聚乙二醇降解菌大谷鞘氨醇单胞菌菌株203N（NBRC 111659）的全基因组序列
Complete Genome Sequence of Sphingopyxis macrogoltabida Strain 203N (NBRC 111659), a Polyethylene Glycol Degrader.
作者信息
Ohtsubo Yoshiyuki, Nonoyama Shouta, Nagata Yuji, Numata Mitsuru, Tsuchikane Keiko, Hosoyama Akira, Yamazoe Atsushi, Tsuda Masataka, Fujita Nobuyuki, Kawai Fusako
机构信息
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
出版信息
Genome Announc. 2016 Jun 9;4(3):e00529-16. doi: 10.1128/genomeA.00529-16.
Abstract
We determined the complete genome sequence of Sphingopyxis macrogoltabida strain 203N, a polyethylene glycol degrader. Because the PacBio assembly (285× coverage) seemed to be full of nucleotide-level mismatches, the Newbler assembly of MiSeq mate-pair and paired-end data was used for finishing and the PacBio assembly was used as a reference. The PacBio assembly carried 414 nucleotide mismatches over 5,953,153 bases of the 203N genome.
摘要
我们测定了聚乙二醇降解菌大戈尔德鞘氨醇单胞菌（Sphingopyxis macrogoltabida）菌株203N的全基因组序列。由于PacBio组装结果（覆盖度为285×）似乎存在大量核苷酸水平的错配，因此使用MiSeq配对末端和双末端数据的Newbler组装结果进行基因组完成工作，并将PacBio组装结果用作参考。在203N基因组的5,953,153个碱基上，PacBio组装结果存在414个核苷酸错配。
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3
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