Insights from 20 years of bacterial genome sequencing.
Insights from 20 years of bacterial genome sequencing.
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DOI：
10.1007/s10142-015-0433-4
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发表时间：
2015-03
影响因子：
2.9
通讯作者：
Ussery, David W.
中科院分区：
文献类型：
--
作者：
Land, Miriam;Hauser, Loren;Jun, Se-Ran;Nookaew, Intawat;Leuze, Michael R.;Ahn, Tae-Hyuk;Karpinets, Tatiana;Lund, Ole;Kora, Guruprased;Wassenaar, Trudy;Poudel, Suresh;Ussery, David W.
关键词：
自 1995 年发表前两个完整的细菌基因组序列以来，细菌科学发生了巨大的变化。使用第三代 DNA 测序，可以在几个小时内对细菌基因组进行完整测序，并识别基因组中某些类型的甲基化位点。细菌基因组序列测序现已成为标准程序，来自数万个细菌基因组的信息对我们对细菌世界的看法产生了重大影响。在这篇综述中，我们探讨了一系列问题，以强调比较基因组学产生的一些见解。迄今为止，已有 50 个不同细菌门和 11 个不同古细菌门的基因组序列。然而，这种分布非常偏向于一些含有模式生物的门。但随着致力于填补特征较少的分类群的项目的开展，其广度正在持续改善。成簇的规则间隔短回文重复序列 (CRISPR)-Cas 系统为细菌提供了针对病毒的免疫力，而病毒的数量是细菌的十倍。我们能走多快？二代测序已产生大量基因组草案（GenBank中接近90%的细菌基因组目前不完整）；第三代测序有可能在几个小时内产生完整的基因组，同时提供整个染色体的甲基化位点。细菌群落的多样性非常广泛，从 50 个不同细菌门和 11 个不同古细菌门的基因组序列中可以明显看出。基因组测序可以帮助对生物体进行分类，并且在同一物种的多个基因组可用的情况下，可以计算泛基因组和核心基因组；通过对2000多个大肠杆菌基因组的比较，发现大肠杆菌核心基因组包含约3100个基因家族，总共约89000个不同的基因家族。为什么我们关心细菌基因组测序？有许多实际应用，例如基因组规模的代谢模型、生物监测、生物法医学和传染病流行病学。在不久的将来，患者宏基因组样本的高通量测序可能会在寻找病原体和了解如何治疗它们的速度和准确性方面彻底改变医学。
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.
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影响因子：
3.7
作者：
Cosentino S;Voldby Larsen M;Møller Aarestrup F;Lund O
通讯作者：
Lund O
影响因子：
11.8
作者：
Aarestrup FM;Brown EW;Detter C;Gerner-Smidt P;Gilmour MW;Harmsen D;Hendriksen RS;Hewson R;Heymann DL;Johansson K;Ijaz K;Keim PS;Koopmans M;Kroneman A;Lo Fo Wong D;Lund O;Palm D;Sawanpanyalert P;Sobel J;Schlundt J
通讯作者：
Schlundt J
DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
影响因子：
46.9
作者：
Bikard, David;Euler, Chad W.;Jiang, Wenyan;Nussenzweig, Philip M.;Goldberg, Gregory W.;Duportet, Xavier;Fischetti, Vincent A.;Marraffini, Luciano A.
通讯作者：
Marraffini, Luciano A.
影响因子：
46.9
作者：
Cho, Byung-Kwan;Zengler, Karsten;Qiu, Yu;Park, Young Seoub;Knight, Eric M.;Barrett, Christian L.;Gao, Yuan;Palsson, Bernhard O.
通讯作者：
Palsson, Bernhard O.