Hi-C Assisted Genome Assembly
Description
The Hi-C technology is a novel technique that combines chromatin conformation capture with high-throughput sequencing. This method cross-links and enriches DNA fragments that are far apart linearly but close in spatial structure, followed by pair-end sequencing. By analyzing the sequencing data, it is possible to reveal the interactions between different DNA regions of the chromatin, thereby deducing the three-dimensional spatial structure of the genome and potential regulatory relationships between genes.
Characteristics of Hi-C:
- 90% of data is mapped to chromosomes
- Does not require population data
- Time-efficient and labor-saving compared to genetic maps
- Intelligent automated scaffolding algorithms
Principle of Hi-C Technology
The Hi-C library preparation and sequencing experiment uses the in situ Hi-C type, which mainly includes the following steps: cell cross-linking, restriction enzyme digestion, end repair, ligation, DNA purification and capture, and next-generation sequencing.
Applications of Hi-C Technology
- Hi-C assisted genome assembly
- Hi-C chromatin structure variation detection
- Hi-C chromatin interaction studies
Advantages of Hi-C Assisted Genome Assembly
- No Need for Population Data: Chromosome Positioning with a Single Individual
Many species, including most higher animals, wild plants, trees, and fruit trees, cannot be used to construct genetic populations. Hi-C achieves chromosome positioning by leveraging differences in interaction frequencies caused by spatial versus linear distances on the chromosomes, thus eliminating the need for a genetic population.
- Higher Marker Density and More Complete Sequence Localization
Compared to genetic maps, the interaction frequencies between chromatin provide a higher marker density. This dense map allows for the accurate placement of both long and short scaffolds. With Hi-C technology, it is generally possible to map over 90% of the genome sequence to chromosomes.
- Error Correction of Assembled Genomes
Interaction frequencies between scaffolds can be used to correct errors in already assembled genome sequences.
Analysis Content
Data Statistics and Filtering
Hi-C Library Assessment
Hi-C Chromosome Positioning
✓ Chromosome grouping of assembled sequences
✓ Ordering within each group of assembled sequences
✓ Orientation within each group of assembled sequences
Statistical Evaluation After Hi-C Positioning
✓ Evaluation against reference genomes of closely related species
✓ Assessment of genetic markers
