A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.
A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.
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DOI：
10.1186/1471-2164-15-1138
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发表时间：
2014-12-18
期刊：
影响因子：
4.4
通讯作者：
Maiden MC
中科院分区：
文献类型：
--
作者：
Bratcher HB;Corton C;Jolley KA;Parkhill J;Maiden MC
高度平行的“第二代”测序技术迅速扩大了可用于研究的细菌全基因组序列的数量，从而允许群体基因组学学科的出现。这些数据中的大多数可作为未组装的短读段序列文件在计算机上获得，这些文件在可用于分析之前需要大量处理。因此，有必要以统一格式提供数据，这些数据的质量易于评估，与来源和表型相联系，并用于分析。使用pubMLST.org奈瑟氏菌数据库评估和评价了108种不同的、代表性的和充分表征的脑膜炎奈瑟氏菌分离株的从头短读组装后自动注释的性能。在从头组装的基因组和四个重新测序的基因组中，获得了>99%的已知脑膜炎球菌基因的高质量序列，并且不到1%的重新组装的基因具有序列差异或错误组装的序列。使用基因组比较工具确定了至少95%群体中存在的1600个基因座的核心基因组。系谱关系兼容，但在更高的分辨率比，通过多位点序列分型确定的核心基因组比较和核糖体蛋白基因分析，揭示了一些先前描述的表型的基因组结构。该用于对基因组中的奈瑟氏菌遗传变异进行编目的统一系统被实施并用于多种分析，并且数据可在PubMLST奈瑟氏菌数据库中检索。从头组装，结合自动化的基因-基因注释，产生高质量的基因组草案，其中大多数蛋白质编码基因以高准确性存在。该方法有效地编目多样性，允许分析单个基因组或多个基因组的比较，是一个实用的方法来解释大的细菌种群样本的WGS数据。该方法对脑膜炎球菌的生物学产生了新的见解，并提高了我们对整个种群结构的理解，而不仅仅是致病谱系。本文的在线版本（doi：10.1186/1471-2164-15-1138）包含补充材料，可供授权用户使用。
Highly parallel, ‘second generation’ sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population genomics. Most of these data are publically available as unassembled short-read sequence files that require extensive processing before they can be used for analysis. The provision of data in a uniform format, which can be easily assessed for quality, linked to provenance and phenotype and used for analysis, is therefore necessary. The performance of de novo short-read assembly followed by automatic annotation using the pubMLST.org Neisseria database was assessed and evaluated for 108 diverse, representative, and well-characterised Neisseria meningitidis isolates. High-quality sequences were obtained for >99% of known meningococcal genes among the de novo assembled genomes and four resequenced genomes and less than 1% of reassembled genes had sequence discrepancies or misassembled sequences. A core genome of 1600 loci, present in at least 95% of the population, was determined using the Genome Comparator tool. Genealogical relationships compatible with, but at a higher resolution than, those identified by multilocus sequence typing were obtained with core genome comparisons and ribosomal protein gene analysis which revealed a genomic structure for a number of previously described phenotypes. This unified system for cataloguing Neisseria genetic variation in the genome was implemented and used for multiple analyses and the data are publically available in the PubMLST Neisseria database. The de novo assembly, combined with automated gene-by-gene annotation, generates high quality draft genomes in which the majority of protein-encoding genes are present with high accuracy. The approach catalogues diversity efficiently, permits analyses of a single genome or multiple genome comparisons, and is a practical approach to interpreting WGS data for large bacterial population samples. The method generates novel insights into the biology of the meningococcus and improves our understanding of the whole population structure, not just disease causing lineages. The online version of this article (doi:10.1186/1471-2164-15-1138) contains supplementary material, which is available to authorized users.
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影响因子：
4.4
作者：
Aury JM;Cruaud C;Barbe V;Rogier O;Mangenot S;Samson G;Poulain J;Anthouard V;Scarpelli C;Artiguenave F;Wincker P
通讯作者：
Wincker P
影响因子：
4.4
作者：
Bennett JS;Bentley SD;Vernikos GS;Quail MA;Cherevach I;White B;Parkhill J;Maiden MC
通讯作者：
Maiden MC
影响因子：
3.3
作者：
Didelot, Xavier;Falush, Daniel
通讯作者：
Falush, Daniel
影响因子：
2.1
作者：
Farrer, Rhys A.;Kemen, Eric;Studholme, David J.
通讯作者：
Studholme, David J.
影响因子：
3.2
作者：
Earl, Ashlee M.;Eppinger, Mark;Ravel, Jacques
通讯作者：
Ravel, Jacques