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. 2023 Jan 10;12(2):320.
doi: 10.3390/plants12020320.

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

Luca Marcolungo  1 , Leonardo Vincenzi  1 , Matteo Ballottari  1 , Michela Cecchin  1 , Emanuela Cosentino  2 , Thomas Mignani  1 , Antonina Limongi  1 , Irene Ferraris  1 , Matteo Orlandi  1 , Marzia Rossato  1   2 , Massimo Delledonne  1   2
Affiliations

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

Luca Marcolungo et al. Plants (Basel). .

Abstract

High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the structural solidity of Hi-C reconstructed scaffolds. Optical maps were used to assess the correctness of five de novo genome assemblies based on long-read sequencing for contig generation and Hi-C for scaffolding. Hundreds of inconsistencies were found between the reconstructions generated using the Hi-C and optical mapping approaches. Manual inspection, exploiting raw long-read sequencing data and optical maps, confirmed that several of these conflicts were derived from Hi-C joining errors. Such misjoins were widespread, involved the connection of both small and large contigs, and even overlapped annotated genes. We conclude that the integration of optical mapping data after, not before, Hi-C-based scaffolding, improves the quality of the assembly and limits reconstruction errors by highlighting misjoins that can then be subjected to further investigation.

Keywords: Hi-C; assembly refinement; de novo genome assembly; optical mapping.

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Conflict of interest statement

Author E.C. is an employee of Genartis srl. Authors M.R. and M.D. are partners of Genartis srl. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Example of inconsistency between optical maps and Hi-C-derived scaffolds in the H. lacustris assembly. (A) Alignment to the NGS assembly scaffolded with Hi-C. Red and green arrows indicate the incongruence points in the BspQI and the BssSI maps, respectively. (B) Raw Bionano molecules aligned on the two maps involved in the conflict.
Figure 2
Figure 2
Integrative Genome Browser of two junction regions identified as potential errors by optical maps. ONT data mapped to the Hi-C-scaffolded H. lacustris genome show either (A) no reads spanning the contig junction or (B) reads spanning the junction but highlighting the incorrect gap size.
Figure 3
Figure 3
Integrative Genome Browser, visualisation of long PacBio, reads aligned on an OM/Hi-C conflict identified on the L. albus genome assemblies. (A) PacBio reads aligned on the PacBio + Hi-C + OM (after anchoring) assembly support the OM-based reconstruction. (B) PacBio reads aligned on the PacBio + Hi-C assembly do not support the HiC-based reconstruction.
See this image and copyright information in PMC

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