Decoding functional regulatory maps via genomic evolutionary footprints in 63 green plants

Systematic identification of functional transcriptional regulatory interactions is essential for understanding regulatory systems. Here, we firstly established genome-wide conservation landscapes for 63 green plants of seven lineages and then developed an algorithm FunTFBS to screen for functional regulatory elements and interactions by coupling base-varied binding affinities of transcription factors with the evolutionary footprints on their binding sites. Using the FunTFBS and the conservation landscapes, we further identified over two million functional interactions for 21,346 TFs, charting functional regulatory maps of these 63 plants. Our work provides plant community with valuable resources to decode plant transcriptional regulatory system and genome sequences.