Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia.
Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia.
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DOI：
10.1186/1754-6834-7-40
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发表时间：
2014
影响因子：
6.3
通讯作者：
Köpke M
中科院分区：
文献类型：
--
作者：
Brown SD;Nagaraju S;Utturkar S;De Tissera S;Segovia S;Mitchell W;Land ML;Dassanayake A;Köpke M
自产乙醇梭菌菌株JA 1 -1（DSM 10061）是能够将CO、CO2和H2（例如来自合成气或废气）发酵成生物燃料乙醇和日用化学品如2，3-丁二醇的产乙酸菌。由100个重叠群组成的基因组序列草案已经公布。一个封闭的、高质量的C. autoethanogenum DSM 10061仅使用最新的单分子DNA测序技术生成，而无需手动整理。它被分配到最复杂的基因组分类的基础上的基因组特征，如重复，原噬菌体，九个拷贝的rRNA基因操纵子。G + C含量低，为31.1%。产生Illumina/454、Illumina/454杂交组装体，然后使用汇总统计、CGAL、QUAST和REAPR生物信息学工具和比较基因组方法与草稿和PacBio组装体进行比较。基于较短读段DNA技术的组装体被大量重复序列及其大小混淆，在rRNA基因操纵子的情况下，其大小约为5 kb。对生物技术相关的梭菌中的CRISPR（重复的规则间隔短回文重复序列）系统进行分类，并将其与质粒含量和原噬菌体相关。质粒含量和CRISPR系统之间的潜在关联可能对历史工业规模的丙酮-丁醇-乙醇（ABE）发酵失败和未来的大规模细菌发酵具有影响。而C.虽然在自产乙醇梭菌中存在活性CRISPR系统，但是在密切相关的扬氏梭菌DSM 13528中不存在这样的系统。一个共同的前噬菌体插入Arg-tRNA之间共享的菌株表明一个共同的祖先。然而，C. ljungdahlii含有几个额外的假定的原噬菌体，并且与C.自产乙醇菌其他差异包括重要的代谢基因的中央代谢（作为一个额外的氢化酶和磷酸烯醇丙酮酸合酶的缺乏）和底物利用途径（甘露糖和芳烃利用），这可能解释表型差异之间的C。autoethanogenum和C.永达利单分子测序将越来越多地用于生产成品微生物基因组。完整的基因组将促进比较基因组学和功能基因组学，并支持梭菌与研究质粒，噬菌体和CRISPR系统进化的研究之间的未来比较。
Clostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published. A closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii. Single molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems.
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影响因子：
3
作者：
Edgar RC
通讯作者：
Edgar RC
影响因子：
3.2
作者：
Brown, Steven D.;Klingeman, Dawn M.;Pelletier, Dale A.
通讯作者：
Pelletier, Dale A.
DOI：
10.1128/genomea.00628-13
发表时间：
2013-07-01
期刊：
GENOME ANNOUNCEMENTS
影响因子：
--
作者：
Bruno-Barcena, Jose M.;Chinn, Mari S.;Grunden, Amy M.
通讯作者：
Grunden, Amy M.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
DOI：
10.1126/science.1159689
发表时间：
2008-08-15
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Brouns SJ;Jore MM;Lundgren M;Westra ER;Slijkhuis RJ;Snijders AP;Dickman MJ;Makarova KS;Koonin EV;van der Oost J
通讯作者：
van der Oost J