Lamichhane Binit, Chua Eng-Guan, Wise Michael J, Laming Connor, Marshall Barry J, Tay Chin-Yen
1Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia.
2Department of Computer Science and Software Engineering, University of Western Australia, Perth, WA Australia.
Gut Pathog. 2019 Feb 20;11:7. doi: 10.1186/s13099-019-0284-y. eCollection 2019.
is a Gram-negative bacterium which mainly causes peptic ulcer disease in human, but is also the predominant cause of stomach cancer. It has been coevolving with human since 120,000 years and, according to Multi-locus sequence typing (MLST), can be classified into seven major population types, namely, hpAfrica1, hpAfrica2, hpNEAfrica, hpEastAsia, hpAsia2, hpEurope and hpSahul. harbours a large number of restriction-modification (R-M) systems. The methyltransferase (MTase) unit plays a significant role in gene regulation and also possibly modulates pathogenicity. The diversity in MTase can act as geomarkers to correlate strains with the phylogeographic origins. This paper describes the complete genome sequence and methylome of gastric pathogen belonging to the population hpNEAfrica.
In this paper, we present the complete genome sequence and the methylome profile of hpNEAfrica strain HP14039, isolated from a patient who was born in Somalia and likely to be infected locally during early childhood prior to migration. The genome of HP14039 consists of 1,678,260 bp with 1574 coding genes and 38.7% GC content. The sequence analysis showed that this strain lacks the cag pathogenicity island. The gene is of S2M2 type. We have also identified 15 methylation motifs, including WCANHNNNNTG and CTANNNNNNNTAYG that were not previously described.
We have described the complete genome of strain HP14039. The information regarding phylo-geography, methylome and associated metadata would help scientific community to study more about hpNEAfrica population type.
幽门螺杆菌是一种革兰氏阴性菌，主要导致人类消化性溃疡疾病，也是胃癌的主要病因。它自12万年前就与人类共同进化，根据多位点序列分型（MLST），可分为七种主要种群类型，即hpAfrica1、hpAfrica2、hpNEAfrica、hpEastAsia、hpAsia2、hpEurope和hpSahul。幽门螺杆菌拥有大量的限制修饰（R-M）系统。甲基转移酶（MTase）单元在基因调控中起重要作用，也可能调节致病性。MTase的多样性可作为地理标记，将菌株与系统发育地理起源相关联。本文描述了属于hpNEAfrica种群的胃病原体的完整基因组序列和甲基化组。
在本文中，我们展示了从一名出生于索马里、可能在幼年移民前于当地感染的患者中分离出的hpNEAfrica菌株HP14039的完整基因组序列和甲基化组图谱。HP14039的基因组由1,678,260 bp组成，有1574个编码基因，GC含量为38.7%。序列分析表明该菌株缺乏cag致病岛。该基因属于S2M2型。我们还鉴定出15个甲基化基序，包括之前未描述过的WCANHNNNNTG和CTANNNNNNNTAYG。
我们描述了幽门螺杆菌菌株HP14039的完整基因组。有关系统发育地理、甲基化组和相关元数据的信息将有助于科学界更多地研究hpNEAfrica种群类型。
