Genomic Basis For Salt Asaptation In A Desert Poplat

Populus euphratica Oliv, the only tree species found in the desert regions of northwest China, is characterized by extraordinary adaptation to salt stress. Notably, at high salinity it maintains higher growth and photosynthetic rates than other poplar species, and has become a model for elucidating both physiological and molecular mechanisms of salt tolerance in tree species. In this study, we report a high quality genome sequence of this desert poplar using high-throughput next generation sequencing technology. We provide essential background for understanding the genetic and molecular mechanisms underlying salt tolerance in P. euphratica by comparing its genome sequences and gene expression differences with those of its salt sensitive congeners.We employed a newly developed fosmid-pooling and hierarchical strategy to sequence and assemble the complex P. euphratica genome. The final assembly covers a total length of496.5Mb, with contig and scaffold N50size of40.4Kb and482Kb, respectively. Sequencing depth distribution showed that over92.5%of the assembly was covered by more than20x. The assembly covered97.3%of the516,712Populus ESTs and97.7%of the seven complete fosmids sequenced by Sanger sequencing. The coverage of the core eukaryotic genes was estimated to be94.35%for the P. euphratica assembly. All of these statistics revealed that our genome sequence has high contiguity, coverage and accuracy. We identified a total of2,434,697heterozygous SNVs in this P. euphratica genome, which is almost twice that in P. trichocarpa. We also identified and designed a total of18,938universal pairs of SSR (simple sequence repeat) primers, which can be converted into genetic markers across most poplar species. These SSR markers provide a desirable marker resource for future genetic mapping, QTL analyses and molecular breeding within the Meta-genome of Populus. We predicted a total of34,279protein-coding genes in the P. euphratica genome, including1,003genes related to the process of wood formation, such as the synthesis of lignin, cellulose and hemicellulose. The divergence time between P. euphratica and P. trichocarpa was estimated to be8million years ago. The genome of P. euphratica is very similar and collinear to that of P. trichocarpa, and they share at least two ancient whole genome duplication events.Gene family clustering analysis revealed that327families comprising841genes are specific to P. euphratica,2,270gene families were substantially expanded in P. euphratica compared to other plant species. For example, the HKT1gene family, which encodes Na+/K+transporters. expanded from one member in the P. trichocarpa genome to four in the P. euphratica genome. Other expanded gene families include those encoding P-type H+-ATPases, heat-shock proteins (HSPs), enzymes involved in biosynthesis of critical solutes (BADH and GolS4) and antioxidative enzymes (CATand GR1). We also detected57positively selected genes in the P. euphratica lineage, including ENH1, CIPK1and PSD1. We further compared the expression profiles of the P. euphratica calluses in response to salt stress with those of the P. tomentosa (a salt-sensitive poplar) calluses. The results showed that2,278differentially expressed genes were specific to P. euphratica, including KUP3, PeNhaD and NCL. Our analyses taken together suggest that P. euphratica may have increased its salt tolerance through duplication and/or up-regulation of multiple genes involved in ion transport and homeostasis.