title: The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome.
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.
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Naito
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Eri
authors.initials: E
authors.lastname: Ogiso-Tanaka
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Takahashi
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Kohtaro
authors.initials: K
authors.lastname: Iseki
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Chiaki
authors.initials: C
authors.lastname: Muto
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan.
authors.forename: Kazuhito
authors.initials: K
authors.lastname: Satou
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan.
authors.forename: Kuniko
authors.initials: K
authors.lastname: Teruya
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan.
authors.forename: Akino
authors.initials: A
authors.lastname: Shiroma
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan.
authors.forename: Makiko
authors.initials: M
authors.lastname: Shimoji
authors.affiliation: Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, 904-2234, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Hirano
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Akito
authors.initials: A
authors.lastname: Kaga
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
authors.forename: Norihiko
authors.initials: N
authors.lastname: Tomooka
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D056890:Eukaryota / Q000235:genetics*; D007887:Fabaceae / Q000235:genetics; D008040:Genetic Linkage; D016678:Genome; D018745:Genome, Plant; D023281:Genomics / Q000295:instrumentation / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation / Q000379:methods*; D058977:Molecular Sequence Annotation; D015203:Reproducibility of Results