An improved and robust method to efficiently deplete repetitive elements from complex plant genomes.

摘要: Genome size and complexity often present major challenges to genome-based approaches in crop plants other agricultural species. For instance, repetitive sequences comprise 80% 90% of the genome hexaploid wheat, which has a haploid approximately 17 Gb. In this study, we developed an improved design procedure for short-read library preparation that uses modified adaptor duplex-specific nuclease (DSN) efficient elimination highly repeated sequence elements within genomes. The adapter, hairpin-like form stability, was constructed from truncated adjacent original Illumina TruSeq adapter can be converted full-length structure during PCR amplification. Using hairpin-structured adaptor, prepared randomly sheared genomic libraries rice diploid, tetraploid, wheat cultivars evaluated efficiency DSN enzymatic depletion elements. According real-time quantitative analysis, relative abundances 18S 25S ribosomal DNA decreased respectively 1.15% 3.54% 1.70%-1.95% 14.71%-20.01% three cultivars. Whole-genome sequencing analysis diploid cultivar, KU104-1, indicated treatment with designed dramatically reduced elements, such as Ty1-Copia Ty3-Gypsy retrotransposons transposons, genome, while reads derived low-copy genes protein coding increased more than 50%. Our new should useful not only genomes but also plant species relatively large complex