Evolution of a ZW sex chromosome system in willows.

Transitions in the heterogamety of sex chromosomes (e.g., XY to ZW or vice versa) fundamentally alter the genetic basis of sex determination, however the details of these changes have been studied in only a few cases. In an XY to ZW transition, the X is likely to give rise to the W because they both carry feminizing genes and the X is expected to harbour less genetic load than the Y. Here, using a new reference genome for Salix exigua, we trace the X, Y, Z, and W sex determination regions during the homologous transition from an XY system to a ZW system in willow (Salix). We show that both the W and the Z arose from the Y chromosome. We find that the new Z chromosome shares multiple homologous putative masculinizing factors with the ancestral Y, whereas the new W lost these masculinizing factors and gained feminizing factors. The origination of both the W and Z from the Y was permitted by an unexpectedly low genetic load on the Y and this indicates that the origins of sex chromosomes during homologous transitions may be more flexible than previously considered.

Antifungal Activity of Cadinane-Type Sesquiterpenes from Eupatorium adenophorum against Wood-Decaying Fungi.

The present study aimed to evaluate the antifungal activities of Eupatorium adenophorum against four strains of wood-decaying fungi, including Inonotus hispida, Inonotus obliquus, and Inonotus cuticularis. Bioguided isolation of the methanol extract of E. adenophorum by silica gel column chromatography and high-performance liquid chromatography afforded six cadinane-type sesquiterpenes. Their structures were identified by nuclear magnetic resonance and MS analyses. According to the antifungal results, the inhibition rate of the compound was between 59.85 % and 77.98 % at a concentration of 200 µg/mL. The EC50 values ranged from 74.5 to 187.4 µg/mL.

A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination.

Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.

Repeated turnovers keep sex chromosomes young in willows.

BACKGROUND: Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. RESULTS: Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the "deleterious mutation load" and "sexually antagonistic selection" theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. CONCLUSIONS: Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species.

PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar.

BACKGROUND: Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of habitats including highly saline ones. However, its triploid genome complicates any detailed investigation of the molecular mechanisms underlying its adaptations. RESULTS: We report a haplotype-resolved genome of this triploid poplar and characterize, using reverse genetics and biochemical approaches, a MYB gene, SALT RESPONSIVE MYB TRANSCRIPTION FACTOR (SRMT), which combines NUCLEAR FACTOR Y SUBUNIT C 9 (PtoNF-YC9) and RESPONSIVE TO DESICCATION 26 (PtoRD26), to regulate an ABA-dependent salt-stress response signaling. We reveal that the salt-inducible PtoRD26 is dependent on ABA signaling. We demonstrate that ABA or salt drives PtoNF-YC9 shuttling into the nucleus where it interacts with SRMT, resulting in the rapid expression of PtoRD26 which in turn directly regulates SRMT. This positive feedback loop of SRMT-PtoRD26 can rapidly amplify salt-stress signaling. Interference with either component of this regulatory module reduces the salt tolerance of this triploid poplar. CONCLUSION: Our findings reveal a novel ABA-dependent salt-responsive mechanism, which is mediated by the PtoNF-YC9-SRMT-PtoRD26 module that confers salt tolerance to this triploid poplar. These genes may therefore also serve as potential and important modification targets in breeding programs.

The U-box E3 ubiquitin ligase PalPUB79 positively regulates ABA-dependent drought tolerance via ubiquitination of PalWRKY77 in Populus.

The abscisic acid (ABA) signalling pathway is involved in the plant response to osmotic stress caused by drought and/or salinity. Although the ABA signalling pathway has been elucidated in Arabidopsis, it remains elusive in woody poplars. In this study, genome-wide analyses of U-box genes in poplars revealed that a U-box E3 ubiquitin ligase gene, PalPUB79, is significantly induced following drought, salinity and ABA signalling. PalPUB79 overexpression enhanced drought tolerance in transgenic poplars, while PalPUB79 RNAi lines were more sensitive to drought. PalPUB79 positively regulated ABA signalling pathway. Furthermore, PalPUB79 interacted with PalWRKY77, a negative transcriptional regulator of ABA signalling, and mediated its ubiquitination for degradation, therefore counteracting its inhibitory effect on PalRD26 transcription. However, the finding that PalWRKY77 negatively regulates PalPUB79 expression was indicative of a negative feedback loop between PalWRKY77 and PalPUB79 during ABA signalling in poplar. These findings provide novel insight into the mechanism through which PalPUB79 enhances the ABA-mediated stress response in woody poplars.

Salicylic acid regulates PIN2 auxin transporter hyperclustering and root gravitropic growth via Remorin-dependent lipid nanodomain organisation in Arabidopsis thaliana.

To adapt to the diverse array of biotic and abiotic cues, plants have evolved sophisticated mechanisms to sense changes in environmental conditions and modulate their growth. Growth-promoting hormones and defence signalling fine tune plant development antagonistically. During host-pathogen interactions, this defence-growth trade-off is mediated by the counteractive effects of the defence hormone salicylic acid (SA) and the growth hormone auxin. Here we revealed an underlying mechanism of SA regulating auxin signalling by constraining the plasma membrane dynamics of PIN2 auxin efflux transporter in Arabidopsis thaliana roots. The lateral diffusion of PIN2 proteins is constrained by SA signalling, during which PIN2 proteins are condensed into hyperclusters depending on REM1.2-mediated nanodomain compartmentalisation. Furthermore, membrane nanodomain compartmentalisation by SA or Remorin (REM) assembly significantly suppressed clathrin-mediated endocytosis. Consequently, SA-induced heterogeneous surface condensation disrupted asymmetric auxin distribution and the resultant gravitropic response. Our results demonstrated a defence-growth trade-off mechanism by which SA signalling crosstalked with auxin transport by concentrating membrane-resident PIN2 into heterogeneous compartments.

A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae.

Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.

Improved genome assembly provides new insights into genome evolution in a desert poplar (Populus euphratica).

Populus euphratica is well adapted to extreme desert environments and is an important model species for elucidating the mechanisms of abiotic stress resistance in trees. The current assembly of P. euphratica genome is highly fragmented with many gaps and errors, thereby impeding downstream applications. Here, we report an improved chromosome-level reference genome of P. euphratica (v2.0) using single-molecule sequencing and chromosome conformation capture (Hi-C) technologies. Relative to the previous reference genome, our assembly represents a nearly 60-fold improvement in contiguity, with a scaffold N50 size of 28.59 Mb. Using this genome, we have found that extensive expansion of Gypsy elements in P. euphratica led to its rapid increase in genome size compared to any other Salicaceae species studied to date, and potentially contributed to adaptive divergence driven by insertions near genes involved in stress tolerance. We also detected a wide range of unique structural rearrangements in P. euphratica, including 2,549 translocations, 454 inversions, 121 tandem and 14 segmental duplications. Several key genes likely to be involved in tolerance to abiotic stress were identified within these regions. This high-quality genome represents a valuable resource for poplar breeding and genetic improvement in the future, as well as comparative genomic analysis with other Salicaceae species.

Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection.

Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of Populus, a model tree genus in the Northern Hemisphere. We constructed phylogenetic trees of 29 Populus taxa using 80 individuals based on re-sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple-species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence. We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection-mediated ancient polymorphisms are prevalent in the genus Populus. These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies.

Intergeneric Relationships within the Family Salicaceae s.l. based on Plastid Phylogenomics.

Many Salicaceae s.l. plants are recognized for their important role in the production of products such as wood, oils, and medicines, and as a model organism in life studies. However, the difference in plastid sequence, phylogenetic relationships, and lineage diversification of the family Salicaceae s.l. remain poorly understood. In this study, we compare 24 species representing 18 genera of the family. Simple sequence repeats (SSRs) are considered effective molecular markers for plant species identification and population genetics. Among them, a total of 1798 SSRs were identified, among which mononucleotide repeat was the most common with 1455 accounts representing 80.92% of the total. Most of the SSRs are located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae s.l. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the inverted repeat (IR) boundary, lacking major structural variations, but we identified six divergence hotspot regions. We obtained phylogenetic relationships of 18 genera in Salicaceae s.l. and the 24 species formed a highly supported lineage. Casearia was identified as the basal clade. The divergence time between Salicaceae s.l. and the outgroup was estimated as ~93 Mya; Salix, and Populus diverged around 34 Mya, consistent with the previously reported time. Our research will contribute to a better understanding of the phylogenetic relationships among the members of the Salicaceae s.l.

The complete chloroplast genome of Azara serrata (Salicaceae) from Chile.

The chloroplast (cp) genome sequence of Azara serrata has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,306 bp in length, containing a large single copy region (LSC) of 85,059 bp and a small single copy region (SSC) of 17,889 bp, which were separated by a pair of 27,679 bp inverted repeat regions (IRs). The genome contained 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content is 36.5%, while the corresponding values of the LSC, SSC, and IR regions are 34.3, 30.0, and 42.0%, respectively. Further, phylogenetic analysis suggested that the A. serrata is a sister of Flacourtia indica and is an outgroup to the remaining genera of Saliaceae.

Polyhydric polymer-functionalized fluorescent probe with enhanced aqueous solubility and specific ion recognition: A test strips-based fluorimetric strategy for the rapid and visual detection of Fe3+ ions.

A polyhydric polymer-functionalized probe with enhanced aqueous solubility was designed initially by coupling 1-pyrenecarboxyaldehyde (Pyr) onto poly(vinyl alcohol) (PVA) via the one-step condensation reaction. Polyhydric PVA polymer chains could facilitate the Pyr fluorophore with largely improved aqueous solubility and especially strong cyan fluorescence. Importantly, the fluorescence of the PVA-Pyr probes could thereby be quenched specifically by Fe3+ ions through the strong PVA-Fe3+ interaction triggering the polymeric probe aggregation. Furthermore, a test strips-based fluorimetric method was developed with the stable and uniform probe distribution by taking advantage of the unique film-forming ability and the depression capacity of "coffee-stain" effects of PVA matrix. The as-developed test strips could allow for the rapid and visual detections of Fe3+ ions simply by a dipping way, showing a linear concentration range of 5.00-300µM, with the detection limit of 0.73µM. Moreover, the proposed method was applied to the evaluation of Fe3+ ions in natural water samples, showing the analysis performances better or comparable to those of current detection techniques. This test strips-based fluorimetric strategy promises the extensive applications for the rapid on-site monitoring of Fe3+ ions in environmental water and the outdoor finding of the potential iron mines.

Transfer-Free Fabrication of Graphene Scaffolds on High-k Dielectrics from Metal-Organic Oligomers.

In situ fabrication of graphene scaffold-ZrO2 nanofilms is achieved by thermal annealing of Zr-based metal-organic oligomers on SiO2 substrates. The structural similarities of the aromatic moieties in the ligand (phenyl-, naphthyl-, anthryl-, and pyrenyl-) compared to graphene play a major role in the ordering of the graphene scaffolds obtained. The depth profiling analysis reveals ultrathin carbon-pure or carbon-rich surfaces of the graphene scaffold-ZrO2 nanofilms. The graphene scaffolds with ∼96.0% transmittance in the visible region and 4.8 nm in thickness can be grown with this non-chemical vapor deposition method. Furthermore, the heterogeneous graphene scaffold-ZrO2 nanofilms show a low sheet resistance of 17.0 kΩ per square, corresponding to electrical conductivity of 3197 S m(-1). The strategy provides a facile method to fabricate graphene scaffolds directly on high-k dielectrics without transferring process, paving the way for its application in fabricating electronic devices.

Interface interaction within nanopores in thin films of an amphiphilic block copolymer and CTAB.

With water droplets as sacrificed templates at a particular humidity, micro-porous solid thin films were successfully fabricated by self-assembly using an amphiphilic block polymer, polystyrene-b-polyacrylic acid (PS-b-PAA). Interface interactions between the micro-porous thin film and a cationic surfactant, cetyltrimethylammonium bromide (CTAB), are investigated by in-situ AFM in aqueous solutions. An interesting phenomenon was observed in water and CTAB solution, which the dimensions of the micropores are remarkably larger than the dimensions of those in air. The solid thin films exhibit different surface morphologies in response to stimulus by different concentrations of CTAB. These observations were explained by positing that the PAA chains in the micropores stretch and contract with interface interactions between PAA and CTAB. A promising electrochemical application of this film is suggested. This study is aimed at strategies for the functionalization of stimulus-responsive micro-porous solid thin films with tunable surface morphologies, and exploring new smart materials.

Photoinduced DNA cleavage by alpha-, beta-, and gamma-cyclodextrin-bicapped C60 supramolecular complexes.

Water-soluble supramolecular inclusion complexes of alpha-, beta-, and gamma-cyclodextrin-bicapped C60 (CD/C60) have been investigated for their photoinduced DNA cleavage activities, with the aim to assess the potential health risks of this class of compounds and to understand the effect of host cyclodextrins having different cavity dimensions. Factors such as incubation temperature, irradiation time, and concentration of NADH or CDs/ C60 supramolecular inclusion complexes have been examined. The results show that alpha-, beta-, and gamma-CDs/C60 are all able to cleave double-stranded DNA under visible light irradiation in the presence of NADH. However, a difference in the photoinduced DNA cleavage efficiency is observed, where the cleavage efficiency increases in the order of alpha-, beta-, and gamma-CD/C60. The difference is attributed to the different aggregation behavior of the inclusion complexes in aqueous solution, which is correlated to the cavity dimension of the host cyclodextrin molecules.

Voltammetric determination of terbinafine in biological fluid at glassy carbon electrode modified by cysteic acid/carbon nanotubes composite film.

The electrochemical oxidation of L-cysteine (CySH) in presence of carbon nanotubes (CNTs) formed a composite film at a glassy carbon electrode (GCE) as a novel modifier for directly electroanalytical determination of terbinafine without sample pretreatment in biological fluid. The determination of terbinafine at the modified electrode with strongly accumulation was studied by differential pulse voltammetry (DPV). The peak current obtained at +1.156 V (vs. SCE) from DPV was linearly dependent on the terbinafine concentration in the range of 8.0 x 10(-8)-5.0 x 10(-5 )M in a B-R buffer solution (0.04 M, pH 1.81) with a correlation coefficient of 0.998. The detection limit (S/N=3) was 2.5 x 10(-8 )M. The low-cost modified electrode showed good sensitivity, selectivity, and stability. This developed method had been applied to the direct determination of terbinafine in human serum samples with satisfactory results. It is hopeful that the modified electrode will be applied for the medically clinical test and the pharmacokinetics in future.