Smukowski Heil Caiti, Burton Joshua N, Liachko Ivan, Friedrich Anne, Hanson Noah A, Morris Cody L, Schacherer Joseph, Shendure Jay, Thomas James H, Dunham Maitreya J
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Genetics, Genomics, and Microbiology, University of Strasbourg, Strasbourg, France.
Yeast. 2018 Jan;35(1):71-84. doi: 10.1002/yea.3280. Epub 2017 Oct 19.
Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the method's application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample. Our assembly method has enabled us to de-convolute four bacterial and four yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed, yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes. Copyright © 2017 John Wiley & Sons, Ltd.
种间杂交是实现基因多样化和适应的常见机制；然而，杂交物种的检测一直颇具难度。微生物杂交种的鉴定更加复杂，因为大多数环境微生物难以培养，必须在其原生混合群落中进行研究。我们之前已将染色体构象捕获方法Hi-C应用于混合群体基因组的组装。在此，我们展示了该方法在直接从自发接种的啤酒样品中的未培养混合群体组装基因组方面的应用。我们的组装方法使我们能够从该样品中解析出四个细菌基因组和四个酵母基因组，包括一个推定的酵母杂交种。对该杂交种的下游分离和分析证实其基因组由膜醭毕赤酵母和另一种相关但未描述的酵母基因组组成。我们的工作表明，基于Hi-C的宏基因组方法可以克服传统测序方法在研究复杂基因组混合物方面的局限性。版权所有© 2017约翰威立父子有限公司。
