Open AccessBioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
Author(s) -
Staňková Helena,
Hastie Alex R.,
Chan Saki,
Vrána Jan,
Tulpová Zuzana,
Kubaláková Marie,
Visendi Paul,
Hayashi Satomi,
Luo Mingcheng,
Batley Jacqueline,
Edwards David,
Doležel Jaroslav,
Šimková Hana
Publication year - 2016
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12513
Subject(s) - biology , genome , physical mapping , computational biology , sequence (biology) , sequence assembly , genetics , gene mapping , evolutionary biology , chromosome , gene , gene expression , transcriptome
Summary 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 (7 DS ) 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 7 DS sequence assemblies obtained by clone‐by‐clone sequencing to the 7 DS genome map provided a valuable tool to improve the BAC ‐contig physical map and validate sequence assembly on a chromosome‐arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome‐by‐chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.