基因组
生物
重组
同源重组
遗传学
霰弹枪测序
基因
GC含量
基因组
DNA测序
计算生物学
作者
Mingzhi Lin,Edo Kussell
出处
期刊:Nature Methods
[Springer Nature]
日期:2019-01-21
卷期号:16 (2): 199-204
被引量:62
标识
DOI:10.1038/s41592-018-0293-7
摘要
We present a robust, computationally efficient method ( https://github.com/kussell-lab/mcorr ) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.
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