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

被引：57

作者：

Sakai, Hiroaki ^{[1
]}

Naito, Ken ^{[2
]}

Ogiso-Tanaka, Eri ^{[2
]}

Takahashi, Yu ^{[2
]}

Iseki, Kohtaro ^{[2
]}

Muto, Chiaki ^{[2
]}

Satou, Kazuhito ^{[3
]}

Teruya, Kuniko ^{[3
]}

Shiroma, Akino ^{[3
]}

Shimoji, Makiko ^{[3
]}

Hirano, Takashi ^{[3
]}

Itoh, Takeshi ^{[1
]}

Kaga, Akito ^{[2
]}

Tomooka, Norihiko ^{[2
]}

机构：

[1] Natl Inst Agrobiol Sci, Agrogen Res Ctr, Tsukuba, Ibaraki 3058602, Japan

[2] Natl Inst Agrobiol Sci, Genet Resources Ctr, Tsukuba, Ibaraki 3058602, Japan

[3] Okinawa Inst Adv Sci, Uruma 9042234, Japan

来源：

SCIENTIFIC REPORTS | 2015年 / 5卷

关键词：

DRAFT GENOME; GENERATION; ALIGNMENT; GENE; ANNOTATION; FRAMEWORK;

D O I：

10.1038/srep16780

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：13

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