title: Effective DNA fragmentation technique for simple sequence repeat detection with a microsatellite-enriched library and high-throughput sequencing.
abstract: Two different techniques for genomic DNA fragmentation before microsatellite-enriched library construction-restriction enzyme (NlaIII and MseI) digestion and sonication-were compared to examine their effects on simple sequence repeat (SSR) detection using high-throughput sequencing. Tens of thousands of SSR regions from 5 species of the plant family Myrtaceae were detected when the output of individual samples was >1 million paired-end reads. Comparison of the two DNA fragmentation techniques showed that restriction enzyme digestion was superior to sonication for identification of heterozygous genotypes, whereas sonication was superior for detection of various SSR flanking regions with both species-specific and common characteristics. Therefore, choosing the most suitable DNA fragmentation method depends on the type of analysis that is planned.
authors.affiliation: NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Tanaka
authors.affiliation: NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan.
authors.forename: Rumi
authors.initials: R
authors.lastname: Ohtake
authors.affiliation: Junior College of Tokyo University of Agriculture, Tokyo, Japan.
authors.forename: Saki
authors.initials: S
authors.lastname: Yoshida
authors.affiliation: Junior College of Tokyo University of Agriculture, Tokyo, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Shinohara
mesh_terms: D003001:Cloning, Molecular / Q000379:methods; D053938:DNA Fragmentation; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics*; D027822:Myrtaceae / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: DNA fragmentation; Myrtaceae; high-throughput sequencing; microsatellite enrichment; restriction enzyme digestion; simple sequence repeat; sonication