A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought tolerance mechanisms

Plants grown under extreme environments represent unique sources for stress-resistant genes and mechanisms. Ammopiptanthus mongolicus (Leguminosae) is a xerophytic legume shrub with evergreen broadleaves native to the semi-arid and desert regions, however, its drought tolerance mechanisms have not been well understood. Here, we report the assembly of a reference-grade genome, its evolutionary history within the legume family, and examination to its drought tolerance mechanisms. The assembled genome size was 843.07 Mb and 98.7% of the assembly was successfully anchored to the nine chromosomes of the plant. 47,611 genes were predicted to be protein-coding and 70.71% of the genome is composed of repetitive sequences dominated by transposable elements, particularly long-terminal-repeat retrotransposons (LTR-RTs). Evolutionary analyses revealed two whole-genome duplication (WGD) events shared by the genus Ammopiptanthus and other legumes at 130 and 58 million years ago (Mya), whereas no species-specific WGD was found within this genus. Further ancestral genome reconstruction indicated that the A. mongolicus genome had fewer rearrangements within the legume family, confirming it is a “relict plant”. Transcriptomic analyses revealed that cuticular wax biosynthesis and transport genes were highly expressed under both normal and polyethylene glycol (PEG)-induced dehydration conditions, and significant induction of ethylene biosynthesis and signaling related genes was also observed in leaves experiencing the dehydration stress, indicating that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in A. mongolicus. Consistently, ectopic expression of AmERF2, an ethylene response factor unique for A. mongolicus, resulted in marked increase of drought tolerance in transgenic Arabidopsis thaliana plants, demonstrating the application potential of A. mongolicus genes in crop improvement.