The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Lejia transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil-microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growthpromoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codonbased methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a "genetic goldmine" to engineer crop resilience to face climate change.
|Journal||Proceedings of the National Academy of Sciences of the United States of America|
|State||Published - 16 Nov 2021|
Bibliographical noteFunding Information:
ACKNOWLEDGMENTS. We thank Alejandro P. Fonseca, Jose Miguel Álvarez, Joaquín Medina, Bernardo Pollack, Sebastián Moreno, Dinka Mandakovic, Mauricio Latorre, Melissa Aguilar, and Angelo Pasquino for their support in the field expeditions. We want to acknowledge Dr. Diego Morata, from the Andean Geothermal Center of Excellence (Centro de Excelencia en Geotermia de los Andes), and his group for performing the total elemental composition determination. This work has been supported by the Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15200002) (to R.A.G.), Millennium Science Initiative Program–iBio ICN17_022 (to R.A.G.), Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT 1180759) (to R.A.G.), US Department of Energy Biological and Environmental Research Grant DE SC0014377 (to G.M.C., R.A.G., D.W.S., R.D., and K.V.), and the Zegar Family Foundation (A16-0051) (to G.M.C.). Powered@NLHPC: This research was partially supported by the supercomputing infrastructure of the National Laboratory for High Performance Computing (NLHPC) (ECM-02). C.W.N. was supported by a Gerstner Scholars Fellowship from the Gerstner Family Foundation at the American Museum of Natural History. H.P.-G. was supported by a FONDECYT Fellowship (Postdoctoral Grant 3130638).
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