Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.
Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.
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DOI：
10.1186/s12859-023-05363-4
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发表时间：
2023-06-09
影响因子：
3
通讯作者：
Weissman, Daniel B.
中科院分区：
文献类型：
--
作者：
Mehta, Rohan S.;Petit III, Robert A.;Read, Timothy D.;Weissman, Daniel B.
关键词：
Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method. The online version contains supplementary material available at 10.1186/s12859-023-05363-4.
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影响因子：
4.5
作者：
Chewapreecha C;Marttinen P;Croucher NJ;Salter SJ;Harris SR;Mather AE;Hanage WP;Goldblatt D;Nosten FH;Turner C;Turner P;Bentley SD;Parkhill J
通讯作者：
Parkhill J
影响因子：
4.2
作者：
McCarthy AJ;Lindsay JA
通讯作者：
Lindsay JA
DOI：
10.1093/bioinformatics/bts396
发表时间：
2012-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cohen O;Ashkenazy H;Burstein D;Pupko T
通讯作者：
Pupko T
影响因子：
2
作者：
Maddison, WP
通讯作者：
Maddison, WP
影响因子：
12.3
作者：
Brynildsrud O;Bohlin J;Scheffer L;Eldholm V
通讯作者：
Eldholm V