July 19, 2019  |  

The power of Single Molecule Real-Time sequencing technology in the de novo assembly of a eukaryotic genome.

Authors: Sakai, Hiroaki and Naito, Ken and Ogiso-Tanaka, Eri and Takahashi, Yu and Iseki, Kohtaro and Muto, Chiaki and Satou, Kazuhito and Teruya, Kuniko and Shiroma, Akino and Shimoji, Makiko and Hirano, Takashi and Itoh, Takeshi and Kaga, Akito and Tomooka, Norihiko

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.

Journal: Scientific reports
DOI: 10.1038/srep16780
Year: 2015

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