Differences in GenBank and RefSeq annotations may affect genomics data interpretation for Pseudomonas putida KT2440

Area of Science:

• Genomics
• Bioinformatics
• Microbial Systems Biology

Background:

• Genomic feature annotations are crucial for omics analyses in organisms like Pseudomonas putida KT2440.
• The GenBank and RefSeq annotated genomes of P. putida KT2440 are widely used but stem from different prediction pipelines.
• Discrepancies between these annotation resources can be overlooked and introduce biases.

Purpose of the Study:

• To systematically compare genomic features between GenBank and RefSeq annotations for P. putida KT2440.
• To quantify the extent of discrepancies in predicted genomic positions of open reading frames (ORFs).
• To assess the impact of these annotation differences on high-throughput omics data analysis, specifically RNAseq.

Main Methods:

• Systematic comparison of P. putida KT2440 genome annotations from GenBank and RefSeq.
• Identification and quantification of differences in predicted genomic positions for shared open reading frames (ORFs).
• Processing of RNAseq expression datasets using both GenBank and RefSeq annotations to evaluate impact on results.

Main Results:

• Approximately 16% of P. putida KT2440 open reading frames (ORFs) exhibit different predicted genomic positions between GenBank and RefSeq annotations.
• These positional discrepancies were observed despite the ORFs sharing equivalent locus tag codes.
• Analysis of RNAseq data revealed that annotation differences can significantly affect the outcomes of high-throughput omics analyses.

Conclusions:

• Significant discrepancies exist between popular P. putida KT2440 genome annotation resources (GenBank vs. RefSeq).
• These differences can lead to overlooked pitfalls and affect the interpretation of omics data, impacting reproducibility.
• Awareness of annotation resource caveats is essential for transparent and reliable P. putida research and potentially other prokaryotes.