Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.
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作者：
Delmont TO;Eren AM
泛基因组提供了在一组密切相关的微生物基因组中发现的核心和辅助基因的详细特征，通常是基于序列同源性对基因进行聚类。相比之下，宏基因组通过读段募集分析促进了微生物基因组和个体基因在环境中的相对分布的高分辨率调查。结合这些互补的方法可以产生独特的见解微生物生态位划分和健身的功能基础，但是，缺乏先进的软件解决方案。在这里，我们提出了一个集成的分析和可视化策略，提供了一个交互式和可重复的框架来生成泛基因组，并结合宏基因组研究它们。为了研究其效用，我们将这种策略应用于大规模海洋宏基因组调查背景下的原绿球藻泛基因组。由此产生的原绿球藻metapangenome揭示了显着的差异丰度模式之间的非常密切相关的菌株，属于同一个系统发育簇，不同的只有少量的基因簇中的泛基因组。虽然这些基因组之间的关系与它们的环境分布模式相关的基因簇的基础上，使用标记基因或串联单拷贝核心基因的系统发育分析没有概括这些模式。metapangenome还揭示了一小组核心基因，主要发生在原绿球藻种群的高变基因组岛屿中，这些岛屿系统地缺乏来自海洋表面宏基因组的读段招募。值得注意的是，这些核心基因簇都与糖代谢有关，这表明糖代谢基因的高序列多样性对原绿球藻有潜在的好处。微生物基因组数量的快速增长和环境宏基因组的可用性的增加为研究微生物种群的功能和生态提供了新的机会，并且宏基因组可以为基因组和足够深的宏基因组数据可用的任何分类群和生物群系提供独特的见解。
Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.
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影响因子：
3.7
作者：
Gómez-Baena G;López-Lozano A;Gil-Martínez J;Lucena JM;Diez J;Candau P;García-Fernández JM
通讯作者：
García-Fernández JM
影响因子：
5.2
作者：
Muñoz-Marín MD;Gómez-Baena G;Díez J;Beynon RJ;González-Ballester D;Zubkov MV;García-Fernández JM
通讯作者：
García-Fernández JM
DOI：
10.1038/ismej.2015.241
发表时间：
2016-07
期刊：
The ISME journal
影响因子：
--
作者：
Bendall ML;Stevens SL;Chan LK;Malfatti S;Schwientek P;Tremblay J;Schackwitz W;Martin J;Pati A;Bushnell B;Froula J;Kang D;Tringe SG;Bertilsson S;Moran MA;Shade A;Newton RJ;McMahon KD;Malmstrom RR
通讯作者：
Malmstrom RR
影响因子：
3.9
作者：
Dutilh, BE;Huynen, MA;Snel, B
通讯作者：
Snel, B
影响因子：
16.6
作者：
Anderson RE;Reveillaud J;Reddington E;Delmont TO;Eren AM;McDermott JM;Seewald JS;Huber JA
通讯作者：
Huber JA