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Updated: Apr 10, 2026
Author Spotlight: Identifying Compensatory Pathways in Malaria Parasites Containing Hypomorphic Allele of Essential Protein Kinases
Published on: November 22, 2024
Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26
Zhi-Yong Tao1, Xu Sui2,3,4, Cao Jun5,6,7
1Department of Parasitology, Bengbu Medical College, Bengbu, People's Republic of China. Bengbucity@163.com.
Abstract:
We found a 47 aa protein sequence that occurs 17 times in the Plasmodium vivax nucleotide database published on PlasmoDB. Coding sequence analysis showed multiple restriction enzyme sites within the 141 bp nucleotide sequence, and a His6 tag attached to the 3' end, suggesting cloning vector origins. Sequences with vector contamination were submitted to NCBI, and BLASTN was used to cross-examine whole-genome shotgun contigs (WGS) from four recently deposited P. vivax whole genome sequencing projects. There are at least 26 genes listed in the PlasmoDB database that incorporate this cloning vector sequence into their predicted provisional protein products.
Insights
A Plasmodium vivax protein sequence was found to be contaminated with cloning vector DNA. This contamination affects at least 26 Plasmodium vivax genes in the PlasmoDB database.
Area of Science:
- Malariology
- Genomics
- Bioinformatics
Background:
- A 47 amino acid (aa) protein sequence was identified 17 times within the Plasmodium vivax nucleotide database on PlasmoDB.
- Analysis revealed multiple restriction enzyme sites and a His6 tag in the 141 bp nucleotide sequence, indicating potential cloning vector origins.
Discussion:
- Vector contamination in genomic data can lead to misinterpretation of gene products.
- Cross-examination of whole-genome shotgun contigs (WGS) from recent P. vivax sequencing projects confirmed the presence of this vector sequence.
- The identified vector sequence is incorporated into the predicted protein products of at least 26 genes in PlasmoDB.
Key Insights:
- Discovery of cloning vector DNA contamination within the Plasmodium vivax genome database.
- Identification of specific vector sequences impacting multiple gene annotations.
- Highlighting the need for rigorous data validation in parasitic disease genomics.
Outlook:
- Recommendations for improved data curation and quality control in Plasmodium databases.
- Implications for future genomic studies of Plasmodium vivax and other parasitic organisms.
- Potential for re-annotation of affected Plasmodium vivax genes to remove vector sequences.
