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PMID: 21324881 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Sequence-based physical mapping of complex genomes by whole genome profiling.

Genome research ·Vol. 21 ·No. 4 ·2011-04-00 ·Pages 618-25

van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R, van Eijk MJ, Prins M

Abstract

We present whole genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (BAC) contigs of complex genomes, using Arabidopsis thaliana as an example. WGP leverages short read sequences derived from restriction fragments of two-dimensionally pooled BAC clones to generate sequence tags. These sequence tags are assigned to individual BAC clones, followed by assembly of BAC contigs based on shared regions containing identical sequence tags. Following in silico analysis of WGP sequence tags and simulation of a map of Arabidopsis chromosome 4 and maize, a WGP map of Arabidopsis thaliana ecotype Columbia was constructed de novo using a six-genome equivalent BAC library. Validation of the WGP map using the Columbia reference sequence confirmed that 350 BAC contigs (98%) were assembled correctly, spanning 97% of the 102-Mb calculated genome coverage. We demonstrate that WGP maps can also be generated for more complex plant genomes and will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data.

MeSH Terms
Arabidopsis/genetics Chromosome Mapping/methods Chromosomes, Artificial, Bacterial/genetics Computational Biology Contig Mapping Genome, Plant/genetics Genomic Library High-Throughput Nucleotide Sequencing
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
van Oeveren Jan
Keygene N.V., Wageningen, The Netherlands.
de Ruiter Marjo
Jesse Taco
van der Poel Hein
Tang Jifeng
Yalcin Feyruz
Janssen Antoine
Volpin Hanne
Stormo Keith E
Bogden Robert
van Eijk Michiel J T
Prins Marcel
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.112094.110
Published
2011-04-00
Epub
2011-00-01
Pages
618-25
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC3065709
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.112094.110 PMC Full Text View journal details
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