Populus euphratica has stronger regrowth ability than Populus pruinosa under salinity stress.

Pest infestation and soil salinization levels are increasing due to climate change. Comprehending plant regrowth after insect damage and salinity stress is crucial to understanding climate change's multifactorial impacts on forest ecosystems. This study examined Populus euphratica and P. pruinosa regrowth after different defoliation levels combined with salinity stress. Specifically, the biomass and regrowth ability, non-structural carbohydrate (NSC) and nitrogen (N) pools in different organs and the whole plant, and the leaf Cl- concentration of both poplars were analyzed. Our results showed that after 50% defoliation and no salt addition, the regrowth of both species recovered similarly to the control level, while their regrowth was about 70% after 90% defoliation. However, under salinity stress, the regrowth (% leaf biomass) of P. euphratica was significantly higher than P. pruinose at either the 50% or 90% defoliation levels. Additionally, P. euphratica had more soluble sugar, starch, NSC and N pools in leaf, stem, root and whole plant than P. pruinose under salinity stress. The regrowth based on leaf biomass increased linearly with soluble sugar, starch, NSC and N pools, and decreased linearly with leaf Cl- concentration across different salinity and defoliation levels. These results indicated that defoliation significantly decreased NSC and N pools, limiting the growth of both poplars, and salinity stress exacerbated the negative effect. Furthermore, when suffering from salinity stress, P. euphratica with higher NSC and N pools exhibited stronger regrowth ability than P. pruinose.

The chromosome-scale genome and population genomics reveal the adaptative evolution of Populus pruinosa to desertification environment.

The Populus pruinosa is a relic plant that has managed to survive in extremely harsh desert environments. Owing to intensifying global warming and desertification, research into ecological adaptation and speciation of P. pruinosa has attracted considerable interest, but the lack of a chromosome-scale genome has limited adaptive evolution research. Here, a 521.09 Mb chromosome-level reference genome of P. pruinosa was reported. Genome evolution and comparative genomic analysis revealed that tandemly duplicated genes and expanded gene families in P. pruinosa contributed to adaptability to extreme desert environments (especially high salinity and drought). The long terminal repeat retrotransposons (LTR-RTs) inserted genes in the gene body region might drive the adaptive evolution of P. pruinosa and species differentiation in saline-alkali desert environments. We recovered genetic differentiation in the populations of the northern Tianshan Mountain and southern Tianshan Mountain through whole-genome resequencing of 156 P. pruinosa individuals from 25 populations in China. Further analyses revealed that precipitation drove the local adaptation of P. pruinosa populations via some genetic sites, such as MAG2-interacting protein 2 (MIP2) and SET domain protein 25 (SDG25). This study will provide broad implications for adaptative evolution and population studies by integrating internal genetic and external environmental factors in P. pruinosa.

Differences in the Functional Traits of Populus pruinosa Leaves in Different Developmental Stages.

Populus pruinosa Schrenk has the biological characteristics of heteromorphic leaves and is a pioneer species for wind prevention and sand fixation. The functions of heteromorphic leaves at different developmental stages and canopy heights of P. pruinosa are unclear. To clarify how developmental stages and canopy height affect the functional characteristics of leaves, this study evaluated the morphological anatomical structures and the physiological indicators of leaves at 2, 4, 6, 8, 10, and 12 m. The relationships of functional traits to the developmental stages and canopy heights of leaves were also analyzed. The results showed that blade length (BL), blade width (BW), leaf area (LA), leaf dry weight (LDW), leaf thickness (LT), palisade tissue thickness (PT), net photosynthetic rate (Pn), stomatal conductance (Gs), proline (Pro), and malondialdehyde (MDA) content increased with progressing developmental stages. BL, BW, LA, leaf dry weight, LT, PT, Pn, Gs, Pro, and the contents of MDA, indoleacetic acid, and zeatin riboside had significant positive correlations with canopy heights of leaves and their developmental stages. The morphological structures and physiological characteristics of P. pruinosa leaves showed more evident xeric structural characteristics and higher photosynthetic capacity with increasing canopy height and progressive developmental stages. Resource utilization efficiency and the defense ability against environmental stresses were improved through mutual regulation of each functional trait.

Multi-omics analysis reveals spatiotemporal regulation and function of heteromorphic leaves 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.

Genome-wide analysis of R2R3-MYB transcription factors reveals their differential responses to drought stress and ABA treatment in desert poplar (Populus euphratica).

The R2R3-MYB transcription factors are widely involved in the regulation of plant growth, biotic and abiotic stress responses. Meanwhile, seed germination, which is stimulated by internal and external environments, is a critical stage in the plant life cycle. However, the identification, characterization, and expression profiling of the Populus euphratica R2R3-MYB family in drought response during seed germination have been unknown. Our study attempted to identify and characterize the R2R3-MYB genes in P. euphratica (PeR2R3-MYBs) and explore how R2R3-MYBs trigger the drought and abscisic acid (ABA) response mechanism in its seedlings. Based on the analysis of comparative genomics, 174 PeR2R3-MYBs were identified and expanded driven by whole genome duplication or segment duplication events. The analysis of Ka/Ks ratios showed that, in contrast to most PeR2R3-MYBs, the other PeR2R3-MYBs were subjected to positive selection in P. euphratica. Further, the expression data of PeR2R3-MYBs under drought stress and ABA treatment, together with available functional data for Arabidopsis thaliana MYB genes, supported the hypothesis that PeR2R3-MYBs involved in response to drought are dependent or independent on ABA signaling pathway during seed germination, especially PeR2R3-MYBs with MYB binding sites (MBS) cis-element and/or tandem duplication. This study is the first report on the genome-wide analysis of PeR2R3-MYBs, as well as the other two Salicaceae species. The duplication events and differential expressions of PeR2R3-MYBs play important roles in enhancing the adaptation to drought desert environment. Our results provide a reference for prospective functional studies of R2R3-MYBs of poplars and lay the foundation for new breeding strategies to improve the drought tolerance of P. euphratica.

Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism.

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.

Structural and Functional Responses of the Heteromorphic Leaves of Different Tree Heights on Populus euphratica Oliv. to Different Soil Moisture Conditions.

Populus euphratica Oliv., a pioneer species of desert riparian forest, is characterized heterophylly. To understand the adaptation strategies of the heteromorphic leaves of P. euphratica to soil drought, we assessed the structural and functional characteristics of the heteromorphic leaves at different heights in suitable soil moisture conditions (groundwater depth 1.5 m) and drought conditions (groundwater depth 5 m), which include morphology, anatomical structure, photosynthetic capacity, water use efficiency, osmotic adjustment capacity, and endogenous hormones. These results indicate that leaf area, leaf thickness, fence tissue, palisade-to-sea ratio, main vein xylem area, vessel area, net photosynthetic rate, transpiration rate, and proline, MDA, IAA, GA3, and ZR contents showed a positive correlation with the tree height under the two soil moisture conditions, but leaf shape index, leaf water potential (LWP), and ABA content showed a decreasing trend. In addition, the main vein vascular bundle area, main vein xylem area, and contents of malondialdehyde, ABA, GA3, and IAA were significantly greater under soil drought conditions than normal soil water content. Under soil drought stress, the heteromorphic leaves of P. euphratica showed more investment in anatomical structure and greater water use efficiency, proline, and hormone contents, and synergistic changes to maintain high photosynthetic efficiency. This is an adaptation strategy to water stress caused by soil drought and tree height changes.

Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of Populus sect. Turanga in Northwest China.

Populus sect. Turanga (hereafter referred to as "Populus"), including Populus euphratica and Populus pruinosa, are the predominant tree species in desert riparian forests in northwestern China. These trees play key roles in maintaining ecosystem balance, curbing desertification, and protecting biodiversity. However, the distribution area of Populus forests has been severely diminished and degraded in recent years due to increased habitat destruction and human activity. Understanding the genetic diversity among Populus individuals and populations is essential for designing conservation strategies, but comprehensive studies of their genetic diversity in northwest China are lacking. Here, we assessed the population structures and genetic diversity of 1,620 samples from 85 natural populations of Populus (59 P. euphratica and 26 P. pruinosa populations) covering all of northwestern China using 120 single nucleotide polymorphism (SNP) markers. Analysis of population structure revealed significant differentiation between these two sister species and indicated that strong geographical distribution patterns, a geographical barrier, and environmental heterogeneity shaped the extant genetic patterns of Populus. Both P. euphratica and P. pruinosa populations in southern Xinjiang had higher genetic diversity than populations in other clades, perhaps contributing to local geographic structure and strong gene flow. Analysis of molecular variance (AMOVA) identified 15% variance among and 85% variance within subpopulations. Mantel tests suggested that the genetic variation among P. euphratica and P. pruinosa populations could be explained by both geographical and environmental distance. The genetic diversity of P. euphratica showed a significant negative correlation with latitude and longitude and a positive correlation with various environmental factors, such as precipitation of warmest quarter and driest month, temperature seasonality, and annual mean temperature. These findings provide insights into how the genetic differentiation of endangered Populus species was driven by geographical and environmental factors, which should be helpful for designing strategies to protect these genetic resources in the future.

Complete chloroplast genome sequence of Populus euphratica from PacBio Sequel platform.

Populus euphratica Oliv., one of tall arbors growing in desert areas, has great stress resistance. The complete chloroplast genome was reported in this study using the PacBio Sequel Platform. The chloroplast genome with a total size of 157,881 bp consisted of two inverted repeats (IRs) (27,666 bp) separated by a large single-copy region (85,906 bp) and a small single-copy region (16,643 bp). Further annotation revealed the chloroplast genome contains 111 genes, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. The information of the chloroplast genome will be useful for study on the evolution of P. euphratica in the future.

Transcriptomic profile analysis of the halophyte Suaeda rigida response and tolerance under NaCl stress.

Suaeda rigida is a lignified, true haplotype that predominantly grows in the Tarim basin, China. It has significant economic and ecological value. Herein, with aim to determine the genes associated with salt tolerance, transcriptome sequencing was performed on its stem, leaves and root over three set NaCl gradients regimens at treatment intervals of 3 h and 5 days. From our findings, we identified 829,095 unigenes, with 331,394 being successfully matched to at least one annotation database. In roots, under 3 h treatment, no up-regulated DEGs were identified in 100 and 500 mM NaCl treated samples. Under 5 days treatment, 97, 60 and 242 up-regulated DEGs were identified in 100, 300, 500 mM NaCl treated samples, respectively. We identified 50, 22 and 255 down-regulated DEGs in 100, 300, 500 mM NaCl treated samples, respectively. GO biological process enrichment analysis established that down-regulated DEGs were associated with nitrogen compound transport, organic substance transport and intracellular protein transport while the up-regulated genes were enriched in cell wall biogenesis, such as plant-type cell wall biogenesis, cell wall assembly, extracellular matrix organization and plant-type cell wall organization. These findings provide valuable knowledge on genes associated with salt tolerance of Suaeda rigida, and can be applied in other downstream haplotype studies.