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The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome.

Scientific reports (2015-12-01)
Hiroaki Sakai, Ken Naito, Eri Ogiso-Tanaka, Yu Takahashi, Kohtaro Iseki, Chiaki Muto, Kazuhito Satou, Kuniko Teruya, Akino Shiroma, Makiko Shimoji, Takashi Hirano, Takeshi Itoh, Akito Kaga, Norihiko Tomooka
ABSTRACT

Second-generation sequencers (SGS) have been game-changing, achieving cost-effective whole genome sequencing in many non-model organisms. However, a large portion of the genomes still remains unassembled. We reconstructed azuki bean (Vigna angularis) genome using single molecule real-time (SMRT) sequencing technology and achieved the best contiguity and coverage among currently assembled legume crops. The SMRT-based assembly produced 100 times longer contigs with 100 times smaller amount of gaps compared to the SGS-based assemblies. A detailed comparison between the assemblies revealed that the SMRT-based assembly enabled a more comprehensive gene annotation than the SGS-based assemblies where thousands of genes were missing or fragmented. A chromosome-scale assembly was generated based on the high-density genetic map, covering 86% of the azuki bean genome. We demonstrated that SMRT technology, though still needed support of SGS data, achieved a near-complete assembly of a eukaryotic genome.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Hexadecyltrimethylammonium bromide, for molecular biology, ≥99%
Sigma-Aldrich
Hexadecyltrimethylammonium bromide, ≥98%
Sigma-Aldrich
Hexadecyltrimethylammonium bromide, BioXtra, ≥99%
Sigma-Aldrich
Hexadecyltrimethylammonium bromide, BioUltra, for molecular biology, ≥99.0% (AT)
SAFC
Hexadecyltrimethylammonium bromide