<b>Field pennycress (</b><b><i>Thlaspi arvense</i></b><b>)</b>

We sequenced and assembled <i>de novo</i> the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2,495 single-copy genes revealed that pennycress is closely related to <i>Eutrema salsugineum</i><i> </i>(estimated divergence 14.32-18.58 Mya),<i> </i>and both species form a sister clade to <i>Schrenkiella parvula</i>, and genus <i>Brassica</i>. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two high- and two low-elevation populations detected 1,256,971 high-quality single-nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high altitude adaptation.<b> </b>Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early-flowering in high-elevation populations.