Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

摘要

Background: Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomicscale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genomesequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number.Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from thestandpoint of genome scaffolding. Results: To gain insight into the best practice of Hi-C scaffolding, we performed amultifaceted methodological comparison using vertebrate samples and optimized various factors during samplepreparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-Cscaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restrictionenzyme(s), and the choice of scaffolding program and its usage. Conclusions: This study provides the first comparison ofmultiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party.We introduce a customized protocol designated “inexpensive and controllable Hi-C (iconHi-C) protocol,” which incorporatesthe optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences ofthe Chinese softshell turtle Pelodiscus sinensis.