Fast growth of single-crystal covalent organic frameworks for laboratory x-ray diffraction.

The imine-exchange strategy makes single-crystal growth of covalent organic frameworks (COFs) with large size (>15 microns) possible but is a time-consuming process (15 to 80 days) that has had limited success (six examples) and restricts structural characterization to synchrotron-radiation sources for x-ray diffraction studies. We developed a CF3COOH/CF3CH2NH2 protocol to harvest single-crystal COFs within 1 to 2 days with crystal sizes of up to 150 microns. The generality was exemplified by the feasible growth of 16 high-quality single-crystal COFs that were structurally determined by laboratory single-crystal x-ray diffraction with resolutions of up to 0.79 angstroms. The structures obtained included uncommon interpenetration of networks, and the details of the structural evolution of conformational isomers and host-guest interaction could be determined at the atomic level.

Bottom-Up Construction of Ni(II)-Incorporated Covalent Organic Framework for Metallaphotoredox Catalysis.

The construction of an all-in-one catalyst, in which the photosensitizer and the transition metal site are close to each other, is important for improving the efficiency of metallaphotoredox catalysis. However, the development of convenient synthetic strategies for the precise construction of an all-in-one catalyst remains a challenging task due to the requirement of precise installation of the catalytic sites. Herein, we have successfully established a facile bottom-up strategy for the direct synthesis of Ni(II)-incorporated covalent organic framework (COF), named LZU-713@Ni, as a versatile all-in-one metallaphotoredox catalyst. LZU-713@Ni showed excellent activity and recyclability in the photoredox/nickel-catalyzed C-O, C-S, and C-P cross-coupling reactions. Notably, this catalyst displayed a better catalytic activity than its homogeneous analogues, physically mixed dual catalyst system, and, especially, LZU-713/Ni which was prepared through post-synthetic modification. The improved catalytic efficiency of LZU-713@Ni should be attributed to the implementation of bottom-up strategy, which incorporated the fixed, ordered, and abundant catalytic sites into its framework. This work sheds new light on the exploration of concise and effective strategies for the construction of multifunctional COF-based photocatalysts.

Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change.

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledge about the shift of evergreen versus deciduous leaf with the impact of paleoclimatic change using genomic data remains rare. Here, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of EBLFs, to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) with eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling and climate niche reconstruction were employed to estimate its origin and diversification pattern. Taking into account studies on other plant lineages dominating EBLFs of East Asia, it was revealed that the prototype of EBLFs in East Asia probably emerged in the Early Eocene (55-50 million years ago [Ma]), facilitated by the greenhouse warming. As a response to the cooling and drying climate in the Middle to Late Eocene (48-38 Ma), deciduous habits were evolved in the dominant lineages of the EBLFs in East Asia. Up to the Early Miocene (23 Ma), the prevailing of East Asian monsoon increased the extreme seasonal precipitation and accelerated the emergence of evergreen habits of the dominant lineages, and ultimately shaped the vegetation resembling that of today.

Synchronization and adaptive control for coupled fractional-order reaction-diffusion neural networks with multiple couplings.

In this paper, two kinds of coupled fractional-order reaction-diffusion neural networks (CFORDNNs) with multiple state couplings or spatial diffusion couplings are proposed. By resorting to the Laplace transform and the properties of Mittag-Leffler functions, sufficient synchronization conditions are derived for the concerned network models. In addition, to guarantee the synchronization of these two networks, several appropriate adaptive control schemes are also developed. Ultimately, the validity of the devised adaptive strategies are verified by adopting some numerical examples with simulation results.

Plastome characteristics and species identification of Chinese medicinal wintergreens (Gaultheria, Ericaceae).

Wintergreen oil is a folk medicine widely used in foods, pesticides, cosmetics and drugs. In China, nine out of 47 species within Gaultheria (Ericaceae) are traditionally used as Chinese medicinal wintergreens; however, phylogenetic approaches currently used to discriminating these species remain unsatisfactory. In this study, we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria. Each Gaultheria plastome contained 110 unique genes (76 protein-coding, 30 tRNA, and four rRNA genes). Duplication of trnfM, rps14, and rpl23 genes were detected, while all plastomes lacked ycf1 and ycf2 genes. Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene. Moreover, plastomes of Gaultheria leucocarpa var. yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene. Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales. Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species. Additionally, seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens. Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria. In addition, our findings provide important resources for identification of Chinese medicinal wintergreens.

Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae.

BACKGROUND: Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly understood. To explore the deep relationships within suborder Dennstaedtiineae and estimate the early diversification of this morphologically heterogeneous group, we analyzed complete plastomes of 57 samples representing all eleven genera of suborder Dennstaedtiineae using maximum likelihood and Bayesian inference. RESULTS: The phylogenetic relationships of all the lineages in the bracken fern family Dennstaedtiaceae were well resolved with strong support values. All six genera of Hypolepidoideae were recovered as forming a monophyletic group with full support, and Pteridium was fully supported as sister to all the other genera in Hypolepidoideae. Dennstaedtioideae (Dennstaedtia s.l.) fell into four clades with full support: the Microlepia clade, the northern Dennstaedtia clade, the Dennstaedtia globulifera clade, and the Dennstaedtia s.s. clade. Monachosorum was strongly resolved as sister to all the remaining genera of suborder Dennstaedtiineae. Based on the well resolved relationships among genera, the divergence between Monachosorum and other groups of suborder Dennstaedtiineae was estimated to have occurred in the Early Cretaceous, and all extant genera (and clades) in Dennstaedtiineae, were inferred to have diversified since the Late Oligocene. CONCLUSION: This study supports reinstating a previously published family Monachosoraceae as a segregate from Dennstaedtiaceae, based on unique morphological evidence, the shady habitat, and the deep evolutionary divergence from its closest relatives.

[Groundwater Pollution Source Identification by Combination of PMF Model and Stable Isotope Technology].

The pollution source identification methods based on traditional water quality monitoring and pollutant discharge loading typically require a high frequency of monitoring and generate a level of uncertainty in the identification results, owing to their limitations on the accurate and quantitative assessment of pollution source identification, migration, and transformation. This study combined multivariate statistical analysis and stable isotope technology to identify groundwater pollution sources in a typical multiple land-use area of the Chengdu Plain. A positive matrix factorization (PMF) model was adopted to reduce the interference of mass environmental factors on source identification and to determine the main factors influencing groundwater quality. Subsequently, a Bayesian stable isotope mixing model was developed to quantify the apportionment of each pollution source to groundwater nitrate (NO3-) with the consideration of hydro-chemical and land-use information. The results showed that the concentrations of NO3-, NO2-, NH4+, Mn, Fe, SO42-, and Cl- in groundwater of the study area exceeded the standard to different extents, presenting spatial variation. The main form of inorganic nitrogen in groundwater was NO3-. In general, concentrations of groundwater NO3- were the highest in vegetable fields (9.29 mg·L-1 on average), followed by livestock and poultry breeding farms (7.66 mg·L-1) and arable land (7.09 mg·L-1), whereas concentrations of groundwater NO3- in industrial areas were the lowest (2.20 mg·L-1). Groundwater quality in the study area was affected by geological processes, agricultural activities, hydrogeochemical evolution, and domestic and industrial discharges. Agricultural activities were the main contributor to the increase in groundwater NO3- in the study area. Chemical fertilizer (32%) and soil nitrogen (25%) contributed greatly to groundwater NO3- in agricultural areas, whereas sewage (28%) and atmospheric precipitation (27%) contributed most groundwater NO3- in industrial areas. Thus, the combination of multivariate statistical analysis and stable isotope technology could identify groundwater pollution sources and their apportionment effectively, providing scientific support for the prevention and control of groundwater pollution.

Structural Variation of Plastomes Provides Key Insight Into the Deep Phylogeny of Ferns.

Structural variation of plastid genomes (plastomes), particularly large inversions and gene losses, can provide key evidence for the deep phylogeny of plants. In this study, we investigated the structural variation of fern plastomes in a phylogenetic context. A total of 127 plastomes representing all 50 recognized families and 11 orders of ferns were sampled, making it the most comprehensive plastomic analysis of fern lineages to date. The samples included 42 novel plastomes of 15 families with a focus on Hymenophyllales and Gleicheniales. We reconstructed a well-supported phylogeny of all extant fern families, detected significant structural synapomorphies, including 9 large inversions, 7 invert repeat region (IR) boundary shifts, 10 protein-coding gene losses, 7 tRNA gene losses or anticodon changes, and 19 codon indels (insertions or deletions) across the deep phylogeny of ferns, particularly on the backbone nodes. The newly identified inversion V5, together with the newly inferred expansion of the IR boundary R5, can be identified as a synapomorphy of a clade composed of Dipteridaceae, Matoniaceae, Schizaeales, and the core leptosporangiates, while a unique inversion V4, together with an expansion of the IR boundary R4, was verified as a synapomorphy of Gleicheniaceae. This structural evidence is in support of our phylogenetic inference, thus providing key insight into the paraphyly of Gleicheniales. The inversions of V5 and V7 together filled the crucial gap regarding how the "reversed" gene orientation in the IR region characterized by most extant ferns (Schizaeales and the core leptosporangiates) evolved from the inferred ancestral type as retained in Equisetales and Osmundales. The tRNA genes trnR-ACG and trnM-CAU were assumed to be relicts of the early-divergent fern lineages but intact in most Polypodiales, particularly in eupolypods; and the loss of the tRNA genes trnR-CCG, trnV-UAC, and trnR-UCU in fern plastomes was much more prevalent than previously thought. We also identified several codon indels in protein-coding genes within the core leptosporangiates, which may be identified as synapomorphies of specific families or higher ranks. This study provides an empirical case of integrating structural and sequence information of plastomes to resolve deep phylogeny of plants.

A revision of Dryopteris sect. Diclisodon (Dryopteridaceae) based on morphological and molecular evidence with description of a new species.

Dryopteris sect. Diclisodon is a small section of ferns with about 12 species mainly distributed in East Asia. Here, we carried out morphological and phylogenetic analyses of this section. A new species from southwest China, D. gaoligongensis, is described and illustrated. Dryopteris gaoligongensis resembles D. indonesiana and D. sparsa, but differs by having a creeping rhizome and large 4-pinnate fronds. We also show that D. glabrior Ching & Z.Y. Liu is a distinct species; however, because it is a later homonym of D. glabrior Copel., it should be renamed D. renchangiana. We conclude that a species previously known as D. nitidula , also an illegitimate homonym, should be recognized with a new name, D. sinonepalensis. We resolve the phylogenetic position of D. yoroii as sister to other sampled species of D. sect. Diclisodon. Our phylogenetic analyses confirm the distinctiveness of D. gaoligongensis, D. renchangiana, and D. sinonepalensis. A key to species of D. sect. Diclisodon in China is provided.

Complex and reticulate origin of edible roses (Rosa, Rosaceae) in China.

While roses are today among the most popular ornamental plants, the petals and fruits of some cultivars have flavored foods for millennia. The genetic origins of these edible cultivars remain poorly investigated. We collected the major varieties of edible roses available in China, assembled their plastome sequences, and phased the haplotypes for internal transcribed spacers (ITS1/ITS2) of the 18S-5.8S-26S nuclear ribosomal cistron. Our phylogenetic reconstruction using 88 plastid genomes, of primarily maternal origin, uncovered well-supported genetic relationships within Rosa, including all sections and all subgenera. We phased the ITS sequences to identify potential donor species ancestral to the development of known edible cultivars. The tri-parental Middle-Eastern origin of R. × damascena, the species most widely used in perfume products and food additives, was confirmed as a descendent of past hybridizations among R. moschata, R. gallica, and R. majalis/R. fedtschenkoana/R. davurica. In contrast, R. chinensis, R. rugosa, and R. gallica, in association with six other wild species, were the main donors for fifteen varieties of edible roses. The domesticated R. rugosa 'Plena' was shown to be a hybrid between R. rugosa and R. davurica, sharing a common origin with R. 'Fenghua'. Only R. 'Jinbian' and R. 'Crimson Glory' featured continuous flowering. All remaining cultivars of edible roses bloomed only once a year. Our study provides important resources for clarifying the origin of edible roses and suggests a future for breeding new cultivars with unique traits, such as continuous flowering.

Characterization of the Complete Chloroplast Genome of Gaultheria nummularioides D.Don 1825 (Ericaceae).

Gaultheria nummularioides D.Don 1825 (Ericaceae) is a traditional Chinese medicinal plant used to treat rheumatoid arthritis. The complete chloroplast genome of G. nummularioides has been sequenced and assembled. The genome is 176,207 bp in total with one large single copy (LSC: 107,726 bp), one small single copy (SSC: 3,389 bp), and two inverted repeat regions (IRa and IRb; each 32,546 bp). The chloroplast genome encoded a total of 110 unique genes; the GC content of these genes is 36.6%. The results based on phylogenetic analysis of the complete chloroplast genome suggests that G. nummularioides diverged later than G. praticola, the sister relationship between G. nummularioides and the clade comprising G. fragrantissima Wall. 1820 and G. hookeri C.B. Clarke 1882 was strongly supported. This study provides additional information on the genetic diversity of G. nummularioides, its closely related taxa, and further exploration of chloroplast genomes in the Ericaceae family.

Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic.

Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems.

Characterization of the complete plastid genome of Gaultheria griffithiana (Ericaceae).

Gaultheria griffithiana is an evergreen shrub in the family Ericaceae. It is used as a source of the Chinese traditional medicine, Tougucao, with distribution of the junction of eastern Himalaya and Hengduan Mountain. The chloroplast genome of G. griffithiana is 175,649 bp in length with 135 genes, including eight rRNA genes, 39 tRNA genes, and 85 protein-coding genes. Phylogenetic analysis has converged on the placement of G. griffithiana as sister to G. praticola, G. nummularioides, and G. hookeri within the Leucothoides clade of Gaultheria in this study.

The complete chloroplast genome of Gaultheria fragrantissima Wall. (Ericaceae) from Yunnan, China, an aromatic medicinal plant in the wintergreens.

Gaultheria fragrantissima (Ericaceae) is an aromatic medicinal plant with high concentrations of the secondarymetabolite methyl salicylate (oil of wintergreen). In this study, the complete chloroplast genomeof G. fragrantissima was sequenced. The complete plastome is 176,196 bp in length, and the GCcontent is 36.6%. The plastome comprises 110 unique genes (76 protein-coding, 30 tRNA and 4 rRNA).Phylogenetic analysis fully supported a sister relationship between G. fragrantissima and G. hookeriwithin the Leucothoides clade of Gaultheria. This chloroplast genome will serve as a valuable referencefor future taxonomic and phylogenetic research.

Adaptation in the Dorsal Belt and Core Regions of the Auditory Cortex in the Awake Rat.

The rat auditory cortex is divided anatomically into several areas, but little is known about the functional differences in information processing among these areas. Three tonotopically organized core fields, namely, the primary (A1), anterior (AAF), and ventral (VAF) auditory fields, as well as one non-tonotopically organized belt field, the dorsal belt (DB), were identified based on their response properties. Compared to neurons in A1, AAF and VAF, units in the DB exhibited little or no response to pure tones but strong responses to white noise. The few DB neurons responded to pure tones with thresholds greater than 60 dB SPL, which was significantly higher than the thresholds of neurons in the core regions. In response to white noise, units in DB showed significantly longer latency and lower peak response, as well as longer response duration, than those in the core regions. Responses to repeated white noise were also examined. In contrast to neurons in A1, AAF and VAF, DB neurons could not follow repeated stimulation at a 300 ms inter-stimulus interval (ISI) and showed a significant steeper ISI tuning curve slope when the ISI was increased from 300 ms to 4.8 s. These results indicate that the DB processes auditory information on broader spectral and longer temporal scales than the core regions, reflecting a distinct role in the hierarchical cortical pathway.

Extreme plastid RNA editing may confound phylogenetic reconstruction: A case study of Selaginella (lycophytes).

Cytidine-to-uridine (C-to-U) RNA editing is common in coding regions of organellar genomes throughout land plants. In most cases RNA editing alters translated amino acids or creates new start codons, potentially confounds phylogenetic reconstructions. In this study, we used the spike moss genus Selaginella (lycophytes), which has the highest frequency of RNA editing, as a model to test the effects of extreme RNA editing on phylogenetic reconstruction. We predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes, and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences, first and second codon positions, and translated amino acid sequences, respectively. We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes. The numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions, but not correlated with the GC content of plastomes as a whole. Contrast phylogenetic analyses showed that there were substantial differences (e.g., the placement of clade B in Selaginella) between the phylogenies generated by the plastome and RNA-edited data sets. This empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction, and might even confound phylogenetic reconstruction. Therefore, RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies, particularly in those lineages with abundant organellar RNA editing sites, such as hornworts, quillworts, spike mosses, and some seed plants.

Characteristics and Mutational Hotspots of Plastomes in Debregeasia (Urticaceae).

Debregeasia is an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from five Debregeasia species and 13 plastomes from other genera. Together with the one published plastome for Debregeasia, we analyzed plastome structure and character, identified mutation hotspots and loci under selection, and constructed phylogenies. The plastomes of Debregeasia were found to be very conservative, with a size from 155,743 bp to 156,065 bp, and no structural variation. Eleven mutation hotspots were identified, including three (rpoB-trnC-GCA, trnT-GGU-psbD and ycf1) that are highly variable both within Debregeasia and among genera; these show high potential value for future DNA barcoding, population genetics and phylogenetic reconstruction. Selection pressure analysis revealed nine genes (clpP, ndhF, petB, psbA, psbK, rbcL, rpl23, ycf2, and ycf1) that may experience positive selection. Phylogenomic analyses results suggest that Debregeasia was monophyletic, and closest to Boehmeria among genera examined. Within Debregeasia, D. longifolia was sister to D. saeneb, whereas D. elliptica, D. orientalis with D. squamata formed the other subclade. This study enriches organelle genome resources for Urticaceae, and highlights the utility of plastome data for detecting mutation hotspots for evolutionary and systematic analysis.

Complete plastome of an endemic fern species from China: Neocheiropteris palmatopedata (Polypodiaceae).

Neocheiropteris palmatopedata (Baker) Christ is an endangered fern species endemic to southwest China. In this study, we sequenced the complete plastid genome of N. palmatopedata. The gene order and structure of the N. palmatopedata plastome are similar to those published plastomes in Polypodiales. The complete plastome is 153,344 bp in length, and the GC content is 42.1%. The plastome comprises 113 unique genes (83 protein-coding genes, 29 tRNA genes and four rRNA genes).

The complete plastid genome sequence of Begonia guangxiensis.

Begonia guangxiensis was assessed as endangered according to Red List of Chinese Plants. In this study, we described the complete plastid genome of B. guangxiensis. The plastid genome sequence of B. guangxiensis is 157,648 bp in size, having a large single-copy region (LSC) of 86,514 bp, a small single-copy region (SSC) of 18,076 bp, and two inverted repeat (IR) regions of 26,529 bp. The complete plastid genome of B. guangxiensis encoding 112 unique genes including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. The overall GC content of the plastid genome is 35.9%. Phylogenetic analysis confirmed that B. guangxiensis is closely related to B. varipeltata.