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An improved and robust method to efficiently deplete repetitive elements from complex plant genomes.
Plant Sci 2019; 280:455-460PS

Abstract

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

Authors+Show Affiliations

RIKEN Nishina Center for Accelerator-Based Science, Saitama 351-0198, Japan. Electronic address: ichida@riken.jp.RIKEN Nishina Center for Accelerator-Based Science, Saitama 351-0198, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30824026

Citation

Ichida, Hiroyuki, and Tomoko Abe. "An Improved and Robust Method to Efficiently Deplete Repetitive Elements From Complex Plant Genomes." Plant Science : an International Journal of Experimental Plant Biology, vol. 280, 2019, pp. 455-460.
Ichida H, Abe T. An improved and robust method to efficiently deplete repetitive elements from complex plant genomes. Plant Sci. 2019;280:455-460.
Ichida, H., & Abe, T. (2019). An improved and robust method to efficiently deplete repetitive elements from complex plant genomes. Plant Science : an International Journal of Experimental Plant Biology, 280, pp. 455-460. doi:10.1016/j.plantsci.2018.10.021.
Ichida H, Abe T. An Improved and Robust Method to Efficiently Deplete Repetitive Elements From Complex Plant Genomes. Plant Sci. 2019;280:455-460. PubMed PMID: 30824026.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - An improved and robust method to efficiently deplete repetitive elements from complex plant genomes. AU - Ichida,Hiroyuki, AU - Abe,Tomoko, Y1 - 2018/11/03/ PY - 2018/08/10/received PY - 2018/10/21/revised PY - 2018/10/23/accepted PY - 2019/3/3/entrez PY - 2019/3/3/pubmed PY - 2019/3/19/medline KW - Duplex-specific nuclease KW - Genome reduction KW - Next-generation sequencing KW - Rice KW - Wheat SP - 455 EP - 460 JF - Plant science : an international journal of experimental plant biology JO - Plant Sci. VL - 280 N2 - Genome size and complexity often present major challenges to genome-based approaches in crop plants and other agricultural species. For instance, repetitive sequences comprise 80% to 90% of the genome of hexaploid wheat, which has a haploid genome size of approximately 17 Gb. In this study, we developed an improved design and procedure for short-read library preparation that uses a modified adaptor and duplex-specific nuclease (DSN) for the efficient elimination of highly repeated sequence elements within genomes. The improved adapter, which has a hairpin-like form for stability, was constructed from truncated sequences adjacent to the original Illumina TruSeq adapter and can be converted to a full-length adapter structure during PCR amplification. Using the hairpin-structured adaptor, we prepared randomly sheared genomic libraries from rice and diploid, tetraploid, and hexaploid wheat cultivars and evaluated the efficiency of DSN for the enzymatic depletion of repetitive elements. According to real-time quantitative PCR analysis, the relative abundances of 18S and 25S ribosomal DNA decreased respectively to 1.15% and 3.54% in rice and 1.70%-1.95% and 14.71%-20.01% in the three wheat cultivars. Whole-genome sequencing analysis of a diploid wheat cultivar, KU104-1, indicated that DSN treatment with the designed hairpin-structured adapter dramatically reduced highly repetitive elements, such as Ty1-Copia and Ty3-Gypsy retrotransposons and DNA transposons, within the genome, while sequencing reads derived from low-copy genes and protein coding sequences increased more than 50%. Our new procedure should be useful not only for wheat genomes but also for other agricultural plant species with relatively large and complex genomes. SN - 1873-2259 UR - https://www.unboundmedicine.com/medline/citation/30824026/An_improved_and_robust_method_to_efficiently_deplete_repetitive_elements_from_complex_plant_genomes_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0168-9452(18)30997-X DB - PRIME DP - Unbound Medicine ER -