The Chromatin Interaction Based Anchoring Of Scaffolds In Arabidopsis Thaliana

For recent progress in next-generation sequencing technologies, DNA sequencing is more efficiently and economically and in greater depth than ever before. One key challenge for genome sequencing project is assembling scaffolds into high-quality chromosome-scale scaffolds. Recently, some studies established an effective and efficient solution to the challenge of chromosome-scale scaffolds assembly by exploiting chromatin interaction data from high-throughput chromosome conformation capture(Hi-C) technology. The aim of this study was to assess the feasibility and validity of the chromatin-interaction-based de novo assembly in the plant, based on a case study of Arabidopsis thaliana ecotype Landsberg erecta(Ler).We followed the previously published Hi-C protocol of Arabidopsis to get the genome-wide chromatin interaction data. We builded a de novo assembly for the Ler with 1,705 scaffolds(total length of 112.61 Mb, N50 = 341.63 Kb) draft by clustering scaffolds to chromosome groups, ordering scaffolds within chromosome groups and assigning relative orientations to individual scaffolds. We found that the assembly results presented a high consistency(99.10% of all length of the scaffolds in clustering, 93.41% of all sequence length in ordering and orientation) with homology to a reference genome. Moreover, we found our predictions were agreement with the previous assembly using a high resolution genetic map generated in Ler. Our study not only demonstrated the capability of this method to accurately assemble the scaffolds in plant, but also taken the advantage of the small scaffolds that are difficult to use by other methods.The development of de novo plant genome assembly based on chromatin interactions creates the new opportunities for building accurate reference sequences and carrying out precise and rigid analyses of unexplored genomes in a very cost-effective way, opening the door for carrying out numerous substantial new analyses on plant.