Summary 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.

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.

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We have identified a synergistic roughening mechanism of 193 nm photoresist, where simultaneous ion bombardment, vacuum ultraviolet (VUV) radiation, and moderate substrate heating in a well‐characterized beam system results in a similar level of surface roughness observed during conditions typical of plasma etching. VUV radiation (147 nm) results in bulk modification of the photoresist polymer, witnessed by the loss of carbon–oxygen bonds through transmission FTIR. Ion bombardment (150 eV) results in the formation of a densified surface layer on the order of a few nanometers in depth. We have shown that elevated levels of roughness are observed only during simultaneous exposure and that sequential exposure is not sufficient to produce surface roughness. In addition, through the use of transmission FTIR we have shown that an etching synergy does not exist and that etch rates are nearly independent of temperature. We propose that the observed roughness could be due to the drastically different mechanical properties of the ion‐modified near‐surface region and VUV‐modified bulk photoresist, where the difference is exaggerated at elevated temperatures. A more complete understanding of plasma‐induced surface roughness will require further study, resulting in the improvement of existing pattern transfer technologies and possibly novel new technologies as well.

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.

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 singlemolecule 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.

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.

0Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly 3 1 in multiple plant lineages. However, the specific mechanisms through which sex 3 2 systems evolve and their commonalities among plant species remain poorly 3 3 understood. With both XY and ZW sex systems, the family Salicaceae provides a 3 4 system to uncover the evolutionary forces driving sex chromosome turnovers. In this 3 5 study, we performed a genome-wide association study to characterize sex 3 6 determination in two Populus species, P. euphratica and P. alba. Our results reveal an 3 7XY system of sex determination on chromosome 14 of P. euphratica, and a ZW 3 8 system on chromosome 19 of P. alba. We further assembled the corresponding sex 3 9 determination regions, and found that their sex chromosome turnovers may be driven 4 0 by the repeated translocations of a Helitron-like transposon. During the translocation, 4 1 this factor may have captured partial or intact sequences that are orthologous to a 4 2 type-A cytokinin response regulator gene. Based on results from this and other 4 3recently published studies, we hypothesize that this gene may act as a master regulator 4 4 of sex determination for the entire family. We propose a general model to explain how 4 5 the XY and ZW sex systems in this family can be determined by the same RR gene. 6Our study provides new insights into the diversification of incipient sex chromosome 4 7 in flowering plants by showing how transposition and rearrangement of a single gene 4 8 can control sex in both XY and ZW systems. 4 9 5 0