Short structural variation fuelled CAM evolution within an explosive bromeliad radiation

1. Abstract

Identifying the drivers of trait evolution and diversification is central to understanding plant diversity and evolution. The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of the water- conserving Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, CAM has evolved independently across many plant families and over short timescales. By producing the first high-quality genome assemblies of a species pair representing a recent CAM/C3 shift, we were able to pinpoint the genomic drivers of trait evolution and diversification in Tillandsia. We combined genome-wide investigations of synteny, TE dynamics, sequence evolution, gene family evolution and differential expression to highlight the crucial role of rapid gene family expansion and transposable element activity associated with differentially expressed genes in fuelling CAM/C3 shifts in this vast plant radiation.