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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies.

David A Yarmosh¹, Juan G Lopera¹, Nikhita P Puthuveetil¹

¹American Type Culture Collection (ATCC), Manassas, Virginia, USA.

|May 2, 2022

Summary

Public microbial genomics data often lack quality and traceability. This study reveals significant issues in NCBI RefSeq bacterial genome assemblies, highlighting the need for authenticated data and improved accountability for reliable research.

Keywords:

DNA sequencing bioinformatics comparative studies culture collection data provenance genome analysis genome authentication genomes genomics microbial genomics

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Area of Science:

Microbial genomics
Bioinformatics
Data science

Background:

Public genomics data are crucial for life sciences research.
Current microbial genome databases like NCBI RefSeq lack strict requirements for data provenance and authenticity of source materials.
This can impact the reliability of microbial genomics research.

Purpose of the Study:

To assess the quality, traceability, and provenance of microbial genome data.
To compare newly assembled ATCC standard reference genomes (ASRGs) with existing NCBI RefSeq assemblies.
To highlight issues in data accuracy and provenance in public microbial genomics resources.

Main Methods:

De novo assembly of 1,113 bacterial genome references from authenticated American Type Culture Collection (ATCC) materials.
Comparative genomics analysis between ASRGs and corresponding NCBI RefSeq bacterial genome assemblies.
Evaluation of metadata completeness, including sample source, sequencing technology, and bioinformatics methods.

Main Results:

Significant issues found in NCBI RefSeq bacterial genome assemblies regarding completeness, mutations, structure, and metadata.
Nearly half of RefSeq assemblies lack essential details on sample source, sequencing technology, or bioinformatics methods.
Widespread discrepancies in genome assembly quality, genetic variability, and metadata completeness were observed.

Conclusions:

Gaps in metadata accuracy and data provenance are a major challenge in microbial genomics research.
There is a need for increased accountability for data depositors and higher quality expectations for reference genome data.
Ensuring data authentication and provenance is critical for the reliability of microbial genomics research.