TY - JOUR T1 - <em>Cis</em>-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids JF - bioRxiv DO - 10.1101/044362 SP - 044362 AU - Carlo G. Artieri AU - Adit Naor AU - Israela Turgeman-Grott AU - Yiqi Zhou AU - Ryan York AU - Uri Gophna AU - Hunter B. Fraser Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/03/17/044362.abstract N2 - The study of allele-specific expression (ASE) in interspecific hybrids has played a central role in our understanding of a wide range of phenomena, including genomic imprinting, X-chromosome inactivation, and cis-regulatory evolution. However across the hundreds of studies of hybrid ASE, all have been restricted to sexually reproducing eukaryotes, leaving a major gap in our understanding of the genomic patterns of cis-regulatory evolution in prokaryotes. Here we introduce a method to generate stable hybrids between two species of halophilic archaea, and measure genome-wide ASE in these hybrids with RNA-seq. We found that over half of all genes have significant ASE, and that genes encoding kinases show evidence of lineage-specific selection on their cis-regulation. This pattern of polygenic selection suggested species-specific adaptation to low phosphate conditions, which we confirmed with growth experiments. Altogether, our work extends the study of ASE to archaea, and suggests that cis-regulation can evolve under polygenic lineage-specific selection in prokaryotes. ER -