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Rhododendron is famous for its high ornamental value. However, the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved. In addition, the origin of key morphological characters with high horticulture value need to be explored. Both problems largely hinder utilization of germplasm resources. Most studies attempted to disentangle the phylogeny of Rhododendron, but only used a few genomic markers and lacked large-scale sampling, resulting in low clade support and contradictory phylogenetic signals. Here, we used restriction-site associated DNA sequencing (RAD-seq) data and morphological traits for 144 species of Rhododendron, representing all subgenera and most sections and subsections of this species-rich genus, to decipher its intricate evolutionary history and reconstruct ancestral state. Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data. Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron. Subg. Therorhodion (clade I) formed the basal lineage. Subg. Tsutsusi and Azaleastrum formed clade II and had sister relationships. Clade III included all scaly rhododendron species. Subg. Pentanthera (clade IV) formed a sister group to Subg. Hymenanthes (clade V). The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence, ten stamens, leaf blade without scales and broadly funnelform corolla with pink or purple color. This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data. It also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary relationships. Additionally, the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.

Abstract Cotoneaster glaucophyllus is a semi-evergreen plant that blossoms in late summer, producing dense, attractive, fragrant white flowers with significant ornamental and ecological value. Here, a chromosome-scale genome assembly was obtained by integrating PacBio and Illumina sequencing data with the aid of Hi-C technology. The genome assembly was 563.3 Mb in length, with contig N50 and scaffold N50 values of ~6 Mb and ~31 Mb, respectively. Most (95.59%) of the sequences were anchored onto 17 pseudochromosomes (538.4 Mb). We predicted 35,856 protein-coding genes, 1,401 miRNAs, 655 tRNAs, 425 rRNAs, and 795 snRNAs. The functions of 34,967 genes (97.52%) were predicted. The availability of this chromosome-level genome will provide valuable resources for molecular studies of this species, facilitating future research on speciation, functional genomics, and comparative genomics within the Rosaceae family.

In this study, a novel composite was engineered by integrating Zr-MOF (NH2-UIO-66) with MXene layers through electrostatic self-assembly. Under simulated sunlight and at 80 °C, this composite material achieved nearly complete conversion of low-concentration atmospheric CO2 to CO and CH4 without additional sacrificial agents or alkaline absorption liquids, marking one of the few reports demonstrating near-complete reduction of low-concentration CO2 directly from the air. For high-concentration CO2 in industrial flue gas, the composite utilized residual heat at 80 °C without additional energy input, exhibiting excellent CO2 reduction efficiency with CO and CH4 production rates of 127 μmol·g-1·h-1 and 330 μmol·g-1·h-1, respectively, resulting in a total production rate 4.76 times higher than that in the air. Compared to most reports on thermocatalytic CO2 reduction (>300 °C), this material shows significant advantages below 100 °C. The performance improvement is attributed to the introduction of Zr-MOF, which provides additional active sites and reduces activation energy. Additionally, the localized surface plasmon resonance (LSPR) effect of MXene facilitates the migration of thermal charge carriers to Zr4+ sites within the MOF. Density Functional Theory (DFT) calculations validate these findings. Overall, Zr-MOF/MXene composite holds potential for reducing CO2 in air and industrial settings, advancing energy conversion and environmental management.

Abstract Microcos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.

Drought stress, as one of the most common environmental factors, seriously affects seed- ling establishment as well as plant growth and productivity. The growth of Toona ciliata is constrained by soil moisture deficit, and drought stress can reduce its productivity and limit its suitable growing environment. To explore the molecular mechanism of Toona ciliata responding to drought stress, leaves of two-year-old Toona ciliata seedlings were used as experimental materials for transcriptome sequencing and physiological index measurements. Under drought stress, the contents of Chl, MDA, POD, SP, SS, and RWC all change differently. We performed transcriptome sequencing, obtaining 4830 differential genes. The enrichment analysis indicates that the primary effects on the leaves of Toona ciliata under drought stress are related to photosynthesis and responses to plant hormone signal transduction. Transcription factor families associated with drought resistance include the NAC, WRKY, bZIP, bHLH, AP2-EREBP, C3H, GRAS, and FRAI transcription factor families. A weighted gene co-expression network analysis (WGCNA) analysis successfully identified 10 hub genes in response to drought stress in Toona ciliata leaves. Real-time quantitative PCR (RT-qPCR) validated the reliability of the transcriptomic data, and the analysis of its results showed a close correlation with the data obtained from RNA-seq. This study clarifies the transcriptional response of Toona ciliata to drought stress, contributing to the revelation of the molecular mechanisms of drought adaptation.

Abstract Rhododendron vialii (subgen. Azaleastrum) is an evergreen shrub with high ornamental value. This species has been listed as a plant species with extremely small populations (PSESP) for urgent protection by China’s Yunnan provincial government in 2021, due to anthropogenic habitat fragmentation. However, limited genomic resources hinder scientifically understanding of genetic threats that the species is currently facing. In this study, we assembled a high-quality haplotype-resolved genome of R. vialii based on PacBio HiFi long reads and Hi-C reads. The assembly contains two haploid genomes with sizes 532.73 Mb and 521.98 Mb, with contig N50 length of 35.67 Mb and 34.70 Mb, respectively. About 99.92% of the assembled sequences could be anchored to 26 pseudochromosomes, and 14 gapless assembled chromosomes were included in this assembly. Additionally, 60,926 protein-coding genes were identified, of which 93.82% were functionally annotated. This is the first reported genome of R. vialii, and hopefully it will lay the foundations for further research into the conservation genomics and horticultural domestication of this ornamentally important species.

Abstract Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of ~4.9 Mb and a scaffold N50 of ~112.6 Mb. ~98.2% of the assembly was anchored into 13 pseudo-chromosomes. It contains ~1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.

BackgroundThe genus Rhododendron (Ericaceae), a species-rich and widely distributed genus of woody plants, is distinguished for the beautiful and diverse flowers. Rhododendron delavayi Franch. and Rhododendron irroratum Franch., are highly attractive species widely distributed in south-west China and abundant new varieties have been selected from their genetic resources.MethodsWe constructed chromosome-scale genome assemblies for Rhododendron delavayi and Rhododendron irroratum. Phylogenetic and whole-genome duplication analyses were performed to elucidate the evolutionary history of Rhododendron. Further, different types of gene duplications were identified and their contributions to gene family expansion were investigated. Finally, comprehensive characterization and evolutionary analysis of R2R3-MYB and NBS-encoding genes were conducted to explore their evolutionary patterns.ResultsThe phylogenetic analysis classified Rhododendron species into two sister clades, ‘rhododendrons’ and ‘azaleas’. Whole-genome duplication (WGD) analysis unveiled only one WGD event that occurred in Rhododendron after the ancestral γ triplication. Gene duplication and gene family expansion analyses suggested that the younger tandem and proximal duplications contributed greatly to the expansion of gene families involved in secondary metabolite biosynthesis and stress response. The candidate R2R3-MYB genes likely regulating anthocyanin biosynthesis and stress tolerance in Rhododendron will facilitate the breeding for ornamental use. NBS-encoding genes had undergone significant expansion and experienced species-specific gain and loss events in Rhododendron plants.ConclusionsThe reference genomes presented here will provide important genetic resources for molecular breeding and genetic improvement of plants in this economically important Rhododendron genus.

Natural hybridization plays an important role in speciation; however, we still know little about the mechanisms underlying the early stages of hybrid speciation. Hybrid zones are commonly dominated by F1s, or backcrosses, which impedes further speciation. In the present study, morphological traits and double digest restriction‐site associated DNA sequencing (ddRAD-seq) data have been used to confirm natural hybridization between Salvia flava and S. castanea, the first case of identification of natural hybridization using combined phenotypic and molecular evidence in the East Asian clade of Salvia. We further examined several reproductive barriers in both pre-zygotic and post-zygotic reproductive stages to clarify the causes and consequences of the hybridization pattern. Our results revealed that reproductive isolation between the two species was strong despite the occurrence of hybridization. Interestingly, we found that most of the hybrids were likely to be F2s. This is a very unusual pattern of hybridization, and has rarely been reported before. The prevalence of geitonogamy within these self-compatible hybrids due to short distance foraging by pollinators might explain the origin of this unusual pattern. F2s can self-breed and develop further, therefore, we might be witnessing the early stages of hybrid speciation. Our study provides a new case for understanding the diversification of plants on the Qinghai-Tibet Plateau.

Understanding the adaptation of plant species will help us develop effective breeding programs, guide the collection of germplasm, and improve the success of population restoration projects for threatened species. Genetic features correlate with species adaptation. Acer yangbiense is a critically endangered plant species with extremely small populations (PSESP). However, no information was available on its seed germination and seedling growth in populations with different genetic characteristics. In this study, we investigated seed germination and compared the performance of 566 seedlings in 10 maternal half-sib families cultivated in Kunming Botanical Garden. The results showed that A. yangbiense seeds required an average of 44 days to start germinating, with a 50% germination rate estimated to take about 47–76 days, indicating slow and irregular germination. There is a trade-off between the growth and survival in A. yangbiense seedlings, with fast growth coming at the cost of low survival. Groups that were able to recover from a recent bottleneck consistently had higher relative growth rates. High genetic diversity and low levels of inbreeding are likely to be responsible for their improved survival during drought conditions and rapid growth under optimal environmental conditions. Our results suggest that maternal genetic traits might be used as indicators for conservation and population restoration. These findings provide us with new information that could be applied to support ex situ conservation and reintroduction of threatened species.

Brandisia hancei (Paulowniaceae) is a widely distributed shrub in karst regions in southwestern China. Its seeds have a membranous wing, and they mature just before the rainy season begins. To assess the effect of the wing on seed dispersal and germination of B. hancei, we measured the dispersal distance at varying wind speeds and release heights, falling duration from different release heights, floating duration on still water, rates of imbibition of water, and drying and soil adherence to seeds. Germination experiments were conducted on intact and de-winged seeds immediately after harvest. The wing increased the falling duration in still air and the floating ability on water. Dispersal distance of winged and de-winged seeds did not differ at a wind speed of 2.8 m s−1, but at 3.6 and 4.0 m s−1 dispersal distances were greater for de-winged than for winged seeds. Seed wing had little effect of absorption and retention of water, but significantly increased soil adherence to the seeds. Mature seeds were non-dormant and germinated to over 90% with a mean germination time of about 10 days. By combining the environmental conditions in karst habitat with the seed traits of B. hancei, we conclude that dispersal and germination of winged seeds are adapted to the precipitation seasonality in heterogeneous habitats absence of soil.

Abstract Background The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, genomes and transcriptomes of members of the Rhododendron genus have been sequenced and published by various laboratories. With increasing amounts of omics data available, a centralized platform is necessary for effective storage, analysis, and integration of these large-scale datasets to ensure consistency, independence, and maintainability. Results Here, we report our development of the Rhododendron Plant Genome Database (RPGD; http://bioinfor.kib.ac.cn/RPGD/ ), which represents the first comprehensive database of Rhododendron genomics information. It includes large amounts of omics data, including genome sequence assemblies for R. delavayi, R. williamsianum, and R. simsii, gene expression profiles derived from public RNA-Seq data, functional annotations, gene families, transcription factor identification, gene homology, simple sequence repeats, and chloroplast genome. Additionally, many useful tools, including BLAST, JBrowse, Orthologous Groups, Genome Synteny Browser, Flanking Sequence Finder, Expression Heatmap, and Batch Download were integrated into the platform. Conclusions RPGD is designed to be a comprehensive and helpful platform for all Rhododendron researchers. Believe that RPGD will be an indispensable hub for Rhododendron studies.

Abstract Background It has been recognized that a certain amount of habitat disturbance is a facilitating factor for the occurrence of natural hybridization, yet to date we are unaware of any studies exploring hybridization and reproductive barriers in those plants preferentially occupying disturbed habitats. Buddleja plants (also called butterfly bush) generally do grow in disturbed habitats, and several species with hybrid origin have been proposed, based solely on morphological evidence. Results In the present study, we test the hypothesis that B. × wardii is of natural hybridization origin in two sympatric populations of three taxa including B. × wardii and its parents (B. alternifolia and B. crispa) plus 4 referenced parental populations, using four nuclear genes and three chloroplast intergenic spacers, as well as with 10 morphological characters. Our results suggest that at both sites B. × wardii is likely to be a hybrid between B. alternifolia and B. crispa, and moreover, we confirm that most of the hybrids examined are F1s. That these plants are F1s is further supported by morphology, as no transgressive characters were detected. B. crispa was found to be the maternal parent in the Bahe (BH) population, from cpDNA evidence. However, in the Taji (TJ) population, the direction of hybridization was difficult to establish due to the shared cpDNA haplotypes between B. alternifolia and B. crispa, however we still predicted a similar unidirectional hybridization pattern due to results from cross-specific pollination treatments which supported the “SI × SC rule”. Conclusions The presence of mainly F1 hybrids can successfully impede gene flow and thus maintain species boundaries in parental species in a typical distribution of Buddleja, i.e. in disturbed habitats.

Abstract Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.

Gene flow between sympatric congeneric plants is thought to be very common and may pose serious threats to endangered species. In the present study, we evaluate the genetic diversity and divergence of three sympatric Rhododendron species in Jiaozi Mountain using newly developed microsatellites through the Illumina MiSeq sequencing approach. Genetic diversity of all three Rhododendron species studied was moderate in comparison to genetic parameters previously reported from species of this genus. Interestingly, genetic structure analysis of the three species identified a possible hybrid origin of the threatened Rh. pubicostatum. This sympatry should be considered a unimodal hybrid zone, since Rh. pubicostatum is predominant here. Unimodal hybrid zones are uncommon in Rhododendron, despite the fact that hybridization frequently occurs in the genus. Issues pertaining to the conservation of Rh. pubicostatum resulting from admixture of genetic material from its parental species are discussed.

Abstract Background Primula is a large genus of flowering herbs well known for their heterostyly. Currently few natural hybrids are known and reproductive barriers in this genus in the wild have received little attention. However, there is instance of hybridization between rare and widely-spread species, and conservation implications of such situation is poorly understood. In the present study, we investigated hybridization patterns and reproductive barriers between a wide spread species, Primula poissonii and a rare species P. anisodora, of which only three populations are currently known. Results Pollinator-mediated reproductive isolation was strong between parental species but not significant between hybrids and parental species. Hand pollination experiments showed significant reduction of both fruit- and seed-set for heterospecific pollination as compared with conspecific pollination for both parental species. Furthermore, hybrids had higher fruit- and seed-set when pollinated with P. anisodora pollen as opposed to P. poissonii pollen. Microsatellites identified backcrosses to P. anisodora in two of the three populations of P. anisodora, and additionally more individuals of P. anisodora showed introgression from P. poissonii than vice versa. Conclusions These results provide evidence for potential genetic swamping of the P. anisodora populations, which could pose a serious threat for this locally endemic species.

Phyllanthus emblica L. is a well-known medicinal and edible plant species. Various medicinal compounds in the fruit make it an important medicinal and promising economic material. The plant is widely distributed in Southwestern and Southern China. However, due to massive deforestation and land reclamation as well as deterioration of its natural habitat in recent years, the wild resources of this species have been sharply reduced, and it is rare to see large-scale wild P. emblica forests so far. In order to effectively protect and rationally utilize this species, we investigated the genetic diversity, genetic structure, and population dynamics of 260 individuals from 10 populations of P. emblica sampled from the dry climate area in Yunnan and wet climate area in Guangxi using 20 polymorphic EST-SSR markers. We found high genetic diversity at the species level (He = 0.796) and within populations (He = 0.792), but low genetic differentiation among populations (FST = 0.084). In addition, most genetic variation existed within populations (92.44%) compared with variation among the populations (7.56%). Meanwhile, the NJ tree, STRUCTURE, and hierarchical analysis suggested that the sampled individuals were clustered into two distinct genetic groups. In contrast, the genetic diversity of the dry climate group (He = 0.786, Na = 11.790, I = 1.962) was higher than that of the wet climate group (He = 0.673, Na = 9.060, I = 1.555), which might be attributed to the combined effects of altitude, precipitation, and geographic distance. Interestingly, only altitude and precipitation had significant pure effects on the genetic diversity, and the former was slightly stronger. In addition, DIYABC analysis suggested the effective population size of P. emblica might have contracted in the beginning of the Last Glacial Maximum. These genetic features provided vital information for the conservation and sustainable development of genetic resources of P. emblica, and they also provided new insights and guidelines for ecological restoration and economic development in dry-hot valleys of Yunnan and karst areas in Guangxi.

Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima’s D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, He = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (Fst from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (Ne) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of Ne over a short period, and a subsequent gradual decline in Ne to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.

The complete plastid genome of Rhododendron griersonianum, a critically endangered plant species with extremely small populations, was obtained using Illumina HiSeq X Ten and ONT PromethION sequencing. The full length of the plastid genome is 206,467 bp with an overall GC content of 35.8%, which encodes 118 unique genes, including 78 protein-coding genes, 36 tRNA and 4 rRNA genes. Phylogenetic analysis revealed that all Rhododendron species formed a monophyletic clade. This study provides a valuable reference and will facilitate future studies related to the general characteristics and evolution of plastid genomes in the genus Rhododendron.

The giant tree rhododendron (R. protistum var. giganteum) is one of the most famous plants in China, and is critically endangered. As previous conservation efforts only focused on the two recorded populations of this variety, key issues regarding relatedness to R. protistum var. protistum still remain. Our field investigations and SSR analysis of the two varieties in China and Nepal suggest that the two varieties are not significantly different, and we suggest that limited conservation resources could be better used elsewhere given the numerous endangered plants urgently needing protection in China. We suspect that the problems we identified in this study will also apply to many other taxa in developing countries identified as endangered on the basis of incomplete information. Keywords: Rhododendron protistum var. giganteum, Conservation priority, Genetic structure

Long-term ecological and genetic studies in natural populations of tree species require marking techniques so that individuals can be re-visited over time, even in difficult terrain. Both GPS coordinates and physical labels have disadvantages that can make re-finding trees difficult. We tested passive and semi-active radio frequency identification (RFID) tags and readers as a means to relocate individual trees. Passive RFID tags do not provide a good solution because of low transmission power of hand-held readers and strong directionality. Semi-active RFID tags provide detection over longer distances, but also suffer from strong directionality. Active RFID tags promise an improvement over semi-passive tags, and could be evaluated in a future study. We conclude that RFID technology has the potential to improve the ability of researchers to locate individual trees repeatedly under natural conditions, and can be used in conjunction with other marking techniques such as physical tags and GPS coordinates.

Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I. cornuta and I. latifolia, we proposed it as a natural hybrid between them. In this study, we sequenced one chloroplast intergenic spacer (trnH-psbA) and two nuclear genes (gapC and nepGS) in I. dabieshanensis and its putative parental species to test the hybrid origin hypothesis. Our results showed that there were one to two differentially fixed sequence differences between I. cornuta and I. latifolia at the two nuclear genes. Twelve of the 14 individuals of I. dabieshanensis exhibited additivity in chromatograms on these differentially fixed sites at both nuclear genes, and the remaining two exhibited additivity in chromatograms on the fixed site at only the nepGS gene. Except one haplotype of I. cornuta at the nepGS gene, all of the haplotypes of I. cornuta at the two nuclear genes were well separated from those of I. latifolia, and most haplotypes of I. dabieshanensis were shared with those of I. cornuta and I. latifolia. Phylogenetic analysis of these haplotypes was largely consistent with haplotype network analysis. I. cornuta and I. latifolia differed by two nucleotide substitutions in the chloroplast intergenic spacer, and 12 individuals of I. dabieshanensis had the same sequences as I. latifolia, while the remaining two were identical with I. cornuta. The molecular data provide convincing evidence for the hybrid origin of I. dabieshanensis and asymmetrical direction of hybridization. One haplotype of I. cornuta at the nepGS gene was nested with those of I. latifolia, indicating introgression to I. cornuta.

Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) markers and 11 simple sequence repeat (SSR) markers. Examination of genetic diversity revealed that the species maintained a relatively high level of genetic diversity at the species level (percentage of polymorphic bands) PPB = 96.36% from ISSRs; PPL (percentage of polymorphic loci) = 95.56% from SSRs, despite several fragmental populations. Low levels of genetic differentiation among the populations of M. coriacea were detected by Nei’s Gst = 0.187 for ISSR and Wright’s Fst = 0.090 for SSR markers, which is further confirmed by Bayesian model-based STRUCTURE and PCoA analysis that could not reveal a clear separation between populations, although YKP was differentiated to other two populations by ISSR markers. Meanwhile, AMOVA analysis also indicated that 22.84% and 13.90% of genetic variation existed among populations for ISSRs and SSRs, respectively. The high level of genetic diversity, low genetic differentiation, and the population, structure imply that the fragmented habitat and the isolated population of M. coriacea may be due to recent over-exploitation. Conservation and management of M. coriacea should concentrate on maintaining the high level of genetic variability through both in and ex-situ conservation actions.

The segmented taper equation has great flexibility and is widely applied in exiting taper systems. The unconstrained least square regression (ULSR) was generally used to estimate parameters in previous applications of the segmented taper equations. The joint point parameters estimated with ULSR may fall outside the feasible region, which leads to the results of the segmented taper equation being uncertain and meaningless. In this study, a combined method of constrained two-dimensional optimum seeking and least square regression (CTOS & LSR) was proposed as an improved method to estimate the parameters in the segmented taper equation. The CTOS & LSR was compared with ULSR for both individual tree-level equation and the population average-level equation using data from three tropical precious tree species (Castanopsis hystrix, Erythrophleum fordii, and Tectona grandis) in the southwest of China. The differences between CTOS & LSR and ULSR were found to be significant. The segmented taper equation estimated using CTOS & LSR resulted in not only increased prediction accuracy, but also guaranteed the parameter estimates in a more meaningful way. It is thus recommended that the combined method of constrained two-dimensional optimum seeking and least square regression should be a preferred choice for this application. The computation procedures required for this method is presented in the article.

Natural hybridization plays an important role in speciation; however, we still know little about the mechanisms underlying the early stages of hybrid speciation. Hybrid zones are commonly dominated by F1s, or backcrosses, which impedes further speciation. In the present study, morphological traits and double digest restriction-site associated DNA sequencing (ddRAD-seq) data have been used to confirm natural hybridization between Salvia flava and S. castanea, the first case of identification of natural hybridization using combined phenotypic and molecular evidence in the East Asian clade of Salvia. We further examined several reproductive barriers in both pre-zygotic and post-zygotic reproductive stages to clarify the causes and consequences of the hybridization pattern. Our results revealed that reproductive isolation between the two species was strong despite the occurrence of hybridization. Interestingly, we found that most of the hybrids were likely to be F2s. This is a very unusual pattern of hybridization, and has rarely been reported before. The prevalence of geitonogamy within these self-compatible hybrids due to short distance foraging by pollinators might explain the origin of this unusual pattern. F2s can self-breed and develop further, therefore, we might be witnessing the early stages of hybrid speciation. Our study provides a new case for understanding the diversification of plants on the Qinghai-Tibet Plateau. [ABSTRACT FROM AUTHOR]

Rhododendron longipedicellatum is an endangered species endemic to southeastern Yunnan,China. Assessment of genetic variation is critical for protecting endangered species. Therefore, we used EST-SSR markers to analyze the genetic characteristics of R. longipedicellatum. The results revealed high genetic diversity at the species level (He = 0.559, NA = 9.529) and within populations (He = 0.507, NA = 5.910) and moderate genetic differentiation between populations (FST = 0.083). In addition, more genetic variation existed within populations (91.25%) compared with variation among populations (8.75%). The STRUCTURE analysis showed that 150 individuals from five existing populations could best be divided into two genetic groups. At the population level, the neighbor-joining (NJ) tree and principal coordinates analysis (PCoA) analyses also divided them into two groups. In addition, Bottleneck analyses using the Two-Phase Model (TPM) and Stepwise Mutation Model (SMM) as well as the Garza-Williamson Index revealed widespread signatures of bottleneck events. These results provide vital information for scientifically formulating conservation strategies for the endangered R . longipedicellatum. [ABSTRACT FROM AUTHOR]

In this work, we investigated the absorption characteristics of SO2 and the effect of inhibitors on the desulfurization performances of Na2SO3. The results showed that the NO2 had a competitive effect with SO2 on SO32- which resulted in a significant decrease in the absorption capacity of SO2. O2 in the flue gas could decrease the absorption capacity of SO2 due to the oxidation of Na2SO3. Besides, Na2S2O3 had more excellent inhibiting effect on the oxidation of SO32-; the inhibition mechanism is understood on the basis of the free radical chain reaction, whereby S2O32- combined with the sulfite free radical to form an inert substance, thus, quenching the reaction of free radical with the dissolved oxygen and invariably inhibiting the oxidation of SO32-. Furthermore, the intrinsic and the apparent oxidation kinetics of Na2SO3 oxidation process with Na2SO3 were investigated to explain the relationships between consumption rates of SO32- and the absorption capacities of SO2 under different components in flue gas and absorption solution. [ABSTRACT FROM AUTHOR]

In this study, the effect of CuO nanoparticles (NPs) on partial nitrification (PN) process was investigated at various pH values. The shortand long-term experiments were carried out in six identical reactors, with or without CuO NPs, at pH values of 6.5, 8.0 and 10.0. The ammonia oxidation, reaction rates, copper content, and the microbial community were investigated. The results of this work suggested that CuO NPs inhibited the ammonia oxidation by aerobic ammonia-oxidizing bacteria (AOB), under both the acid and alkali conditions. AOB could resist the acid condition but was significantly suppressed when CuO NPs was fed, and the low pH did not aggravate the inhibition level. Almost all the bacteria lost bioactivity under the pH as 10.0, while anaerobic ammonia-oxidizing bacteria survived. The acid condition increased the Nitrosomonas relative abundance while the alkali condition lowered it. More than 60% of the supplied CuO NPs was discharged via effluent. [ABSTRACT FROM AUTHOR]

Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to different environments. Here, we report the genome assembly and gene annotation of R. delavayi var. delavayi (the second genome sequenced in the Ericaceae), which will facilitate the study of the family. The genome assembly will have further applications in genome-assisted cultivar breeding. The final size of the assembled R. delavayi var. delavayi genome (695.09 Mb) was close to the 697.94 Mb, estimated by k-mer analysis. A total of 336.83 gigabases (Gb) of raw Illumina HiSeq 2000 reads were generated from 9 libraries (with insert sizes ranging from 170 bp to 40 kb), achieving a raw sequencing depth of x482.6. After quality filtering, 246.06 Gb of clean reads were obtained, giving x352.55 coverage depth. Assembly using Platanus gave a total scaffold length of 695.09 Mb, with a contig N50 of 61.8 kb and a scaffold N50 of 637.83 kb. Gene prediction resulted in the annotation of 32 938 protein-coding genes. The genome completeness was evaluated by CEGMA and BUSCO and reached 95.97% and 92.8%, respectively. The gene annotation completeness was also evaluated by CEGMA and BUSCO and reached 97.01% and 87.4%, respectively. Genome annotation revealed that 51.77% of the R. delavayi genome is composed of transposable elements, and 37.48% of long terminal repeat elements (LTRs). The de novo assembled genome of R. delavayi var. delavayi (hereinafter referred to as R. delavayi) is the second genomic resource of the family Ericaceae and will provide a valuable resource for research on future comparative genomic studies in Rhododendron species. The availability of the R. delavayi genome sequence will hopefully provide a tool for scientists to tackle open questions regarding molecular mechanisms underlying environmental interactions in the genus Rhododendron, more accurately understand the evolutionary processes and systematics of the genus, facilitate the identification of genes encoding pharmaceutically important compounds, and accelerate molecular breeding to release elite varieties. [ABSTRACT FROM AUTHOR]

Long-term ecological and genetic studies in natural populations of tree species require marking techniques so that individuals can be re-visited over time, even in difficult terrain. Both GPS coordinates and physical labels have disadvantages that can make re-finding trees difficult. We tested passive and semi-active radio frequency identification (RFID) tags and readers as a means to relocate individual trees. Passive RFID tags do not provide a good solution because of low transmission power of hand-held readers and strong directionality. Semi-active RFID tags provide detection over longer distances, but also suffer from strong directionality. Active RFID tags promise an improvement over semi-passive tags, and could be evaluated in a future study. We conclude that RFID technology has the potential to improve the ability of researchers to locate individual trees repeatedly under natural conditions, and can be used in conjunction with other marking techniques such as physical tags and GPS coordinates. [ABSTRACT FROM AUTHOR]

Elemental mercury (Hg0) in flue gases can be efficiently captured by mercury chloride (HgCl2) solution. However, the absorption behaviors and the influencing effects are still poorly understood. The mechanism of Hg0 absorption by HgCl2 and the factors that control the removal were studied in this paper. It was found that when the mole ratio of Cl− to HgCl2 is 10:1, the Hg0 removal efficiency is the highest. Among the main mercury chloride species, HgCl3− is the most efficient ion for Hg0 removal in the HgCl2 absorption system when moderate concentrations of chloride ions exist. The Hg0 absorption reactions in the aqueous phase were investigated computationally using Moller-Plesset perturbation theory. The calculated Gibbs free energies and energy barriers are in excellent agreement with the results obtained from experiments. In the presence of SO32− and SO2, Hg2+ reduction occurred and Hg0 removal efficiency decreased. The reduced Hg0 removal can be controlled through increased chloride concentration to some degree. Low pH value in HgCl2 solution enhanced the Hg0 removal efficiency, and the effect was more significant in dilute HgCl2 solutions. The presence of SO42− and NO3− did not affect Hg0 removal by HgCl2. [ABSTRACT FROM AUTHOR]

The slip ammonia from selective catalytic reduction (SCR) of NOx in coal-fired flue gas can result in deterioration of the utilities or even the environmental issues. To achieve selective catalytic oxidation (SCO) of slip ammonia, Ru-modified Ce-Zr solid solution catalysts were prepared and evaluated under various conditions . It was found that the Ru / Ce0.6Zr0.4O2(polyvinylpyrrolidone (PVP)) catalyst displayed significant catalytic activity and the slip ammonia was almost completely removed with the coexistence of NOx and SOz. Interestingly, the effect of SO2 on NH3 oxidation was bifacial, and the N2 selectivity of the resulting products was as high as 100% in the presence of SO2 and NH3. The mechanism of the SCO of NH3 over Ru/Ce0.6Zr0.4O2(PVP) was studied using various techniques, and the results showed that NH3 oxidation follows an internal SCR (iSCR) mechanism. The adsorbed ammonia was first activated and reacted with lattice oxygen atoms toform an -HNO intermediate. Then, the -HNO mainly reacted with atomic oxygen from O2 toform NO. Meanwhile, the formed NO interacted with -NH2 to N2 with N2O as the byproduct, but the presence of SO2 can effectively inhibit the production of N2O . [ABSTRACT FROM AUTHOR]

Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) markers and 11 simple sequence repeat (SSR) markers. Examination of genetic diversity revealed that the species maintained a relatively high level of genetic diversity at the species level (percentage of polymorphic bands) PPB = 96.36% from ISSRs; PPL (percentage of polymorphic loci) = 95.56% from SSRs, despite several fragmental populations. Low levels of genetic differentiation among the populations of M. coriacea were detected by Nei's Gst = 0.187 for ISSR and Wright's Fst = 0.090 for SSR markers, which is further confirmed by Bayesian model-based STRUCTURE and PCoA analysis that could not reveal a clear separation between populations, although YKP was differentiated to other two populations by ISSR markers. Meanwhile, AMOVA analysis also indicated that 22.84% and 13.90% of genetic variation existed among populations for ISSRs and SSRs, respectively. The high level of genetic diversity, low genetic differentiation, and the population, structure imply that the fragmented habitat and the isolated population of M. coriacea may be due to recent over-exploitation. Conservation and management of M. coriacea should concentrate on maintaining the high level of genetic variability through both in and ex-situ conservation actions. [ABSTRACT FROM AUTHOR]

• Premise of the study: One potential threat to rare species is genetic swamping caused by hybridization, but few studies have quantified this threat. Rhododendron cyanocarpum is a narrow endemic species that occurs sympatrically with potentially interfertile congeners throughout its range within Yunnan, China. We searched the entire distribution of R. cyanocarpum for hybrids and examined the patterns of hybridization to assess potential threat from hybridization. • Methods: In a comprehensive field survey, we detected only one instance of hybridization involving R. cyanocarpum, with R. delavayi, at Huadianba near Dali. Material of both species and putative hybrids was examined using morphology, chloroplast DNA, nuclear ribosomal DNA, and Bayesian analysis of AFLP profiles. • Key results: Of 10 putative hybrids, two were F1's and at least seven were F2's. Four backcrosses to R. delavayi were detected among material with R. delavayi-like morphology within the hybrid zone. Backcrosses to R. cyanocarpum were not detected. Therefore F2's outnumbered all other classes within the hybrid zone, a situation not previously confirmed for plants and extremely rare generally. Hybridization was asymmetrical, with R. delavayi as the maternal parent in all but one of the hybrids detected. • Conclusions: Although natural hybridization is common in Rhododendron, it is rare in R. cyanocarpum and is apparently not accompanied by backcrossing toward R. cyanocarpum. Hence, there is no immediate risk of genetic swamping, unless habitat disturbance increases and changes the patterns of hybridization. Our study is the first to report a plant hybrid zone dominated by F2 hybrids. This pattern might contribute to species barrier maintenance. [ABSTRACT FROM AUTHOR]