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Related Concept Videos

Genomic DNA in Prokaryotes00:46

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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A practical guide on environmental genomics for prokaryotic systematics.

Nathan M Ernster1, Luis M Rodriguez-R2

  • 1Department of Microbiology, University of Innsbruck, Innsbruck, Austria.

Systematic and Applied Microbiology
|August 6, 2025
PubMed
Summary

The Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) provides standards for naming uncultivated prokaryotes using DNA sequences. This guide aids new users in metagenomics and systematics, improving data communication.

Keywords:
MetagenomicsNomenclatureSeqCodeTaxonomy

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Area of Science:

  • Microbial ecology
  • Genomics
  • Bioinformatics

Background:

  • Environmental shotgun sequencing and single-cell amplified genomes (SAGs) yield vast microbial data.
  • Many recovered genomes lack valid names due to uncultivability and traditional nomenclature challenges.
  • This hinders communication and data usability in microbial genomics.

Purpose of the Study:

  • To provide a guide for new users in metagenomics and systematics.
  • To clarify topics including genome quality, taxonomy, and nomenclature.
  • To promote the adoption of standardized nomenclature for uncultivated prokaryotes.

Main Methods:

  • Review of metagenomic pipelines and genome quality assessment criteria.
  • Discussion of taxonomy and trait prediction tools.
  • Explanation of source metadata, abundance measurement, and nomenclature registration.

Main Results:

  • The Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) offers a framework for naming prokaryotes from sequence data.
  • SeqCode incorporates genome quality criteria and nomenclature standards.
  • Standardized nomenclature is essential for effective communication and data integration.

Conclusions:

  • Validly naming uncultivated prokaryotes using SeqCode is crucial for advancing microbial genomics.
  • Community efforts in generating high-quality, named genomes will enhance data usability.
  • Standardized nomenclature facilitates scientific communication and data sharing in environmental genomics.