Populus euphratica Oliv., the Euphrates poplar, is the tallest tree species in the arid desert areas of Northwest China. Investigation of its drought-resistance genes is valuable to increase understanding of drought resistance mechanisms. RNA-seq of leaves and roots under drought simulation by 25% polyethylene glycol-6000 (PEG 6000) were performed at 0, 4, and 12 h. Leaves and roots responded differently to drought via differentially upregulated and downregulated genes; more genes were downregulated than upregulated in both leaves and roots. Additionally, these differentially expressed genes were enriched in different GO terms and KEGG pathways. For example, GO term ‘response to organic substance’ and KEGG pathway ‘nitrogen metabolism’ were enriched for drought-stressed leaves, while GO term ‘cell wall organization or biogenesis’ and KEGG pathway ‘zeatin biosynthesis’ were enriched for drought-stressed roots. The enrichment of the GO term ‘enzyme linked receptor protein signalling pathway’ in both leaf and root drought responses suggests that these tissues may also have similar mechanisms. However, roots under drought stress for four hs responded by activating programed cell death. The KEGG pathway ‘plant hormone signal transduction’ was detected for 4- and 12-h drought-stressed leaves and 12-h drought-stressed roots, suggesting that plant hormone signal transduction plays an important role in both roots and leaves. GO enrichment of upregulated and downregulated genes for leaves and roots reflect differentially regulatory mechanisms of response to drought stress via different biological processes such as the regulation of photosynthesis and auxin signalling pathway in leaves, and the regulation of defence response and water homeostasis in roots. Fifteen candidate genes, including transcription factors, protein kinase, transporter, late embryogenesis abundant protein and mannitol dehydrogenase, were further selected to determine their response to drought using qRT-PCR. The results show that the expression patterns of 13 of the 15 genes correspond to the RNA-seq results. This study provides new insights into the drought response mechanism of P. euphratica and suggests new candidate gene resources.

Reference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus.

Despite the high economic and ecological importance of forests, our knowledge of the adaptive evolution of leaf traits remains very limited. Euphrates poplar (Populus euphratica), which has high tolerance to arid environment, has evolved four heteromorphic leaf forms, including narrow (linear and lanceolate) and broad (ovate and broad-ovate) leaves on different crowns. Here, we revealed the significant functional divergence of four P. euphratica heteromorphic leaves at physiological and cytological levels. Through global analysis of transcriptome and DNA methylation across tree and leaf developmental stages, we revealed that gene expression and DNA epigenetics differentially regulated key processes involving development and functional adaptation of heteromorphic leaves, such as hormone signaling pathways, cell division, and photosynthesis. Combined analysis of gene expression, methylation, ATAC-seq, and Hi-C-seq revealed longer interaction of 3D genome, hypomethylation, and open chromatin state upregulates IAA-related genes (such as PIN-FORMED1 and ANGUSTIFOLIA3) and promotes the occurrence of broad leaves while narrow leaves were associated with highly concentrated heterochromatin, hypermethylation, and upregulated abscisic acid pathway genes (such as Pyrabactin Resistance1-like10). Therefore, development of P. euphratica heteromorphic leaves along with functional divergence was regulated by differentially expressed genes, DNA methylation, chromatin accessibility, and 3D genome remodeling to adapt to the arid desert. This study advances our understanding of differential regulation on development and functional divergence of heteromorphic leaves in P. euphratica at the multi-omics level and provides a valuable resource for investigating the adaptive evolution of heteromorphic leaves in Populus.

Euphrates poplar (Populus euphratica Oliv.) has heteromorphic leaves including strip, lanceolate, ovate, and broad‐ovate leaves from base to top in the mature canopy. To clarify how diameter at breast height (DBH) and tree height affect the functional characteristics of all kinds of heteromorphic leaves, we measured the morphological anatomical structure and physiological indices of five crown heteromorphic leaves of P. euphratica at 2, 4, 6, 8, 10, and 12 m from the same site. We also analysed the relationships between morphological structures and physiological characteristics of heteromorphic leaves and DBH and the height of heteromorphic leaves. The results showed that the number of abnormalities regarding blade width, leaf area, leaf thickness, leaf mass per area, cuticle layer thickness, palisade tissue thickness, and palisade tissue/sponge tissue ratio increased with size order and sampling height gradient. Net photosynthetic rate, transpiration rate, stomatal conductance, instantaneous water use efficiency, stable delta carbon isotope ratio, proline and malondialdehyde (MDA) content increased with DBH and sampling height. By contrast, blade length, leaf shape index, and intercellular CO2 concentration decreased with the increase in path order and sampling height gradient. Although MDA content and leaf sponge thickness were not correlated with DBH or sampling height, other morphological structure and physiological parameters were significantly correlated with these variables. In addition, correlations were found among leaf morphology, anatomical structure, and physiological index parameters indicating that they changed with path order and tree height gradient. The differences in the morphology, anatomic structure and physiological characteristics of the heteromorphic leaves ofP. euphratica are related to ontogenesis stage and coronal position.