Pantoea varia

Citation

Formal styling

Pantoea varia Crosby et al., 2023

Effective publication

Crosby et al., 2023

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:xfaladud (validated)

Cannonical URL

https://seqco.de/i:31357

Nomenclature

Rank

Species

Syllabication

va'ri.a

Etymology

L. fem. adj. varia, varied, corresponding to the varying sources of isolation for members of this species

Nomenclatural type

NCBI Assembly: GCF_900115075.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

This species consists of the genomes of two strains: OV426, isolated during characterization of Populus root and rhizosphere microbial communities in Tennessee, USA, and AF015A5, isolated from an indoor dust sample in Oregon, USA (GCF_004798195.1). The two genomes have a pairwise ANI of approximately 97% and thus clearly belong to the same species. The genome of strain OV426 does not contain the enterobactin biosynthesis cluster, while it does contain the pagRI genes encoding the autoinducer system (Sulja et al. 2022). This strain also contains a Hrp-2a T3SS, but its functionality has not been examined (Moretti et al. 2021). The nomenclatural type for the species is the genome of OV426^Ts, available under the NCBI assembly accession number GCF_900115075.1.

Classification

Bacteria » Pseudomonadota » Gammaproteobacteria » Enterobacterales » Erwiniaceae » Pantoea » Pantoea varia

Parent

Pantoea ncbi

Genomics

Accession

NCBI Assembly:GCF_900115075.1

Type

Isolate Genome

Estimated Quality Metrics

• Completeness: 100.0%
• Contamination: 0.49%
• Quality: 97.55

Ribosomal and transfer RNA genes

• 1 16S rRNA (up to 100.0%)
• 1 23S rRNA (up to 100.0%)
• tRNAs for 18 amino acids

Sequencing depth

269.0 ×

Source

• SRA: SRX2156480

Other features

• G+C Content: 55.18%
• Coding Density: 87.29%
• Codon Table: 11
• N50: 568,987 bp
• Contigs: 12
• Largest Contig: 2,306,547 bp
• Assembly Length: 4,751,258 bp
• Ambiguous Assembly Fraction: 0.012%

Submitter comments

Quality assessed with CheckM v. 1. rRNA prediction performed with barrnap v. 0.9, and tRNA prediction performed with tRNAscan-SE v. 2.0.9.

Automated checks

Complete

See additional details

Metadata

Outside links and data sources

• NCBI Taxonomy: 1881036
• GTDB Genome: GCF_900115075.1
• Global Biodiversity Information Facility (GBIF)

Search sequences

• NCBI Nucleotide
• NCBI Genomes

Local history

• This name was last modified 3 months ago
• Submission process status
• Quality checks before valid publication

Registered by

Palmer, Marike 11 months ago

Submitted by

Palmer, Marike 9 months ago

Curators

• Rodriguez-R, Luis M
• Chuvochina, Maria

Endorsed by

Chuvochina, Maria 9 months ago

Validated by

Rodriguez-R, Luis M 5 months ago