使用PacBio单分子实时技术测定的来自日本冲绳岛患有不同胃肠道疾病患者的8株具有不同毒力因子基因型和甲基化谱的幽门螺杆菌菌株的全基因组序列。
Complete Genome Sequences of Eight Helicobacter pylori Strains with Different Virulence Factor Genotypes and Methylation Profiles, Isolated from Patients with Diverse Gastrointestinal Diseases on Okinawa Island, Japan, Determined Using PacBio Single-Molecule Real-Time Technology.
作者信息
Satou Kazuhito, Shiroma Akino, Teruya Kuniko, Shimoji Makiko, Nakano Kazuma, Juan Ayaka, Tamotsu Hinako, Terabayashi Yasunobu, Aoyama Misako, Teruya Morimi, Suzuki Rumiko, Matsuda Miyuki, Sekine Akihiro, Kinjo Nagisa, Kinjo Fukunori, Yamaoka Yoshio, Hirano Takashi
机构信息
Okinawa Institute of Advanced Sciences, Uruma, Japan.
出版信息
Genome Announc. 2014 Apr 17;2(2):e00286-14. doi: 10.1128/genomeA.00286-14.
Abstract
We report the complete genome sequences of eight Helicobacter pylori strains isolated from patients with gastrointestinal diseases in Okinawa, Japan. Whole-genome sequencing and DNA methylation detection were performed using the PacBio platform. De novo assembly determined a single, complete contig for each strain. Furthermore, methylation analysis identified virulence factor genotype-dependent motifs.
摘要
我们报告了从日本冲绳胃肠道疾病患者中分离出的8株幽门螺杆菌菌株的完整基因组序列。使用PacBio平台进行全基因组测序和DNA甲基化检测。从头组装确定了每个菌株的单个完整重叠群。此外，甲基化分析确定了毒力因子基因型依赖性基序。
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本文引用的文献
1
Reducing assembly complexity of microbial genomes with single-molecule sequencing.利用单分子测序降低微生物基因组的组装复杂性
Genome Biol. 2013;14(9):R101. doi: 10.1186/gb-2013-14-9-r101.
2
Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes.单分子实时测序在高 GC 含量基因组中的优势。
PLoS One. 2013 Jul 23;8(7):e68824. doi: 10.1371/journal.pone.0068824. Print 2013.
3
Choosing a benchtop sequencing machine to characterise Helicobacter pylori genomes.选择台式测序仪来分析幽门螺杆菌基因组。
PLoS One. 2013 Jun 28;8(6):e67539. doi: 10.1371/journal.pone.0067539. Print 2013.
4
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.非杂交、基于长读长 SMRT 测序数据的完成微生物基因组组装。
Nat Methods. 2013 Jun;10(6):563-9. doi: 10.1038/nmeth.2474. Epub 2013 May 5.
5
Pathogenesis of Helicobacter pylori-Related Gastroduodenal Diseases from Molecular Epidemiological Studies.从分子流行病学研究看幽门螺杆菌相关胃十二指肠疾病的发病机制。
Gastroenterol Res Pract. 2012;2012:371503. doi: 10.1155/2012/371503. Epub 2012 Jul 5.
6
Association between Helicobacter pylori virulence factors and gastroduodenal diseases in Okinawa, Japan.日本冲绳地区幽门螺杆菌毒力因子与胃十二指肠疾病的相关性研究。
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7
BIGSdb: Scalable analysis of bacterial genome variation at the population level.BIGSdb：在群体水平上对细菌基因组变异进行可扩展的分析。
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8
Mechanisms of disease: Helicobacter pylori virulence factors.发病机制：幽门螺杆菌毒力因子。
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Direct detection of DNA methylation during single-molecule, real-time sequencing.单分子实时测序中 DNA 甲基化的直接检测。
Nat Methods. 2010 Jun;7(6):461-5. doi: 10.1038/nmeth.1459. Epub 2010 May 9.
10
Clinical practice. Helicobacter pylori infection.临床实践。幽门螺杆菌感染。
N Engl J Med. 2010 Apr 29;362(17):1597-604. doi: 10.1056/NEJMcp1001110.
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