Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Repetitive DNA sequences are prevalent across all life forms.
• These sequences pose significant challenges in genome sequencing, assembly, and gene annotation.
• Existing genome and protein databases may contain unacknowledged errors stemming from repetitive DNA handling.

Purpose of the Study:

• To review the problems associated with tandem repeats throughout the genome data workflow.
• To highlight how these issues propagate into public databases.
• To raise awareness among database users and creators about data integrity.

Main Methods:

• Literature review of challenges in handling repetitive DNA sequences.
• Analysis of the sequencing-assembly-annotation-deposition workflow.
• Case studies including the Atlantic cod genome and other species with propagated errors.

Main Results:

• Tandem repeats cause errors at multiple stages of genome data generation and curation.
• These errors can lead to unreliable data in public repositories, impacting research.
• The Atlantic cod genome assembly was notably affected by a high frequency of tandem repeats.

Conclusions:

• Errors originating from repetitive DNA are widespread in public genomic databases.
• Improved handling of repetitive sequences is crucial for accurate genome assembly and annotation.
• Scientists must be aware of potential data inaccuracies and the biological significance of repetitive elements.