Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Genome scaffolding is essential for chromosome-level assembly.
• High-throughput chromatin conformation capture (Hi-C) is a common scaffolding method.
• Haplotype-resolved genomes offer deeper genetic insights into variations.

Purpose of the Study:

• To develop a reference-independent allele-aware scaffolding tool.
• To improve chromosome assignment and contig ordering/orientation.
• To analyze challenges in allele-aware scaffolding.

Main Methods:

• Developed HapHiC, a novel allele-aware scaffolding tool.
• Performed comprehensive analyses of factors affecting scaffolding.
• Applied HapHiC to construct a haplotype-resolved allotriploid genome.

Main Results:

• HapHiC demonstrates superior performance in chromosome assignment and contig manipulation.
• Identified key challenges and adverse factors in allele-aware scaffolding.
• Successfully assembled the haplotype-resolved allotriploid genome of Miscanthus × giganteus.

Conclusions:

• HapHiC overcomes limitations of existing tools like ALLHiC.
• Provides a robust method for reference-independent haplotype-resolved genome assembly.
• Facilitates genomic studies of complex polyploid species.