RT Journal
A1 Jiao, Wen-Biao
A1 Accinelli, Gonzalo Garcia
A1 Hartwig, Benjamin
A1 Kiefer, Christiane
A1 Baker, David
A1 Severing, Edouard
A1 Willing, Eva-Maria
A1 Piednoel, Mathieu
A1 Woetzel, Stefan
A1 Madrid-Herrero, Eva
A1 Huettel, Bruno
A1 Hümann, Ulrike
A1 Reinhard, Richard
A1 Koch, Marcus A.
A1 Swan, Daniel
A1 Clavijo, Bernardo
A1 Coupland, George
A1 Schneeberger, Korbinian
T1 Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
JF Genome Research 
JO Genome Research 
YR 2017 
FD May 01 
VO 27 
IS 5 
SP 778 
OP 786 
DO 10.1101/gr.213652.116 
UL http://genome.cshlp.org/content/27/5/778.abstract 
AB Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.