Kamada Mayumi, Hase Sumitaka, Sato Kengo, Toyoda Atsushi, Fujiyama Asao, Sakakibara Yasubumi
Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan.
Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
PLoS One. 2014 Oct 16;9(10):e109999. doi: 10.1371/journal.pone.0109999. eCollection 2014.
De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.
从头进行的微生物基因组测序随着第三代测序（TGS）平台迎来了一个转折点，并且一些微生物基因组已通过TGS长读长得到了改进。纳豆芽孢杆菌与实验室标准菌株枯草芽孢杆菌马尔堡168密切相关，并且它在传统日本发酵食品“纳豆”的生产中具有作用。纳豆芽孢杆菌BEST195的基因组先前已使用短读长进行了测序，但其中包含一些不完整区域。我们使用PacBio RS测序仪对BEST195基因组进行了重测序，并且成功地从一个无间隙的支架中获得了完整的基因组序列，我们还应用了Illumina MiSeq短读长来提高质量。与先前的BEST195草图基因组和马尔堡168基因组相比，我们发现先前基因组序列中的不完整区域归因于GC偏差和重复序列，并且我们还鉴定出了一些仅在新基因组中发现的新基因。
