Phylogeny and Whole-genome Duplication
A total of 279,614 coding sequences from M. pygmaea and genomes representing the two Brassicaceae Lineages (I and II) were assessed, and clustered into 28,151 gene families. Species were grouped into phylogenetic lineages according to their COG gene profiles. M. pygmaea shared a total of 17,919 with Lineage I species and 18,018 with Lineage II, with 292 genes unique to M. pygmaea (Fig. 2A ). Whole-genome duplication (WGD) analyses based on collinear paralogous genes revealed that M. pygmaea , along withA. thaliana and C. rubella , did not experience an independent WGD subsequent to the Brassicaceae-specific At-α WGD (Kiefer et al., 2014) (Fig. 2B ). However, consistent with previous studies, B. rapa had a clade-specific whole genome triplication (Cheng et al., 2014; Zhang et al., 2018). This further supports the cytogenetic evidence of the diploid status of M. pygmaea . M. pygmaea was placed as an independent clade of Lineage II, divergent from other representatives in the phylogenetic tree (Fig. 2C ). M. pygmaea was estimated to diverge from other Lineage II genera around 27.04 (19.11-36.60) million years ago.