Chromosome Scaffolding of Diploid Genomes Using ALLHiC

Background

Construction of a chromosome-scale assembly is a step-by-step process, including generating a contig-level assembly and linking contigs into scaffolds or chromosomes by long-range linking information, such as optical maps, 10× Genomics Linked-Reads, or Hi-C (Zhang et al., 2019; Zhang et al., 2020a). Hi-C (Lieberman-Aiden et al., 2009) is a technology derived from 3C (Chromosome Conformation Capture) technology integrated with next-generation sequencing, which serves as an economical and robust method widely used in many genome projects (Dudchenko et al., 2017; Zhang et al., 2020b). Hi-C can capture many chromatin proximities in parallel and span a long distance of genomic regions, even separated by >200 Mb. Hence, based on proximity information from Hi-C, contigs can be linked into chromosome-scale assemblies with great clarity.

In the past decade, several Hi-C scaffolding algorithms have been developed, including LACHESIS (Burton et al., 2013), SALSA (Ghurye et al., 2017), and 3D-DNA (Dudchenko et al., 2017). Our team also developed a Hi-C scaffolding algorithm, namely ALLHiC. Although initially designed for chromosome phasing in polyploid genomes (Zhang et al., 2019), ALLHiC also shows capability for chromosome-scale assembly in diploid genomes. Here, we describe a pipeline for chromosome scaffolding of diploid genomes by ALLHiC, from an initial contig-level assembly to a high-quality chromosomal-scale assembly (Figure 1). This pipeline uses the Hi-C paired-end reads to generate a mosaic genome assembly of diploids and provides a method to correct chimeric scaffolds. Moreover, this pipeline has been successfully applied in the diploid chromosome scaffolding in the banyan tree (Zhang et al., 2020b) and oolong tea genomes (Zhang et al., 2021).

Figure 1. Workflow of our pipeline of chromosome-scale scaffolding using ALLHIC.