title: Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.
abstract: Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
authors: Genome Center, University of California Davis, Davis, California, USA.
authors: Marta
authors: M
authors: Matvienko
authors: Alexander
authors: A
authors: Kozik
authors: Lutz
authors: L
authors: Froenicke
authors: Dean
authors: D
authors: Lavelle
authors: Belinda
authors: B
authors: Martineau
authors: Bertrand
authors: B
authors: Perroud
authors: Richard
authors: R
authors: Michelmore
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics; D001482:Base Composition; D019295:Computational Biology / Q000379:methods; D003851:Deoxyribonucleases; D020869:Gene Expression Profiling; D015723:Gene Library; D061125:Genes, Chloroplast; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D018545:Lactuca / Q000187:drug effects / Q000235:genetics; D016366:Open Reading Frames; D000644:Quaternary Ammonium Compounds / Q000494:pharmacology; D012091:Repetitive Sequences, Nucleic Acid; D059467:Transcriptome
chemical_list: D000644:Quaternary Ammonium Compounds; D003851:Deoxyribonucleases; C027917:tetramethylammonium