Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data.
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 plantArabidopsis thalianaand 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.
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Wen-Biao
WB
Jiao
Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
Gonzalo Garcia
GG
Accinelli
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Benjamin
B
Hartwig
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Christiane
C
Kiefer
Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
David
D
Baker
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Edouard
E
Severing
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Eva-Maria
EM
Willing
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Mathieu
M
Piednoel
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Stefan
S
Woetzel
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Eva
E
Madrid-Herrero
Max Planck-Genome-center Cologne, 50829 Cologne, Germany.
Bruno
B
Huettel
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Ulrike
U
Hümann
Max Planck-Genome-center Cologne, 50829 Cologne, Germany.
Richard
R
Reinhard
Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, 69120 Heidelberg, Germany.
Marcus A
MA
Koch
Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
Daniel
D
Swan
Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
Bernardo
B
Clavijo
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
George
G
Coupland
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
Korbinian
0000-0002-5512-0443
K
Schneeberger
D017360:Arabidopsis / Q000235:genetics; D032461:Chromosomes, Plant / Q000737:chemistry* / Q000235:genetics; D020451:Contig Mapping / Q000379:methods* / Q000592:standards; D018745:Genome, Plant; D023281:Genomics / Q000379:methods* / Q000592:standards; D012984:Software