Local Assemblies of Paired-End Reduced Representation Libraries Sequenced with the Illumina Genome Analyzer in Maize
Joint Authors
Zhang, Yun
Deschamps, Stéphane
Hayes, Kevin
Nannapaneni, Kishore
Source
International Journal of Plant Genomics
Issue
Vol. 2012, Issue 2012 (31 Dec. 2012), pp.1-8, 8 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2012-10-09
Country of Publication
Egypt
No. of Pages
8
Main Subjects
Abstract EN
The use of next-generation DNA sequencing technologies has greatly facilitated reference-guided variant detection in complex plant genomes.
However, complications may arise when regions adjacent to a read of interest are used for marker assay development, or when reference sequences are incomplete, as short reads alone may not be long enough to ascertain their uniqueness.
Here, the possibility of generating longer sequences in discrete regions of the large and complex genome of maize is demonstrated, using a modified version of a paired-end RAD library construction strategy.
Reads are generated from DNA fragments first digested with a methylation-sensitive restriction endonuclease, sheared, enriched with biotin and a selective PCR amplification step, and then sequenced at both ends.
Sequences are locally assembled into contigs by subgrouping pairs based on the identity of the read anchored by the restriction site.
This strategy applied to two maize inbred lines (B14 and B73) generated 183,609 and 129,018 contigs, respectively, out of which at least 76% were >200 bps in length.
A subset of putative single nucleotide polymorphisms from contigs aligning to the B73 reference genome with at least one mismatch was resequenced, and 90% of those in B14 were confirmed, indicating that this method is a potent approach for variant detection and marker development in species with complex genomes or lacking extensive reference sequences.
American Psychological Association (APA)
Deschamps, Stéphane& Nannapaneni, Kishore& Zhang, Yun& Hayes, Kevin. 2012. Local Assemblies of Paired-End Reduced Representation Libraries Sequenced with the Illumina Genome Analyzer in Maize. International Journal of Plant Genomics،Vol. 2012, no. 2012, pp.1-8.
https://search.emarefa.net/detail/BIM-465819
Modern Language Association (MLA)
Deschamps, Stéphane…[et al.]. Local Assemblies of Paired-End Reduced Representation Libraries Sequenced with the Illumina Genome Analyzer in Maize. International Journal of Plant Genomics No. 2012 (2012), pp.1-8.
https://search.emarefa.net/detail/BIM-465819
American Medical Association (AMA)
Deschamps, Stéphane& Nannapaneni, Kishore& Zhang, Yun& Hayes, Kevin. Local Assemblies of Paired-End Reduced Representation Libraries Sequenced with the Illumina Genome Analyzer in Maize. International Journal of Plant Genomics. 2012. Vol. 2012, no. 2012, pp.1-8.
https://search.emarefa.net/detail/BIM-465819
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-465819