Contigs Scaffolding with Hi-C for Plant Genomes

Background

A plant genome provides valuable information to researchers for all kinds of molecular biological studies. In recent years, the development of sequencing technology has allowed faster and more affordable genome sequencing. Nevertheless, chromosome-scale genome sequences are still hard to obtain with only next-generation sequencing (NGS) or long-read sequencing due to some complicated genomic structures, like long interspersed repeats or highly homologous genome blocks. To conquer this, a genetic linkage map or optical map has been applied, to order and orient contigs into chromosome-scale sequences (Yamaguchi et al., 2021). However, the genetic linkage map is labour- and time-consuming in the Plantae kingdom. Meanwhile, the optical map requires a large quantity and high quality of high molecular weight DNA, which makes its production relatively difficult. In contrast, the quickly developed Hi-C scaffolding only requires 100 mg of plant tissue, and short-read sequencing on the NGS platform. This makes the Hi-C scaffolding both tissue- and cost-affordable. However, we need to be aware of the Hi-C library preparation, which will determine the success of the genome scaffolding. Young leaf tissue is commonly used in Hi-C library preparation for plants. Multi-round quality control is recommended during library preparation (Kadota et al., 2020). In particular, small-scale sequencing is highly recommended to evaluate the quality of the library, including the proportion of valid interaction reads, and estimation of the proper read pairs for further deep sequencing. Hi-C scaffolding has become one of the main solutions to obtain chromosome-scale scaffolds, having been widely utilized in recent plant genome sequencing projects. Meanwhile, multiple open-source software have been developed to compute the interact matrix, and order and orient assembled contigs into scaffolds (Table 1). Among these tools, the 3D-DNA pipeline is a widely used software that supports interactively visualizing and manually modifying the scaffolds.

Table 1. Overview of the major Hi-C scaffolding software