Consequences of Normalizing Transcriptomic and Genomic Libraries of Plant Genomes Using a Duplex-specific Nuclease and Tetramethylammonium Chloride

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2013 Feb 15

PMID 23409088

Citations 20

Authors

Marta Matvienko

Alexander Kozik

Lutz Froenicke

Dean Lavelle

Belinda Martineau

Bertrand Perroud

Richard Michelmore

Affiliations

Soon will be listed here.

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.

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