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The landscape of coadaptation in Vibrio parahaemolyticus

By Yujun Cui, Chao Yang, Hongling Qiu, Hui Wang, Ruifu Yang, Daniel Falush

Posted 22 Jul 2018
bioRxiv DOI: 10.1101/373936 (published DOI: 10.7554/eLife.54136)

Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of Vibrio parahaemolyticus , a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups involving 1,560 coding genes. 82 of these interaction groups are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 interaction groups involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. Preliminary experiments imply that the strategies influence biofilm formation and bacterial growth rate in vitro. One strategy involves a divergent profile in multiple genome regions, implying that strains have irreversibly specialized, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.

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