Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions.

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• High-throughput chromosome conformation capture (Hi-C) is a key technology for de novo genome assembly, enabling highly contiguous genome reconstructions.
• However, the statistical nature of Hi-C can lead to connection errors within the generated scaffolds.
• Orthogonal validation methods are crucial for assessing the structural integrity of Hi-C-based assemblies.

Purpose of the Study:

• To evaluate the structural accuracy of Hi-C scaffolding in de novo genome assemblies.
• To assess the utility of optical mapping as an orthogonal technology for validating Hi-C reconstructions.
• To determine the optimal integration strategy for optical mapping and Hi-C data in genome assembly.

Main Methods:

• Utilized long-read sequencing for initial contig generation.
• Employed Hi-C for scaffolding contigs into larger chromosomal structures.
• Applied optical mapping (Bionano Genomics) to generate genome-wide structural maps for validation.
• Performed manual inspection of discrepancies using raw sequencing and optical map data.

Main Results:

• Identified hundreds of inconsistencies between Hi-C and optical mapping reconstructions across five de novo assemblies.
• Confirmed that Hi-C scaffolding introduced misjoins, connecting both small and large contigs.
• Observed that Hi-C misjoins occurred within annotated genes, impacting gene structure accuracy.
• Demonstrated that optical mapping effectively highlights these widespread Hi-C errors.

Conclusions:

• Optical mapping serves as a critical orthogonal validation tool for Hi-C scaffolding.
• Integrating optical mapping data *after* Hi-C scaffolding significantly improves genome assembly quality.
• This post-scaffolding integration strategy effectively identifies and facilitates the correction of Hi-C-derived misjoins, leading to more accurate genome reconstructions.