Tracing foreign sequences in plant transcriptomes and genomes using OCT4, a POU domain protein

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Computational Biology

Background:

• Contaminants in sequencing data, particularly reference genomes and transcriptomes, introduce errors into downstream analyses.
• Such contaminants can misrepresent the molecular basis of biological interactions.
• POU domain proteins are a family of proteins not previously reported in plants and fungi.

Purpose of the Study:

• To report the presence of plant transcriptomes contaminated with RNAs encoding POU domain proteins.
• To identify foreign DNA sequences within plant reference genomes and draft genomes.
• To highlight the implications of such contaminations for genomic and transcriptomic research.

Main Methods:

• Bioinformatic analysis of plant transcriptome and genome sequencing data.
• Identification and characterization of foreign RNA and DNA sequences.
• Comparative genomics to trace the origin of contaminant sequences.

Main Results:

• A significant number of plant transcriptomes were found to be contaminated with RNAs encoding POU domain proteins.
• The reference genome of Rhodamnia argentea contained four POU domain protein-coding sequences of arthropod origin.
• Draft genomes of Humulus lupulus and Cannabis sativa contained complete rDNA sequences from Tetranychus species (arthropods).

Conclusions:

• Foreign fragments, including arthropod-related sequences, are present in plant sequencing data.
• These contaminants can be misidentified as endogenous elements, impacting biological interpretation.
• Thorough screening of sequencing data for contaminants before public release and checking existing genomes is crucial.