Stepwise evolution of root nodule symbiosis [DAP-seq]

Root nodule symbiosis (RNS) represents a significant phenotypic adaptation in plants to thrive in nitrogen-deficient environments. Recent findings propose a single gain of RNS at the crown of the nitrogen-fixing clade (NF clade). However, the genetic mechanisms underlying the origin and subsequent evolution of RNS remain largely unexplored. Here, we newly sequenced and assembled eleven genomes from the NF clade and studied genetic change along the evolution of RNS. Our results elucidated three key evolutionary stages leading to the formation of stable RNS between plants and symbiotic nitrogen-fixing bacteria. Overall design: For cross species RNA-Seq analysis, we newly conducted RNA-Seq of the roots and nodules of five species (Coriaria nepalensis, Elaeagnus umbellata, Alnus trabeculosa, Chamaecrista pumila, Mimosa pudica), as well as the mycorrhizal and non-mycorrhizal roots of Populus deltoides x Populus euramericana cv. "Nanlin895". DNAaffinitypurificationsequencing (DAP-Seq) for transcription factor MtNIN and INPUT100 in Medicago truncatula.