Current status of human endogenous retrovirus annotation

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Human endogenous retroviruses (HERVs) are integral to the human genome, influencing physiological and pathological processes.
• Inconsistent annotation of HERV elements across public databases hinders research.
• Accurate HERV cataloging is crucial for understanding their biological roles.

Purpose of the Study:

• To conduct a comparative analysis of major HERV annotation resources: DFAM, HERVd, and RepBase.
• To assess the concordance and discrepancies in HERV annotations across these databases.
• To provide recommendations for effective utilization of HERV resources in research.

Main Methods:

• Systematic examination of HERV database content, classification, and postprocessing workflows.
• Comparative analysis of genomic coordinates for HERV element annotations.
• Development of refined matching criteria to reconcile HERV records across databases.

Main Results:

• Substantial discrepancies were found in element counts, genome coverage, and fragmentation strategies due to differing curation methodologies.
• Up to 93% of HERV records can be reconciled across DFAM, HERVd, and RepBase using refined criteria.
• Each database contributes unique HERV elements, underscoring their complementary value.

Conclusions:

• HERV annotation resources exhibit significant variability, impacting research consistency.
• Harmonized standards for retroelement annotation are essential for comprehensive HERV cataloging.
• The study provides practical guidance for researchers utilizing HERV databases and informs future cataloging efforts, including those for new genome assemblies like T2T-CHM13.