Pantoea symbiotica

Citation

Formal styling

Pantoea symbiotica 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:31363

Nomenclature

Rank

Species

Syllabication

sym.bi.o'ti.ca

Etymology

N.L. fem. adj. symbiotica, living together, symbiotic

Nomenclatural type

NCBI Assembly: GCF_900114175.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

This species includes nine genomes that belong to P. symbiotica sp. nov. The clade corresponding to this group is a sister clade of the "P. endophytica" clade. Pairwise ANI between the eight genomes is over 97%, while ANI between them and "P. endophytica" genomes, which represent the most closely related known species, is approximately 93%, showing that these strains do in fact represent a separate species. The strains were isolated from poplar (Populus deltoides) roots along the Caney Fork River in Tennessee, USA; Eastern cottonwood poplar roots on the Yadkin River in North Carolina, USA (Brown et al. 2012); from fungi in New York State, USA (Wong et al. 2020); and as endophytes of grapevine. Based on these isolation sources, this species appears to be adapted to the rhizosphere. The nomenclatural type for the species is the genome of strain YR512^Ts, available under the GenBank assembly accession number GCF_900114175.1.

Classification

Bacteria » Pseudomonadota » Gammaproteobacteria » Enterobacterales » Erwiniaceae » Pantoea » Pantoea symbiotica

Parent

Pantoea ncbi

Genomics

Accession

NCBI Assembly:GCF_900114175.1

Type

Isolate Genome

Estimated Quality Metrics

• Completeness: 99.84%
• Contamination: 0.91%
• Quality: 95.29

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

273.0 ×

Source

• SRA: SRX2156477

Other features

• G+C Content: 54.57%
• Coding Density: 89.24%
• Codon Table: 11
• N50: 402,499 bp
• Contigs: 27
• Largest Contig: 766,167 bp
• Assembly Length: 5,277,081 bp
• Ambiguous Assembly Fraction: 0.011%

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: 1884370
• GTDB Genome: GCF_900114175.1
• 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