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Changes in temperature during reactor operation may cause changes in physical parameters, leading to core overheating and accidents. It is essential to analyze and assess the safety parameters of the core under different operating conditions. This paper investigates the effects of fuel temperature, moderator density, boron concentration, and control rod state on AP1000 safety parameters. The study uses RMC and NJOY to calculate the changes in reactivity factor, effective delayed neutron fraction, and neutron generation time of the AP1000 reactor under different operating conditions. The changes in reactivity coefficients, neutron fluxes, and relative power densities of AP1000 reactors are analyzed for normal and accidental operating conditions. The results indicated that the reactivity coefficient remained negative under accident conditions, which ensured the safe operation of the reactor. The delayed neutron fraction, neutron flux, and power density distributions are affected by fuel temperature, moderator density, and control rod position. The control rod worth was sufficient for the emergency shutdown of the reactor under accidental conditions. It is demonstrated that the operation of the AP1000 reactor under study conditions is safe and controllable. [ABSTRACT FROM AUTHOR]

Based on commercial CFD software, a 700 °C ultra-supercritical tangential boiler was simulated by the orthogonal test method, and the thermal deviation of flue gas at the furnace outlet section was used as the optimization index. Three horizontal optimization treatments are designed respectively for the air distribution mode of secondary air (factor A), the reverse tangent angle of the separate over-fire air (factor B), and the upper swing angle of the burner (factor C). The range analysis method, variance analysis method, and weight matrix analysis method are used to determine the factor and level combination of the best optimization effect and the weight of each factor. The research results show that the significance of the influence of each factor on the optimization index is: B > C > A (reverse tangent angle of the separate over-fire air > the upper swing angle of the burner > the secondary air distribution mode); the weight ratios of the three factors are: factor A is 0.080, factor B is 0.543, and factor C is 0.241; based on the three analysis methods, it is concluded that factor B has a highly significant impact on the optimization index, factor C has an impact on the optimization index, and factor A has no impact on the optimization index, and it is determined that the optimal factor and level combination of the orthogonal test is A1B3C3. Under this combination, the thermal deviation in the furnace is 1.349 K, and the problem of thermal deviation is basically eliminated, being 116.066 K lower than the highest thermal deviation of 117.415 K, which is very obvious. [ABSTRACT FROM AUTHOR]

In order to study the evolution process and hydraulic characteristics of pressurizer insurge in CPR1000 pressurized water reactor (PWR), the computational fluid dynamics (CFD) of three-dimensional unsteady heat transfer was used to capture the temperature and velocity fluctuation intensity of the mixing of the hot and cold. The results show that Realizable k–ε Turbulence Model combined with VOF multiphase heat transfer model can effectively predict the development trend of pressurizer insurge process. The small diameter pressurizer surge line of CPR1000 enhances the intensity of velocity fluctuation. From the essence of flow and heat transfer, it is concluded that buoyancy force can increase the degree of fluctuation and make an accelerated effect on the influx cold fluid. The electric heater inside the pressurizer should be arranged as far as possible in z<-0.45m and z>0.45m; it is beneficial to improve its harsh operating environment. This research can provide reference for the structural design of pressurizer and the layout optimization of the electric heater. [ABSTRACT FROM AUTHOR]

Keywords: Buddleja (Scrophulariaceae); hybridization; polyploidization EN Buddleja (Scrophulariaceae) hybridization polyploidization v vii 1 10/06/23 20230701 NES 230701 Reticulate evolution involves hybrid speciation events that combine two species to produce a third one with or without polyploidization, introgression and horizontal gene transfer between different species (Fig. Their results further show that the Quaternary climatic oscillations, which possibly led to range changes following hybridizations between previously isolated species, have greatly contributed to a pattern of species diversification through both allopatric and (sympatric) hybrid speciation (Fig. The high proportion of polyploid species obviously suggests that polyploidization should have contributed greatly to the species diversification of this genus in the Sino-Himalayan region, in contrast to the early predication that the species diversification in this region mainly occurs at the diploid level ([10]). Hybridization and polyploidization generate evolutionary diversification of the genus Buddleja in the Sino-Himalayan region. [Extracted from the article]

Abstract: Divergence during the early stage of speciation can be driven by a population bottleneck via reduced gene flow and enhanced lineage sorting. In this study, we aimed to examine whether such bottlenecks occurred during the initial speciation of two closely related spruce species Picea asperata and P. crassifolia occurring on the Qinghai–Tibet Plateau (QTP). We analyzed sequences of three chloroplast, two mitochondrial DNA fragments and a further 13 nuclear loci from 216 individuals of the two species. Both species showed a low level of genetic diversity in contrast to other congeners occurring in the QTP and adjacent regions. The estimated population sizes of P. asperata and P. crassifolia are less than the ancestral population size before splitting. These results together with multiple statistical tests (Tajima's D, Fu and Li's D* and F*) suggest that these two species underwent recent bottlenecks. Based on approximate Bayesian computation (ABC), we also determined that the period of the population shrinkage was consistent with the interspecific divergence during the late Pleistocene. The reduced population sizes and the divergent selection may together have triggered the initial divergence under high gene flow between these two species. Our results therefore highlight the importance of climatic oscillations during the late Pleistocene in promoting speciation through changing demographic sizes of the ancestral species on the QTP and in adjacent regions. [ABSTRACT FROM AUTHOR]

• Many plant species comprising the present-day Arctic flora are thought to have originated in the high mountains of North America and Eurasia, migrated northwards as global temperatures fell during the late Tertiary period, and thereafter attained a circumarctic distribution. However, supporting evidence for this hypothesis that provides a temporal framework for the origin, spread and initial attainment of a circumarctic distribution by an arctic plant is currently lacking. • Here we examined the origin and initial formation of a circumarctic distribution of the arctic mountain sorrel (Oxyria digyna) by conducting a phylogeographic analysis of plastid and nuclear gene DNA variation. • We provide evidence for an origin of this species in the Qinghai-Tibet Plateau of southwestern China, followed by migration into Russia c. 11 million yr ago (Ma), eastwards into North America by c. 4 Ma, and westwards into Western Europe by c. 1.96 Ma. Thereafter, the species attained a circumarctic distribution by colonizing Greenland from both sides of the Atlantic Ocean. • Following the arrival of the species in North America and Europe, population sizes appear to have increased and then stabilized there over the last 1 million yr. However, in Greenland a marked reduction followed by an expansion in population size is indicated to have occurred during the Pleistocene. [ABSTRACT FROM AUTHOR]

We investigate a two-way relay (TWR) fading channel where two source nodes wish to exchange information with the help of a relay node. Given traditional TWR protocols, transmission rates in both directions are known to be limited by the hop with lower capacity, i.e., the min operations between uplink and downlink. In this paper, we propose a new transmission protocol, called alternative awaiting and broadcast (AAB), to cancel the min operations in the TWR fading channels. The operational principles, a new upper bound on ergodic sum capacity (ESC), and a convergence behavior of the average delay of signal transmission (ST) (in the relay buffer) for the proposed AAB protocol are analyzed. Moreover, we propose a suboptimal encoding/decoding solution for the AAB protocol and derive an achievable ergodic sum rate (ESR) with a corresponding average delay of ST. Numerical results show that 1) the proposed AAB protocol significantly improves the achievable ESR compared with the traditional TWR protocols, and 2) considering the average delay of system service (SS) (in the source buffer), the average delay of ST induced by the proposed AAB protocol is very small and negligible. [ABSTRACT FROM PUBLISHER]

Partial decoding has the potential to achieve a larger capacity region than full decoding in two-way relay (TWR) channels. Existing partial decoding realizations are however designed for Gaussian channels and with a static physical layer network coding (PLNC). In this paper, we propose a new solution for joint network coding and channel decoding at the relay, called pairwise check decoding (PCD), for low-density parity-check (LDPC) coded TWR system over block fading channels. The main idea is to form a check relationship table (check-relation-tab) for the superimposed LDPC coded packet pair in the multiple access (MA) phase in conjunction with an adaptive PLNC mapping in the broadcast (BC) phase. Using PCD, we then present a partial decoding method, two-stage closest-neighbor clustering with PCD (TS-CNC-PCD), with the aim of minimizing the worst pairwise error probability. Moreover, we propose the minimum correlation optimization (MCO) for selecting the better check-relation-tabs. Simulation results confirm that the proposed TS-CNC-PCD offers a sizable gain over the conventional XOR with belief propagation (BP) in fading channels. [ABSTRACT FROM AUTHOR]

The global expansion of photovoltaic (PV) power plants, especially in ecologically fragile regions like the Gobi Desert, highlights the suitability of such areas for large-scale PV development. The most direct impact of PV development in the Gobi Desert is temperature change that results from the land-use-induced albedo changes; however, the detailed and systemic understanding of the effects of PV expansion on land surface temperature remains limited. This study focuses on the 16 largest PV plants in the Chinese Gobi Desert, utilizing remote sensing data to assess their effects on land surface temperature. Our result showed a cooling effect during the daytime (−0.69 ± 0.10 °C), but a warming effect during the nighttime (0.23 ± 0.05 °C); the overall effect on the daily mean was a cooling effect (−0.22 ± 0.05 °C). Seasonal variations were observed, with the most significant cooling effect in autumn and the weakest in summer. The PV area was the most significant factor which influenced the temperature variation across PV plants. Our findings enrich our understanding of the environmental effects arising from the construction of PV plants and provide vital information for the design and management of increasingly renewable electricity systems globally. [ABSTRACT FROM AUTHOR]

The authors discuss the paper of Qi and colleagues which focuses on the response of relict genus Cercidiphyllum to climatic or geological changes using genetic information from chloroplast (cp) and nuclear DNAs. They mention that Qi and colleagues who used ecological niche modelling (ENM) estimated that the specie split from its sister lineage during late Cretaceous period based on cpDNA evidence. They state that the paper draws detailed pictured o the evolutionary history of Cercidiphyllum.

Background: Long noncoding RNAs (lncRNAs) have emerged as key players in tumorigenesis and tumour progression. However, the biological functions and potential mechanisms of lncRNAs in colorectal cancer (CRC) are unclear. Methods: The novel lncRNA POU6F2-AS1 was identified through bioinformatics analysis, and its expression in CRC patients was verified via qRT–PCR and FISH. In vitro and in vivo experiments, such as BODIPY staining, Oil Red O staining, triglyceride (TAG) assays, and liquid chromatography mass spectrometry (LC-MS) were subsequently performed with CRC specimens and cells to determine the clinical significance, and functional roles of POU6F2-AS1. Biotinylated RNA pull-down, RIP, Me-RIP, ChIP, and patient-derived organoid (PDO) culture assays were performed to confirm the underlying mechanism of POU6F2-AS1. Results: The lncRNA POU6F2-AS1 is markedly upregulated in CRC and associated with adverse clinicopathological features and poor overall survival in CRC patients. Functionally, POU6F2-AS1 promotes the growth and lipogenesis of CRC cells both in vitro and in vivo. Mechanistically, METTL3-induced m6A modification is involved in the upregulation of POU6F2-AS1. Furthermore, upregulated POU6F2-AS1 could tether YBX1 to the FASN promoter to induce transcriptional activation, thus facilitating the growth and lipogenesis of CRC cells. Conclusions: Our data revealed that the upregulation of POU6F2-AS1 plays a critical role in CRC fatty acid metabolism and might provide a novel promising biomarker and therapeutic target for CRC. [ABSTRACT FROM AUTHOR]

Trees are vital to the survival of numerous species and to forest ecosystem functioning. However, the current distribution, vulnerability to extinction, and conservation priorities of globally endangered trees are not well known. We mapped the global distribution of 1686 tree species listed as endangered on the International Union for the Conservation of Nature Red List and identified conservation priority for them based on species richness, life‐history traits, evolutionary distinctiveness, future climate change, and intensity of human activities. We also evaluated the impacts of various threats to these endangered tree species and evaluated the effectiveness of their protection based on the percentage of the species' range inside protected areas. The worldwide distribution of endangered trees, from the tropics through temperate zones, was uneven. Most endangered tree species were not protected in their native ranges, and only 153 species were fully protected. Hotspots of tree diversity occurred primarily in the tropics, and 79.06% of these were highly vulnerable to threats. We identified 253 areas of high priority for the conservation of endangered trees that are highly threatened and insufficiently protected. In particular, 43.42% of unprotected tree species in priority areas lacked recommended conservation measures or had no associated conservation plan. The priority conservation areas and unprotected trees we identified serve as a guideline for future management underpinning the post‐2020 global biodiversity framework. [ABSTRACT FROM AUTHOR]

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants. A chromosome-level genome assembly for the glasshouse plant Rheum nobile (noble rhubarb) combined with phylogenetic, transcriptomic, and metabolomic analyses provides insight into how alpine plants have adapted to growth in extreme environments. [ABSTRACT FROM AUTHOR]

Long noncoding ribonucleic acids (lncRNAs) play crucial roles in regulating key biological processes; however, our knowledge of lncRNAs' roles in plant adaptive evolution is still limited. Here, we determined the divergence of conserved lncRNAs in closely related poplar species that were either tolerant or sensitive to salt stress by comparative transcriptome analysis. Among the 34,363 identified lncRNAs, ~3% were shared among poplar species with conserved sequences but diversified in their function, copy number, originating genomic region and expression patterns. Further cluster analysis revealed that the conserved lncRNAs showed more similar expression patterns within salt-tolerant poplars (Populus euphratica and P. pruinosa) than between salt-tolerant and salt-sensitive poplars. Among these lncRNAs, the antisense lncRNA lncERF024 was induced by salt and the differentiated expression between salt-sensitive and salt-tolerant poplars. The overexpression of lncERF024 in P. alba var. pyramidalis enhanced poplar tolerance to salt stress. Furthermore, RNA pull-down and RNA-seq analysis showed that numerous candidate genes or proteins associated with stress response and photosynthesis might be involved in salt resistance in PeulncERF024-OE poplars. Altogether, our study provided a novel insight into how the diversification of lncRNA expression contributes to plant adaptation traits and showed that lncERF024 may be involved in the regulation of both gene expression and protein function conferring salt tolerance in Populus. [ABSTRACT FROM AUTHOR]

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity. [ABSTRACT FROM AUTHOR]

Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation. [ABSTRACT FROM AUTHOR]

Summary: Salt and drought impair plant osmotic homeostasis and greatly limit plant growth and development. Plants decrease stomatal aperture to reduce water loss and maintain osmotic homeostasis, leading to improved stress tolerance. Herein, we identified the C2H2 transcription factor gene OSMOTIC STRESS INDUCED C2H21 (OSIC1) from Populus alba var. pyramidalis to be induced by salt, drought, polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). Overexpression of OSIC1 conferred transgenic poplar more tolerance to high salinity, drought and PEG6000 treatment by reducing stomatal aperture, while its mutant generated by the CRISPR/Cas9 system showed the opposite phenotype. Furthermore, OSIC1 directly up‐regulates PalCuAOζ in vitro and in vivo, encoding a copper‐containing polyamine oxidase, to enhance H2O2 accumulation in guard cells and thus modulates stomatal closure when stresses occur. Additionally, ABA‐, drought‐ and salt‐induced PalMPK3 phosphorylates OSIC1 to increase its transcriptional activity to PalCuAOζ. This regulation of OSIC1 at the transcriptional and protein levels guarantees rapid stomatal closure when poplar responds to osmotic stress. Our results revealed a novel transcriptional regulatory mechanism of H2O2 production in guard cells mediated by the OSIC1‐PalCuAOζ module. These findings deepen our understanding of how perennial woody plants, like poplar, respond to osmotic stress caused by salt and drought and provide potential targets for breeding. [ABSTRACT FROM AUTHOR]

Kobresia pygmaea meadows are typical of Tibetan Plateau landscapes in the 3,000 to 5,500 m elevation range and constitute the most extensive alpine ecosystem in the world. Kobresia pygmaea forms turf mats that stabilize the surface and shelter the underlying soils from water erosion. Large tracts of the Plateau, however, exhibit signs of ongoing degradation of the turf and erosion of the underlying soil. Despite the crucial role played by K. pygmaea turf mats in the stabilization of the headwaters of major Asian rivers, the mechanisms responsible for their degradation remain poorly investigated. Here we develop a process-based model of land degradation of Tibetan Plateau slopes, which accounts for (i) turf cracking, (ii) water flow concentration in the cracks, (iii) crack widening by scouring, and (iv) sheet-flow erosion. As expected, soil erosion increases with the slope and drainage area (hence the observation of stronger erosion in relatively steep downhill sites). Model simulations indicate that with a sensible set of parameters representative of soil and hydrologic conditions in the region, Tibetan Plateau landscapes are vulnerable to turf mat degradation and soil erosion. As soon as polygonal cracks develop, water flow widens them until the landscape is completely barren. At this point sheet flow eventually erodes the mineral soil leaving behind a highly degraded landscape. [ABSTRACT FROM AUTHOR]

Background: Two widely cultivated annual buckwheat crops, Fagopyrum esculentum and F. tataricum, differ from each other in both rutin concentration and reproductive system. However, the underlying genetic mechanisms remain poorly elucidated. Results: Here, we report the first haplotype-resolved chromosome-level genome assemblies of the two species. Two haplotype genomes of F. esculentum were assembled as 1.23 and 1.19 Gb with N50 = 9.8 and 12.4 Mb, respectively; the two haplotype genomes of F. tataricum were 453.7 and 446.2 Mb with N50 = 50 and 30 Mb, respectively. We further annotated protein-coding genes of each haplotype genome based on available gene sets and 48 newly sequenced transcriptomes. We found that more repetitive sequences, especially expansion of long terminal repeat retrotransposons (LTR-RTs), contributed to the large genome size of F. esculentum. Based on the well-annotated sequences, gene expressions, and luciferase experiments, we identified the sequence mutations of the promoter regions of two key genes that are likely to have greatly contributed to the high rutin concentration and selfing reproduction in F. tartaricum. Conclusions: Our results highlight the importance of high-quality genomes to identify genetic mutations underlying phenotypic differences between closely related species. F. tataricum may have been experienced stronger selection than F. esculentum through choosing these two non-coding alleles for the desired cultivation traits. These findings further suggest that genetic manipulation of the non-coding promoter regions could be widely employed for breeding buckwheat and other crops. [ABSTRACT FROM AUTHOR]

Background: Calf muscle venous thrombosis (CMVT) is among the most important medical complications after hip surgery. CMVT has been known for many years, but many opinions about the incidence and risk factors of CMVT are still controversial. The objective of this retrospective study was to investigate the incidence and associated risk factors of postoperative CMVT in patients with hip fractures. Methods: Patients with hip fractures from January 2020 to April 2022 (n = 320) at Shenzhen Second People's Hospital were recruited in this study. The personal characteristics and clinical data of CMVT and no-CMVT patients were compared and analyzed. Binary logistic regression analyses were performed to identify potential risk factors of CMVT in patients with hip fractures. Finally we performed a receiver operating characteristic (ROC) curve analysis to compare the diagnostic values of different variables. Results: The overall incidence of new-onset CMVT in patients with hip fractures was 18.75% (60 of 320). Among the 60 CMVT patients, 70% (42 of 60) were diagnosed with femoral neck fractures, 28.3% (17 of 60) with intertrochanteric fractures, and 1.7% (1 of 60) with subtrochanteric fractures. No pulmonary embolism (PE) occurred. High preoperative D-dimer (OR = 1.002, 95%CI 0.97–1.03), sex (OR = 1.22, 95%CI 0.51–2.96), the caprini score (OR = 2.32, 95%CI 1.05–5.16) and the waterlow score (OR = 1.077, 95%CI 0.35–3.36) significantly increased the risk of developing postoperative new-onset CMVT. Conclusions: CMVT has become a common clinical disease, and its harm should not be underestimated. Our study found that D-dimer, sex, the caprini score and the waterlow score were independent risk factors for postoperative CMVT. According to our clinical work, we should pay attention to identifying the risk factors of CMVT formation and targeted intervention measures to prevent new-onset CMVT. [ABSTRACT FROM AUTHOR]

•The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). • Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. • Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. • These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes. [ABSTRACT FROM AUTHOR]

Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth. To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses, there is a need for convenient and accurate toolkits. To meet this need, we developed WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping) that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes. Significantly, it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution. This toolkit is freely available at GitHub (https://github.com/SunPengChuan/wgdi). As an example of its application, WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots. This work reports an integrated and user-friendly toolkit, WGDI,for polyploid inference, hierarchical inference of genomic homology, and ancestral chromosome karyotyping. WGDI can improve the detection of whole-genome duplication and facilitates dynamic illumination of karyotype evolution. [ABSTRACT FROM AUTHOR]

The coexistence of closely related species is key to understanding the nature of biodiversity hotspots where in situ diversification has yielded rich communities of close relatives. Limiting similarity predicts that co‐occurring species are differentiated in their niches; identifying the axes of differentiation in sympatric close relatives can thus help reveal the eco‐evolutionary dynamics of community assembly. For flowering plants, these axes may be temporal (related to reproductive phenology) or morphological (related to functional traits).We collected fine‐scale data on abundance, morphology and phenology over a flowering season for 34 species of Rhododendron (Ericaceae) spanning a 2700 m elevation gradient in a nature reserve in the eastern Hengduan Mountains, China. We used null models to test for patterns of clustering versus overdispersion in species' abundances, phylogenetic relatedness and functional traits across sites, and applied joint distribution models to examine the correlates of pairwise associations.We found that species tended to be spatially aggregated, indicating that communities are not strongly structured by competitive exclusion. At higher elevation sites, species tended to be vegetatively more similar (clustered) and closely related. Environmental variables, including climate and topography, were strong predictors of species' ranges. No evidence of niche differentiation was detected along spatial or morphological (functional) axes, but along the temporal axis, the phenology of co‐occurring species showed significant divergence, and was less phylogenetically conserved compared to morphological traits.Synthesis. Local communities of Rhododendron in its centre of diversity are structured by environmental filtering and the effects of limiting similarity. Evidence for the latter is apparent in the pervasive phenological divergence of co‐occurring species, likely driven by reproductive interference from shared pollinators. The evolutionary lability of flowering time appears to render it the quickest path to coexistence for recently diverged species that experience secondary contact in this biodiversity hotspot. [ABSTRACT FROM AUTHOR]

Background: Structural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. However, they are still a largely unexplored feature in most plant genomes. Here, we present the whole-genome landscape of SVs between two model legume Medicago truncatula ecotypes–Jemalong A17 and R108– that have been extensively used in various legume biology studies. Results: To catalogue SVs, we first resolved the previously published R108 genome assembly (R108 v1.0) to chromosome-scale using 124 × Hi-C data, resulting in a high-quality genome assembly. The inter-chromosomal reciprocal translocations between chromosomes 4 and 8 were confirmed by performing syntenic analysis between the two genomes. Combined with the Hi-C data, it appears that these translocation events had a significant effect on chromatin organization. Using both whole-genome and short-read alignments, we identified the genomic landscape of SVs between the two genomes, some of which may account for several phenotypic differences, including their differential responses to aluminum toxicity and iron deficiency, and the development of different anthocyanin leaf markings. We also found extensive SVs within the nodule-specific cysteine-rich gene family which encodes antimicrobial peptides essential for terminal bacteroid differentiation during nitrogen-fixing symbiosis. Conclusions: Our results provide a near-complete R108 genome assembly and the first genomic landscape of SVs obtained by comparing two M. truncatula ecotypes. This may provide valuable genomic resources for the functional and molecular research of legume biology in the future. [ABSTRACT FROM AUTHOR]

Background: Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. Results: Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. Conclusions: Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots. [ABSTRACT FROM AUTHOR]

The increase in species number from poles to the equator is one of the most fundamental patterns in ecology. Although several hypotheses have been proposed, there is a lack of consensus on the mechanisms underlying this pattern. While most hypotheses provide plausible explanation for high tropical diversity of tropical clades, it is unclear if similar mechanisms drive the diversity of extra‐tropical clades. Here, we investigated the environmental drivers influencing the diversity pattern of a Mediterranean plant genus Medicago and dissect their effects across continents and biomes. We compiled a comprehensive dataset on the distribution of all Medicago species and mapped their distribution at the spatial resolution of 100 × 100 km2. We used generalized linear models to quantify the relative effects of environmental factors on the richness patterns of Medicago and its two life forms. Next, using geographically weighted regression, we explored the variation in richness–environment relationship across latitude. We found that Quaternary climate change and environmental energy were important explanatory variables, and their effects were consistent at global, continental and biome scales. However, we found contrasting effect of environmental energy in temperate and tropical regions, with species richness increasing with energy in the temperate and decreasing in the tropics. We also found strong affinity of Medicago species to its ancestral Mediterranean climatic niche. Our results suggest that the spatial variation in Medicago richness patterns may be strongly influenced by heat tolerance as opposed to the tropical clades that depend upon cold tolerance. This dependency on heat tolerance can be attributed to strong niche conservatism exhibited by Medicago species. Our findings provide new insights into the richness‐energy hypothesis and suggest that high environmental energy may not necessarily yield high species diversity but may also lower species diversity, especially of extra‐tropical clades towards the tropics. [ABSTRACT FROM AUTHOR]

Objectives: To screen and verify differential genes affecting the prognosis of breast cancer. Methods: Breast cancer gene expression datasets were downloaded from the GEO database, and original data were analyzed in R. The TIMER database was used to analyze the relationship between ANLN and UBE2T and immune cell infiltration. Results: Ten hub-key genes were identified, and survival analysis showed that UBE2T and ANLN were upregulated in breast cancer and their upregulation was associated with a poor prognosis. ANLN and UBE2T upregulation was associated with the prevalence of Th1 and Th2 cells, shifting the Th1/Th2 balance to Th2 in Basal and Luminal-B breast cancers, which indicates a poor prognosis (P < 0.05). Conclusion: ANLN and UBE2T are potential biomarkers for predicting the prognosis of breast cancer. [ABSTRACT FROM AUTHOR]

Summary: The Qinghai–Tibet Plateau (QTP) sensu lato (sl), comprising the platform, the Himalaya and the Hengduan Mountains, is characterized by a large number of endemic plant species. This evolutionary cradle may have arisen from explosive species diversification because of geographic isolation. However, gene flow has been widely detected during the speciation processes of all groups examined, suggesting that natural selection may have also played an important role during species divergence in this region. In addition, natural hybrids have been recovered in almost all species‐rich genera. This suggests that numerous species in this region are still 'on the speciation pathway to complete reproductive isolation (RI)'. Such hybrids could directly develop into new species through hybrid polyploidization and homoploid hybrid speciation (HHS). HHS may take place more easily than previously thought through alternate inheritance of alleles of parents at multiple RI loci. Therefore, isolation, selection and hybridization could together have promoted species diversification of numerous plant genera on the QTP sl. We emphasize the need for identification and functional analysis of alleles of major genes for speciation, and especially encourage investigations of parallel adaptive divergence causing RI across different lineages within similar but specific habitats in this region. [ABSTRACT FROM AUTHOR]

Background: Structural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. However, they are still a largely unexplored feature in most plant genomes. Here, we present the whole-genome landscape of SVs between two model legume Medicago truncatula ecotypes–Jemalong A17 and R108– that have been extensively used in various legume biology studies. Results: To catalogue SVs, we first resolved the previously published R108 genome assembly (R108 v1.0) to chromosome-scale using 124 × Hi-C data, resulting in a high-quality genome assembly. The inter-chromosomal reciprocal translocations between chromosomes 4 and 8 were confirmed by performing syntenic analysis between the two genomes. Combined with the Hi-C data, it appears that these translocation events had a significant effect on chromatin organization. Using both whole-genome and short-read alignments, we identified the genomic landscape of SVs between the two genomes, some of which may account for several phenotypic differences, including their differential responses to aluminum toxicity and iron deficiency, and the development of different anthocyanin leaf markings. We also found extensive SVs within the nodule-specific cysteine-rich gene family which encodes antimicrobial peptides essential for terminal bacteroid differentiation during nitrogen-fixing symbiosis. Conclusions: Our results provide a near-complete R108 genome assembly and the first genomic landscape of SVs obtained by comparing two M. truncatula ecotypes. This may provide valuable genomic resources for the functional and molecular research of legume biology in the future. [ABSTRACT FROM AUTHOR]

Summary: Achnatherum splendens Trin. (Gramineae) is a constructive species of the arid grassland ecosystem in Northwest China and is a major forage grass. It has good tolerance of salt and drought stress in alkaline habitats. Here, we report its chromosome‐level genome, determined through a combination of Illumina HiSeq sequencing, PacBio sequencing and Hi‐C technology. The final assembly of the ~1.17 Gb genome sequence had a super‐scaffold N50 of 40.3 Mb. A total of 57 374 protein‐coding genes were annotated, of which 54 426 (94.5%) genes have functional protein annotations. Approximately 735 Mb (62.37%) of the assembly were identified as repetitive elements, and among these, LTRs (40.53%) constitute the highest proportion, having made a major contribution to the expansion of genome size in A. splendens. Phylogenetic analysis revealed that A. splendens diverged from the Brachypodium distachyon–Hordeum vulgare–Aegilops tauschii subclade around 37 million years ago (Ma) and that a clade comprising these four species diverged from the Phyllostachys edulis clade ~47 Ma. Genomic synteny indicates that A. splendens underwent an additional species‐specific whole‐genome duplication (WGD) 18–20 Ma, which further promoted an increase in copies of numerous saline–alkali‐related gene families in the A. splendens genome. By transcriptomic analysis, we further found that many of these duplicated genes from this extra WGD exhibited distinct functional divergence in response to salt stress. This WGD, therefore, contributed to the strong resistance to salt stress and widespread arid adaptation of A. splendens. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Background: Although plastomes are highly conserved with respect to gene content and order in most photosynthetic angiosperms, extensive genomic rearrangements have been reported in Fabaceae, particularly within the inverted repeat lacking clade (IRLC) of Papilionoideae. Two hypotheses, i.e., the absence of the IR and the increased repeat content, have been proposed to affect the stability of plastomes. However, this is still unclear for the IRLC species. Here, we aimed to investigate the relationships between repeat content and the degree of genomic rearrangements in plastomes of Medicago and its relatives Trigonella and Melilotus, which are nested firmly within the IRLC. Results: We detected abundant repetitive elements and extensive genomic rearrangements in the 75 newly assembled plastomes of 20 species, including gene loss, intron loss and gain, pseudogenization, tRNA duplication, inversion, and a second independent IR gain (IR ~ 15 kb in Melilotus dentata) in addition to the previous first reported cases in Medicago minima. We also conducted comparative genomic analysis to evaluate plastome evolution. Our results indicated that the overall repeat content is positively correlated with the degree of genomic rearrangements. Some of the genomic rearrangements were found to be directly linked with repetitive sequences. Tandem repeated sequences have been detected in the three genes with accelerated substitution rates (i.e., accD, clpP, and ycf1) and their length variation could be explained by the insertions of tandem repeats. The repeat contents of the three localized hypermutation regions around these three genes with accelerated substitution rates are also significantly higher than that of the remaining plastome sequences. Conclusions: Our results suggest that IR reemergence in the IRLC species does not ensure their plastome stability. Instead, repeat-mediated illegitimate recombination is the major mechanism leading to genome instability, a pattern in agreement with recent findings in other angiosperm lineages. The plastome data generated herein provide valuable genomic resources for further investigating the plastome evolution in legumes. [ABSTRACT FROM AUTHOR]

Semiconductor quantum dots (QDs) are among the most promising emerging fluorescent labels for cellular imaging. However, it is unclear whether QDs, which are nanoparticles rather than small molecules, can specifically and effectively label molecular targets at a subcellular level. Here we have used QDs linked to immunoglobulin G (IgG) and streptavidin to label the breast cancer marker Her2 on the surface of fixed and live cancer cells, to stain actin and microtubule fibers in the cytoplasm, and to detect nuclear antigens inside the nucleus. All labeling signals are specific for the intended targets and are brighter and considerably more photostable than comparable organic dyes. Using QDs with different emission spectra conjugated to IgG and streptavidin, we simultaneously detected two cellular targets with one excitation wavelength. The results indicate that QD-based probes can be very effective in cellular imaging and offer substantial advantages over organic dyes in multiplex target detection. [ABSTRACT FROM AUTHOR]

Background and Aims Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis – Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. Methods A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. Key Results Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. Conclusions Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies. [ABSTRACT FROM AUTHOR]

Oxygen deprivation caused by flooding activates acclimation responses to stress and restricts plant growth. After experiencing flooding stress, plants must restore normal growth; however, which genes are dynamically and precisely controlled by flooding stress remains largely unknown. Here, we show that the Arabidopsis thaliana ubiquitin E3 ligase SUBMERGENCE RESISTANT1 (SR1) regulates the stability of the transcription factor WRKY33 to modulate the submergence response. SR1 physically interacts with WRKY33 in vivo and in vitro and controls its ubiquitination and proteasomal degradation. Both the sr1 mutant and WRKY33 overexpressors exhibited enhanced submergence tolerance and enhanced expression of hypoxia-responsive genes. Genetic experiments showed that WRKY33 functions downstream of SR1 during the submergence response. Submergence induced the phosphorylation of WRKY33, which enhanced the activation of RAP2.2 , a positive regulator of hypoxia-response genes. Phosphorylated WRKY33 and RAP2.2 were degraded by SR1 and the N-degron pathway during reoxygenation, respectively. Taken together, our findings reveal that the on-and-off module SR1-WRKY33- RAP2.2 is connected to the well-known N-degron pathway to regulate acclimation to submergence in Arabidopsis. These two different but related modulation cascades precisely balance submergence acclimation with normal plant growth. [ABSTRACT FROM AUTHOR]

Summary: It is critically important for plants to control the trade‐off between normal growth and pathogen immunity. However, the underlying molecular mechanism remains largely unknown. Here we report such a mechanism controlled by WRKY70 and its partner CHYR1 in Arabidopsis.We found that both levels of the WRKY70 target gene SARD1 and the phosphorylated forms of WRKY70 were increased in WRKY70OE plants upon Pst DC3000 infection. Mechanistically, phosphorylation of WRKY70 at Thr22 and Ser34 occurs, which then activates SARD1 expression through binding to a WT box.Phosphorylated WRKY70 is degraded by 26S proteasome via CHYR1 when resuming normal growth after infection. In addition, nonphosphorylated WRKY70 represses SARD1 expression by binding to both W (inhibitory activity site) and WT (active activity site) boxes.The binding of WRKY70 to alternative cis‐elements of SARD1 through a phosphorylation‐mediated switch controlled by CHYR1 contributes to modulating the balance between immunity and growth. [ABSTRACT FROM AUTHOR]

Summary: High salinity, one of the most widespread abiotic stresses, inhibits photosynthesis, reduces vegetation growth, blocks respiration and disrupts metabolism in plants. In order to survive their long‐term lifecycle, trees, such as Populus species, recruit the abscisic acid (ABA) signaling pathway to adapt to a saline environment. However, the molecular mechanism behind the ABA‐mediated salt stress response in woody plants remains elusive. We have isolated a WRKY transcription factor gene, PalWRKY77, from Populus alba var. pyramidalis (poplar), the expression of which is repressed by salt stress. PalWRKY77 decreases salt tolerance in poplar. Furthermore, PalWRKY77 negatively regulated ABA‐responsive genes and relieved ABA‐mediated growth inhibition, indicating that PalWRKY77 is a repressor of the ABA response. In vivo and in vitro assays revealed that PalWRKY77 targets the ABA‐ and salt‐induced PalNAC002 and PalRD26 genes by binding to the W‐boxes in their promoters. In addition, overexpression of both PalNAC002 and PalRD26 could elevate salt tolerance in transgenic poplars. These findings reveal a novel negative regulation mechanism for the ABA signaling pathway mediated by PalWRKY77 that results in more sensitivity to salt stress in poplar. This deepens our understanding of the complex responses of woody species to salt stress. Significance Statement: This work reveals a novel negative regulation mechanism for the abscisic acid (ABA) signaling pathway mediated by PalWRKY77 that results in more sensitivity to salt stress in poplar. This deepens our understanding of the complex responses of woody species to salt stress and of the relationship between ABA signaling and salt stress responses. [ABSTRACT FROM AUTHOR]

It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown. In this study, we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of alternate alleles at genes that determine parental premating isolation. The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron. We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent. In this way, it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation (iron tolerance). These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers. Using integrated approaches, the authors reveal that reproductive isolation originated in one homoploid hybrid plant species (Ostryopsis intermedia) through the inheritance of alternate alleles at genes that determine parental premating isolation (flowering time and habitat adaptation, i.e., iron tolerance). Their findings and further modeling results suggest that homoploid hybrid speciation can occur easily via the inheritance of alternate, pre-existing, parental reproductive isolations. [ABSTRACT FROM AUTHOR]

Summary: Tolerance of hypoxia is essential for most plants, but the underlying mechanisms are largely unknown. Here we show that adaptation to submergence induced hypoxia in Arabidopsis involves up‐regulation of RAP2.2 through interactive action of WRKY33 and WRKY12.WRKY33‐ or WRKY12‐overexpressing plants showed enhanced resistance to hypoxia. Y2H, BiFC, Co‐IP and pull‐down experiments confirmed the interaction of WRKY33 with WRKY12. Genetic experiments showed that RAP2.2 acts downstream of WRKY33/WRKY12.WRKY33 and WRKY12 can bind to and activate RAP2.2 individually. Genetic and molecular experiments demonstrate that the two WRKYs can synergistically enhance activation towards RAP2.2 to increase hypoxia tolerance. WRKY33 expression is increased in RAP2.2‐overexpressing plants, indicating a feedback regulation by RAP2.2 during submergence process, which was corroborated by EMSA, ChIP, dual‐LUC and genetic experiments.Our results show that a regulatory cascade module involving WRKY33, WRKY12 and RAP2.2 plays a key role in submergence induced hypoxia response of Arabidopsis and illuminate functions of WRKYs in hypoxia tolerance. See also the Editorial on this article by Sasidharan et al., 229: 5–7. [ABSTRACT FROM AUTHOR]

SUMMARY: Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome‐wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome‐wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species. Significance Statement: Whole‐genome sequencing of Populus ilicifolia, a vulnerable and isolated poplar tree from the Tropics that can reproduce both sexually and asexually, was used to explore how population history and reproduction affected its genetic characteristics, genetic load, and its potential for tropical adaptation. [ABSTRACT FROM AUTHOR]

Salinity restricts the growth of trees to varying extents, but the regulatory mechanisms involved in their varying salt tolerance are largely unknown. In an effort to elucidate these mechanisms, we identified a total of 99 genes in the Ethylene Responsive Factor (ERF) family of transcription factors and examined their expression patterns under salt stress in Populus alba var. pyramidalis. We found that a B4 group gene, PalERF109 , was rapidly induced by salt treatment and preferentially expressed in stems and petioles, where it is probably involved in transport of ions and water in xylem. Overexpression of PalERF109 enhanced the salt tolerance of the poplar, and further analysis showed that it directly upregulated a high-affinity K + transporter (HKT) gene, PalHKT1;2. The results clearly indicate that PalERF109 enhances salt tolerance at least partially through direct activation of PalHKT1;2 and extends understanding of the roles of ERF genes in tree stress responses. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Numbers and sizes of photovoltaic solar power plants have grown unprecedentedly over the last few years in China, which aims to achieve a carbon emission peak by 2030 and carbon neutrality by 2060. Thus, timely and accurate monitoring of photovoltaic solar power plants is crucial to the design and management of renewable electricity systems in China. Random forest algorithm has been used to map photovoltaic solar power plants at multiple scales, however, it always causes several salt-and-pepper noises, limiting its application at larger spatial scales. Here we first develop a photovoltaic solar power plant mapping method through integrating time series Landsat imagery, random forest, and morphological characteristics. Then we apply this method in Gansu Province, which has abundant solar and wind energy resources and provide large amounts of potential lands for photovoltaic development, and generate the annual photovoltaic maps from 2015 to 2020. We further analyze the spatial-temporal dynamics of sizes and areas of photovoltaic solar power plants and major land cover conversion of expansive photovoltaic regions. Finally, we discuss the reliability, uncertainties, implications, and future development of our improved methods. We find our photovoltaic mapping method can remove most of salt-and-pepper noises effectively, and the resultant maps in Gansu for 2020 have very high accuracies with user's and producer's accuracies of 97.57% and 99.22%, respectively. There are 165.29 km2 photovoltaic solar power plants in Gansu for 2020, and most of which are located in the northwestern Gansu. In addition, the photovoltaic with patch size > 1 km2 and ≤ 2 km2 (53.4 km2, 32.3%) has largest patch number (39, 15.7%). The improved photovoltaic mapping methods and further analysis in this study provide critical information for accurate and automatic classification of photovoltaic solar power plants in the future, as well as the environmental and sustainable development of solar energy in China. • Improved random forest mapping algorithm of photovoltaic solar power plants. • An updated annual map of photovoltaic solar power plants in Gansu Province with improved accuracy. • Detailed spatial-temporal dynamics and major land cover conversion of photovoltaic solar power plants in Gansu. [ABSTRACT FROM AUTHOR]

Summary: Nonbifurcating divergence caused by introgressive hybridization is continuously reported for groups of closely related species. In this study, we aimed to reconstruct the genome‐scale classification of deep lineages of the conifer genus Picea, establish their phylogenetic relationships and test the bifurcating hypothesis between deeply branching lineages based on genomic data.We sequenced the transcriptomes of 35 individuals of 27 taxa covering all main lineages of the genus. Four major lineages, comprising three to 12 taxa each, largely consistent with morphological evidence, were recovered across the coalescent and integrated nuclear phylogeny. However, many of the individual gene trees recovered contradict one another. Moreover, the well‐supported coalescent tree inferred here differs from previous studies based on various DNA markers, with respect to topology and inter‐lineage relationships.We identified the shared polymorphisms between four major lineages. ABBA–BABA tests confirmed the inter‐lineage gene flow and thus violated the bifurcating divergence model. Gene flow occurred more frequently between lineages distributed in the same continent than those disjunct between continents.Our results indicate that introgression and nonbifurcating diversification apply, even between deeply branching lineages of the conifer genus Picea. [ABSTRACT FROM AUTHOR]

Background and Aims Rapid evolutionary divergence and reticulate evolution may result in phylogenetic relationships that are difficult to resolve using small nucleotide sequence data sets. Next-generation sequencing methods can generate larger data sets that are better suited to solving these puzzles. One major and long-standing controversy in conifers concerns generic relationships within the subfamily Cupressoideae (105 species, approx. 1/6 of all conifers) of Cupressaceae, in particular the relationship between Juniperus, Cupressus and the Hesperocyparis – Callitropsis – Xanthocyparis (HCX) clade. Here we attempt to resolve this question using transcriptome-derived data. Methods Transcriptome sequences of 20 species from Cupressoideae were collected. Using MarkerMiner, single-copy nuclear (SCN) genes were extracted. These were applied to estimate phylogenies based on concatenated data, species trees and a phylogenetic network. We further examined the effect of alternative backbone topologies on downstream analyses, including biogeographic inference and dating analysis. Results Based on the 73 SCN genes (>200 000 bp total alignment length) we considered, all tree-building methods lent strong support for the relationship (HCX, (Juniperus, Cupressus)); however, strongly supported conflicts among individual gene trees were also detected. Molecular dating suggests that these three lineages shared a most recent common ancestor approx. 60 million years ago (Mya), and that Juniperus and Cupressus diverged about 56 Mya. Ancestral area reconstructions (AARs) suggest an Asian origin for the entire clade, with subsequent dispersal to North America, Europe and Africa. Conclusions Our analysis of SCN genes resolves a controversial phylogenetic relationship in the Cupressoideae, a major clade of conifers, and suggests that rapid evolutionary divergence and incomplete lineage sorting probably acted together as the source for conflicting phylogenetic inferences between gene trees and between our robust results and recently published studies. Our updated backbone topology has not substantially altered molecular dating estimates relative to previous studies; however, application of the latest AAR approaches has yielded a clearer picture of the biogeographic history of Cupressoideae. [ABSTRACT FROM AUTHOR]

The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Evidence of genetic exchange between diverging taxa is reported frequently, although most studies fail to show how hybridization and introgression contribute to the adaptation and differentiation of introgressed taxa. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex, which comprises four taxa occurring in the biodiversity hotspot of the Hengduan–Himalayan mountains. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree‐like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA–BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa. [ABSTRACT FROM AUTHOR]

Scaffolds play an important role in tissue engineering and their structure and biocompatibility have great influence on cell behaviors. In this study, poly(l-lactide-co-ε-caprolactone) (PLCL) scaffolds were printed by a 3D printing technology, low-temperature deposition manufacturing (LDM), and then PLCL scaffolds were treated by alkali and coated with collagen type I (COLI). The scaffolds were characterized by scanning electron microscopy (SEM), porosity test, mechanical test, and infrared spectroscopy. The prepared PLCL and PLCL-COLI scaffolds had three-dimensional (3D) porous structure and they not only have macropores but also have micropores in the deposited lines. Although the mechanical property of PLCL-COLI was slightly lower than that of PLCL scaffold, the hydrophilicity of PLCL-COLI was significantly enhanced. Rabbit articular chondrocytes were extracted and were identified as chondrocytes by toluidine blue staining. To study the biocompatibility, the chondrocytes were seeded on scaffolds for 1, 3, 5, 7, and 10 days. MTT assay showed that the proliferation of chondrocytes on PLCL-COLI scaffold was better than that on PLCL scaffold. And the morphology of cells on PLCL-COLI after 1-day culture was much better than that on PLCL. This 3D-printed PLCL scaffold coated with COLI shows a great potential application in tissue engineering. [ABSTRACT FROM AUTHOR]

Species delimitation through which infers species boundaries is emerging as a major work in modern systematics. Hop-hornbeam species in Ostrya (Betulaceae) are well known for their hard and heavy woods. Five species were described in China and their interspecific delimitations remain unclear. In this study, we firstly explored their distributions in all recorded field sites distributed in China. We then selected 110 samples from 22 natural populations of five species from this genus and one type specimen of O. yunnanensis, for molecular barcoding analyses. We sequenced four chloroplast (cp) DNA fragments ( trnH-psbA, trnL-trnF, rps16, and trnG) and the nuclear internal transcribed spacer ( ITS) region for all samples. Sequence variations of Ostrya from four cp DNA fragments identified three groups that showed no correspondence to any morphological delimitation because of the incomplete lineage sorting and/or possible interspecific introgression in the history. However, phylogenetic analyses of ITS sequence variations discerned four species, O. japonica, O. rehderiana, O. trichocarpa, and O. multinervis while O. yunnanensis nested within O. multinervis. Morphological clustering also discerned four species and showed the complete consistency with molecular evidence. Moreover, our phylogenetic analyses-based ITS sequence variations suggested that O. trichocarpa comprised an isolated lineage different from the other Eurasian ones. Based on these results, hop-hornbeams in China should be treated as four separate species. Our results further highlight the importance of ITS sequence variations in delimitating and discerning the closely related species in plants. [ABSTRACT FROM AUTHOR]

Gentiana straminea is a popular Tibetan medicine that has been used for thousands of years in China to treat various diseases and conditions. Although it has multiple pharmaceutical purposes and important economic plant resource in China, transcriptome and molecular base still known limited. In flowering season, samples were collected from different tissues, using the NGS Illumina. Solexa platform, about 58.85 million sequencing reads were generated and assembled de novo, yielding 78,764 high quality unigenes with an average length of 1090 bp. Gene Ontology (GO), KEGG pathway mapping showed that 49,033 of these were identified as putative homologs of annotated sequences in the protein databases. Among them, candidate genes associated with iridoid, flavonoid and anthocyanin were identified. Further the key enzymes involved to iridoid and flavonoid synthesis pathway were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) on different tissues, the flower and root had the higher expression than leaves. In addition, 7591 SSR markers were identified from the unigenes of the G . straminea transcriptome. The foundation of G . straminea provided the important resource for facilitating to study molecular and functional genomics of it and related this species on the Qinghai–Tibet Plateau. [ABSTRACT FROM AUTHOR]