Cis -regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids

Carlo G. Artieri, Adit Naor, Israela Turgeman-Grott, Yiqi Zhou, Ryan York, Uri Gophna, Hunter B. Fraser

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article number3986
JournalScientific Reports
Volume7
Issue number1
DOIs
StatePublished - 1 Dec 2017

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