Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

Background Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the 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. 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. Conclusions Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.

Germination Patterns in Seeds Produced in Apical and Basal Fruits of Two Thlaspi arvense Populations

The aim of the present work is to study possible differences in the germination behavior of apical and basal seeds (produced in the upper and lower fruits of the infruitescence), of two populations of field pennycress (Thlaspi arvense), both produced in a Mediterranean and a continental temperate climate. The results showed that among the three studied factors (population, seed type, production site), only the production site was relevant for the total germination, germinating those produced in Morris in a greater amount than those produced in Lleida. Germination models could be applied only to seeds produced at Morris (>10% germination), and despite the lack of differences in the total germination percentage, germination rates (speed—b parameter—and time to 50% germination—G50) differed between population and seed types—apical seeds from the Spanish population germinated faster (lower b parameter) than the rest, while apical seeds of both populations germinated faster than the corresponding basal seeds (lower G50). The results show, on the one hand, the importance of the seed production site if this species was considered as a commercial oilseed crop and, on the other hand, differences that will help seed selection for seed germination and establishment improvement of pennycress.

Growing Biofuel Feedstocks in Copper-Contaminated Soils of a Former Superfund Site

Copper mining in the Upper Peninsula of Michigan in the mid-19th century generated millions of tons of mining waste, called stamp sand, which was deposited into various offshoots of Lake Superior. The toxic stamp sand converted the area into barren, fallow land. Without a vegetative cover, stamp sand has been eroding into the lakes, adversely affecting aquatic life. Our objective was to perform a greenhouse study, to grow cold-tolerant oilseed crops camelina (Camelina sativa) and field pennycress (Thlaspi arvense) on stamp sand, for the dual purpose of biofuel production and providing a vegetative cover, thereby decreasing erosion. Camelina and field pennycress were grown on stamp sands in columns, using compost to supply nutrients. A greenhouse study in wooden panels was also done to evaluate the effectiveness of camelina in reducing erosion. Results show that camelina significantly reduced erosion and can also be used commercially for generating biodiesel. A 25-fold reduction in Cu content in the surface run-off was observed in the panels with camelina compared to those of the control. Stamp sand-grown camelina seeds contained 20% and 22.7% oil and protein respectively, and their fatty acid composition was similar to previous studies performed on uncontaminated soils.