A Chinese research team led by Prof. Gao Caixia has developed Programmable Chromosome Engineering (PCE) systems enabling precise genetic manipulations at the megabase scale in higher organisms, especially plants. By innovating novel asymmetric Lox recombination sites, engineering Cre recombinase via AI-informed evolution for enhanced efficiency, and implementing scarless editing methods using prime editors, this breakthrough addresses longstanding limitations in chromosome engineering. These advances, published in Cell, pave the way for sophisticated genome editing applications across diverse fields including agriculture and therapeutics.