BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

Plant Biotechnology Journal
Helena StaňkováHana Šimková

Abstract

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assem...Continue Reading

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Datasets Mentioned

BETA
GM19
GM243
GM158

Methods Mentioned

BETA
Genome Sequencing
flow
chip
PCR

Software Mentioned

IWGSC
BioNano
Irys
SASSY assembler
FPC
IrysView
fasta
BLAST

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