acids Research

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“…The majority was retrieved from NCBI RefSeq. 16 However, 80 datasets were only identified through a literature survey, as they did not have an associated genome assembly deposited. In total, 28 studies were identified spanning 16 countries (Figure 1A and B, Table S1).…”

Section: Resultsmentioning

confidence: 99%

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

Viehweger

Blumenscheit

Lippman

et al. 2021

Preprint

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Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening more than ten thousand genomes, 500 thousand metagenomes, and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available.

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“…No plasmid was detected. The sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP), version March 2021 (Li et al, 2021). The genome was found to contain 5 258 ORFs, among which there are 5 158 CDSs (CoDing Sequences), 74 tRNAs, 22 rRNAs, 3 ncRNAs and 1 tmRNA.…”

Section: Genome Announcementmentioning

confidence: 99%

High-quality complete genome resource of tomato rhizosphere strain Pseudomonas donghuensis P482, a representative of a species with biocontrol activity against plant pathogens

Krzyżanowska

Iwanicki

Czajkowski

et al. 2021

Preprint

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Strain P482 was isolated from a tomato rhizosphere and classified as Pseudomonas donghuensis. The P. donghuensis species was first established in 2015 and currently comprises only four strains: P482, HYST, SVBP6, and 22G5. P. donghuensis strains antagonize plant pathogens, including bacteria, fungi and oomycetes, and therefore are of high interest regarding their biological control potential to combat plant diseases. The antimicrobial activity of P. donghuensis P482 is based on the production of iron scavenging compound 7-hydroxytropolone, antifungal volatile organic compounds, and yet unidentified secondary metabolite(s). Here, we report a complete genome resource for P. donghuensis strain P482. The genome consists of a single chromosome (5 656 185 bp) with 5258 ORFs (5158 protein-coding genes, 74 tRNAs, 22 rRNAs, 3 ncRNAs and 1 tmRNA) and no plasmid. We believe that the information of the first high-quality, complete genome of P. donghuensis will provide resources for analyses targeting the biological control potential of this species and understanding the traits essential for plant-microbe interaction.

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RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Cited by 704 publications

References 26 publications

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

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

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

High-quality complete genome resource of tomato rhizosphere strain Pseudomonas donghuensis P482, a representative of a species with biocontrol activity against plant pathogens

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