A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity

Abstract

Abstract Camelina sativa , an oilseed crop of the Brassicaceae family, has close relatives that vary in ploidy levels, providing a unique platform for studying plant genome evolution. Here, we report an improved assembly of the widely used C. sativa reference DH55 and three additional genome assemblies of Camelina microcarpa : one tetraploid, and two hexaploids with divergent chromosome numbers, Type 1 (2n = 40) and Type 2 (2n = 38). We uncover the fourth subgenome of the Camelina genus that of C. microcarpa Type 2, which shows numerous unique chromosomal rearrangements differentiating it from other characterized Camelina subgenomes. In this recently formed species, the second subgenome displays gene expression dominance, contrary to expectations from the two-step evolutionary process invoked in the generation of related Brassicaceae species. The observed gene dominance is negatively correlated with inter-subgenome chromatin interaction frequencies, suggesting chromosome conformation and proximity in the nucleus contribute to this mechanism of genome evolution.