Marbouty Martial, Cournac Axel, Flot Jean-François, Marie-Nelly Hervé, Mozziconacci Julien, Koszul Romain
Groupe Régulation Spatiale des Génomes, Département Génomes et Génétique, Institut Pasteur, Paris, France.
Biological Physics and Evolutionary Dynamics Group, Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.
Elife. 2014 Dec 17;3:e03318. doi: 10.7554/eLife.03318.
Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis.
对自然环境中微生物群体的基因组分析仍然受到难以组装单个物种完整基因组的限制。因此，仅在少数模式物种中研究了微生物的染色体组织，但所描述的特征能在多大程度上推广到其他分类群仍不清楚。我们利用细菌和酵母物种的受控混合物，开发了meta3C，这是一种宏基因组染色体构象捕获方法，可用于在混合生物体中表征单个基因组及其平均组织情况。meta3C不仅可以应用于已测序的物种，而且单个meta3C文库可用于组装、搭建支架和表征未知基因组的三维组织。通过将meta3C应用于半复杂环境样本，我们证实了其广阔的潜力。总体而言，这项首次meta3C研究突出了微生物染色体组织的显著多样性，同时为宏基因组分析提供了一种简洁且综合的方法。
