Going broad and deep: sequencing driven insights into plant physiology, evolution and crop domestication.

Deep-sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely), high quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 plant transcriptomes project has long been completed (One Thousand Plant Transcriptomes, 2019). The EarthBioGenome project will dwarf even these milestones (Lewin et al., 2022). That said, massive progress in understanding plant physiology, evolution and crop domestication have been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches namely genome wide association- and transcriptome wide association- studies as well as the compilation of pan-genomes. This will include both the most commonly used methods reliant on single nucleotide polymorphisms and short indels as well as more recent examples which consider structural variants. We will subsequently present case-studies exemplifying how their application have brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches both to different species, tissues and biological processes.