Genomic Evolution Of Populus Pruinosa

Adaptive evolution driven by natural selection is the origin of biodiversity, as well as the most important driver of speciation. For the two sister desert poplar species, Populus pruinosa and P. euphratica, both grow in dry desert areas with high summer temperatures in northwest China. They are characterized by extraordinary adaptation to desert environment such as high salinity and drough stress. Both of them play an important role retaining both water and soil in the arid desert ecosystems and have been used as precious biological resources and model species for studying abiotic responses to salt or drought stress. In addition to differences in leaf and hair morphology between two species, they also occur in different habitats. P. pruinosa occurs in deserts with the underground water closer to the surface, but more salts near to ancient or extant rivers while P. euphratica is distributed in dry deserts with deep underground water. It is obvious that these two species might have diverged due to ecological differentiation, in spite of ongoing gene flow. Hence, these two species also together comprise a good model for studying adaptive speciation.In this study, we reported the high quality genome sequence of P. pruinosa using high-throughput next generation sequencing technology in addition to the already published genomes of Salicaceae, P. trichocarpa, P. euphratica and Salix suchowensis. Additionally, we examined temporal gene expressions of the calli cultivated from four poplar species(P. pruinosa, P. euphratica, P. trichocarpa and P. tomentosa) under salt stress, via a series of transcriptome sequencings. Then, we examined genomic evolutions of the ancestor clade of both P. pruinosa and P. euphratica from other poplars and between themselves at the gene sequence level and gene expression level through comparative genomics, comparative transcriptomics and adaptive evolutionary analysis. Main results and conclusions are listed as follows.(1) We employed the whole-genome shotgun sequencing to sequence P. pruinosa genome. The final assembly covers a total length of452.2Mb, with scaffold N50size of65.2Kb. Sequencing depth distribution showed that over90%of the assembly was covered by more than20×. We predicted a total of34,637protein-coding genes in the P. pruinosa genome. Additionally, we assembled the transcriptome of P. tomentosa and recovered34,177high-quality protein-coding genes with the average length of961bp by RNA sequencing.(2) We detected25positively selected genes in the ancestral clade of P. pruinosa and P. euphratica. They are mainly involved in’cation transmembrane transporter activity’,’response to stress’and’transporter proteins’. These genes may have played important roles in adaptive divergence of the ancestral clade from other poplars.(3) The expression patterns of genes were significantly different between two salt-tolerant species (P. pruinosa and P. euphratica) and the two salt-sensitive ones (P. trichocarpa and P. tomentosa). We further identified18genes which showed adaptive gene expressions in both P. pruinosa and P. euphratica.(4) We reconstructed phylogenetic relationships between these four poplar species and estimated the divergence P. pruinosa and P. euphratica betwen1.0-3.5million years ago. We further confirmed that P. pruinosa and P. euphratica diverged with gene flow based on coalescent tests.(5) In order to test the adaptive divergence between P. pruinosa and P. euphratica, we also identified1424rapidly evolving genes between two species. Among these genes, we detected28and22positively selected genes in the P. pruinosa lineage and the P. euphratica lineage respectively. These genes are mainly involved in ’protein kinase activity’,’transferase activity’,’catalytic activity’and’protein ubiquitination’.(6) Transcriptome comparisons of P. pruinosa and P. euphratica under salt stress suggested that these two species may have developed different genetic pathways in order to adapt to different desert habitats.Overall, all results together provided an extensive genetic basis for the adaptive evolution in the ancestor clade of P. pruinosa and P. euphratica and adaptive divergence between these poplars at the gene sequence level and gene expression level. These findings not only provide a good example for understanding adaptive evolution of plants and ecological speciation driven by natural habitat selection, but also provide critical genetic resources for further functional analyses of the genes identified here.