Whole Genome Duplication Events Likely Contributed to the Aquatic Adaptive Evolution of Parkerioideae.

As the only aquatic lineage of Pteridaceae, Parkerioideae is distinct from many xeric-adapted species of the family and consists of the freshwater Ceratopteris species and the only mangrove ferns from the genus Acrostichum. Previous studies have shown that whole genome duplication (WGD) has occurred in Parkerioideae at least once and may have played a role in their adaptive evolution; however, more in-depth research regarding this is still required. In this study, comparative and evolutionary transcriptomics analyses were carried out to identify WGDs and explore their roles in the environmental adaptation of Parkerioideae. Three putative WGD events were identified within Parkerioideae, two of which were specific to Ceratopteris and Acrostichum, respectively. The functional enrichment analysis indicated that the lineage-specific WGD events have played a role in the adaptation of Parkerioideae to the low oxygen concentrations of aquatic habitats, as well as different aquatic environments of Ceratopteris and Acrostichum, such as the adaptation of Ceratopteris to reduced light levels and the adaptation of Acrostichum to high salinity. Positive selection analysis further provided evidence that the putative WGD events may have facilitated the adaptation of Parkerioideae to changes in habitat. Moreover, the gene family analysis indicated that the plasma membrane H+-ATPase (AHA), vacuolar H+-ATPase (VHA), and suppressor of K+ transport growth defect 1 (SKD1) may have been involved in the high salinity adaptation of Acrostichum. Our study provides new insights into the evolution and adaptations of Parkerioideae in different aquatic environments.

Neottiamaolanensis, a replacement name for Neottiabifida M.N.Wang (Orchidaceae).

According to Articles 53.1 of the International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code), Neottiabifida M.N.Wang (as 'bifidus'; PhytoKeys 229: 222, 2023) is an illegitimate name, and hence a new name Neottiamaolanensis M. N. Wang is proposed here.

Neottiabifidus (Orchidaceae, Epidendroideae, Neottieae), a new mycoheterotrophic species from Guizhou, China.

Neottiabifidus, a new mycoheterotrophic orchid, found in Maolan National Nature Reserve in Guizhou Province, China, is described and illustrated here. The new species is close to N.nidus-avis, N.kiusiana and N.papilligera but differs in having a finely pubescent rachis with fewer flowers, a finely pubescent pedicel, and a fishtail-shaped lip that is deeply bilobed to the middle of the lip, with the lobes diverging at an acute angle (45°) to each other and mesochile with many papillae. Additionally, N.bifidus is well supported as a new species by molecular phylogenetic results based on ITS and chloroplast genome. The chloroplast genome of the novelty, which contains an LSC region of 33,819 bp, SSC region of 5,312 bp and IRs of 46,762 bp was assembled and annotated. A key to mycoheterotrophic Neottia species in China is also provided.

Insights into cryptic speciation of quillworts in China.

Cryptic species are commonly misidentified because of high morphological similarities to other species. One group of plants that may harbor large numbers of cryptic species is the quillworts (Isoëtes spp.), an ancient aquatic plant lineage. Although over 350 species of Isoëtes have been reported globally, only ten species have been recorded in China. The aim of this study is to better understand Isoëtes species diversity in China. For this purpose, we systematically explored the phylogeny and evolution of Isoëtes using complete chloroplast genome (plastome) data, spore morphology, chromosome number, genetic structure, and haplotypes of almost all Chinese Isoëtes populations. We identified three ploidy levels of Isoëtes in China-diploid (2n = 22), tetraploid (2n = 44), and hexaploid (2n = 66). We also found four megaspore and microspore ornamentation types in diploids, six in tetraploids, and three in hexaploids. Phylogenetic analyses confirmed that I. hypsophila as the ancestral group of the genus and revealed that Isoëtes diploids, tetraploids, and hexaploids do not form monophyletic clades. Most individual species possess a single genetic structure; however, several samples have conflicting positions on the phylogenetic tree based on SNPs and the tree based on plastome data. All 36 samples shared 22 haplotypes. Divergence time analysis showed that I. hypsophila diverged in the early Eocene (∼48.05 Ma), and most other Isoëtes species diverged 3-20 Ma. Additionally, different species of Isoëtes were found to inhabit different water systems and environments along the Yangtze River. These findings provide new insights into the relationships among Isoëtes species in China, where highly similar morphologic populations may harbor many cryptic species.

Supramolecular Chemistry of Windmill-like Al10 Clusters: Adjustable Guests and Hydrogen-Bonding Networks for Enhanced Optical Limiting.

The interest in cluster chemistry lies not only in the development of new types of geometric structures but also in the higher-level connectivity and assembly of clusters at the supramolecular level. Here, we report a novel windmill-like Al10 cluster and consider this geometrically unique cluster as an anionic node assembled together with different cationic guests such as imidazolium and guanidinium. These guests with different hydrogen-bond angles can help to obtain a series of diverse hydrogen-bonding networks and then manipulate the stacking mode of hosts and guests. Furthermore, we realized a supramolecular approach to fine-tune the optical limiting properties of the cluster. This work not only enriches the host-guest chemistry of ionic windmill-like clusters but also opens up more possibilities for aluminum oxo cluster-based hydrogen-bonded frameworks.

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns.

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.

Population Diversity Analysis Provide Insights into Provenance Identification of Dendrobium catenatum.

Dendrobium catenatum (Dendrobium officinale) is a valuable genuine herb. The source of this species is difficult to be identified by traditional methods including morphology, spectroscopy, and chromatography. We used the restriction site-associated DNA sequencing (RAD-seq) approach to perform the high-throughput sequencing of 24 D. catenatum provenances. In this study, 371.18 Gb clean data were obtained, and 655,057 high-quality SNPs were selected after their filtration. We used phylogenetic tree, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 109 accessions. We found that D. catenatum could be divided into two groups, and each group was closely related to the distribution of the sampling sites. At the population level, the average nucleotide diversity (π) of the D. catenatum population mutation parameters was 0.1584 and the expected heterozygosity (HE) was 0.1575. The GXLPTP07 accessions showed the highest genetic diversity in terms of the private allele number, observed heterozygosity, and nucleotide diversity. The Mantel test showed a significant positive correlation between the genetic and geographic distances among the overall distribution. A genetic information database of D. catenatum was established, which confirmed that RAD-seq technology has the potential to be applied in the identification of medicinal Dendrobium of different origins.

The complete chloroplast genome sequence of Thrixspermum amplexicaule (Orchidaceae, Aeridinae).

The complete chloroplast genome sequence of Thrixspermum amplexicaule was assembled and analyzed in this work. The total chloroplast genome size of T. amplexicaule was 148,124 bp in length, containing a large single-copy (LSC) region of 86,079 bp, a small single-copy (SSC) region of 10,799 bp, and a pair of inverted repeat (IR) regions of 25,623 bp. The GC content of T. amplexicaule was 36.4%. It encoded a total of 120 unique genes, including 75 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of phylogenetic analysis strongly supported that all four samples of Thrixspermum are monophyletic and T. amplexicaule was closely related to T. centipeda.

Carbon monoxide poisoning: a prediction model using meteorological factors and air pollutant.

BACKGROUND: While the influence of meteorology on carbon monoxide (CO) poisoning has been reported, few data are available on the association between air pollutants and the prediction of CO poisoning. Our objective is to explore meteorological and pollutant patterns associated with CO poisoning and to establish a predictive model. RESULTS: CO poisoning was found to be significantly associated with meteorological and pollutant patterns: low temperatures, low wind speeds, low air concentrations of sulfur dioxide (SO2) and ozone (O38h), and high daily temperature changes and ambient CO (r absolute value range: 0.079 to 0.232, all P values < 0.01). Based on the above factors, a predictive model was established: "logitPj = aj - 0.193 * temperature - 0.228 * wind speed + 0.221 * 24 h temperature change + 1.25 * CO - 0.0176 * SO2 + 0.0008 *O38h; j = 1, 2, 3, 4; a1 = -4.12, a2 = -2.93, a3 = -1.98, a4 = -0.92." The proposed prediction model based on combined factors showed better predictive capacity than a model using only meteorological factors as a predictor. CONCLUSION: Low temperatures, wind speed, and SO2 and high daily temperature changes, O38h, and CO are related to CO poisoning. Using both meteorological and pollutant factors as predictors could help facilitate the prevention of CO poisoning.

The complete chloroplast genome of an endangered species Apostasia ramifera (Orchidaceae).

Apostasia ramifera S. C. Chen & K. Y. Lang 1986 is a Chinese endemic and endangered orchid. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of A. ramifera. The cp genome was 157,518 bp in length with a typical quadripartite structure, which was comprised of one large single-copy region (LSC, 86,353 bp) and one small single-copy region (SSC, 16,445 bp) separated by two inverted repeat regions (IRs, 27,360 bp). The cp genome encoded 133 genes, which included 87 protein-coding genes, 38 tRNAs and eight rRNAs. The average GC content of the genome is 35.8%. The phylogenetic analysis showed that A. ramifera was sister with A. wallichii and then nested in the other Apostasia species.

Two new dibenzyl derivatives from the stems of Dendrobium catenatum.

Two new dibenzyl derivatives, dendrocandins V-W (1-2), together with six known compounds (3-8), have been isolated from the dried stems of Dendrobium catenatum. Their structures were mainly elucidated on the basis of HRESIMS, one- and two-dimensional NMR techniques. The isolated compounds 5-8 were evaluated in vitro for their antioxidant and hypoglycemic activities. Compound 8 showed moderate potent DPPH scavenging activity with IC50 value of 34.45 ± 1.07 µM. And compounds 5, 7-8 exhibited significant ABTS radical scavenging activities with IC50 values of 10.03 ± 0.88, 5.32 ± 1.13 and 9.01 ± 1.39 µM. Compounds 6-7 showed potent α-glucosidase inhibitory activities with IC50 values of 36.05 ± 0.67 and 159.59 ± 0.86 µM.

Dipterisshenzhenensis, a new endangered species of Dipteridaceae from Shenzhen, southern China.

Dipterisshenzhenensis, a new species of ferns from Shenzhen, Guangdong, southern China, is identified and described. It closely resembles D.chinensis but possesses several unique traits, such as long rhizome scales, castaneous stipe, and abaxially pale fronds with two fan-shaped fronds connected by a broad wing. Molecular evidence showed that D.shenzhenensis is allied to D.conjugata, whereas it has morphologically significant differences (P < 0.05) on the basis of quantitative trait statistical analysis. Overall, the morphological evidence, taken together with the result of cpDNA indicated that D.shenzhenensis is a distinct species.

Using Hebbian-Type Stimulation to Rescue Arm Function After Stroke: Study Protocol for a Randomized Clinical Trial.

BACKGROUND: Upper-extremity hemiplegia after stroke remains a significant clinical problem. The supplementary motor area (SMA) is vital to the motor recovery outcomes of chronic stroke patients. Therefore, rebuilding the descending motor tract from the SMA to the paralyzed limb is a potential approach to restoring arm motor function after stroke. Paired associative stimulation (PAS), which is based on Hebbian theory, is a potential method for reconstructing the connections in the impaired motor neural circuits. The study described in this protocol aims to assess the effects of cortico-peripheral Hebbian-type stimulation (HTS), involving PAS, for neural circuit reconstruction to rescue the paralyzed arm after stroke. METHODS: The study is a 4-month double-blind randomized sham-controlled clinical trial. We will recruit 90 post-stroke individuals with mild to moderate upper limb paralysis. Based on a 1:1 ratio, the participants will be randomly assigned to the HTS and sham groups. Each participant will undergo 5-week HTS or sham stimulation. Assessments will be conducted at baseline, immediately after the 5-week treatment, and at a 3-month follow-up. The primary outcome will be the Wolf Motor Function Test (WMFT). The secondary outcomes will be Fugl-Meyer Assessment for Upper Extremity (FMA-UE), Functional Independence Measure (FIM), and functional near-infrared spectroscopy (fNIRS) parameters. The adverse events will be recorded throughout the study. DISCUSSION: Upper-limb paralysis in stroke patients is due to neural circuit disruption, so the reconstruction of effective motor circuits is a promising treatment approach. Based on its anatomical structure and function, the SMA is thought to compensate for motor dysfunction after focal brain injury at the cortical level. Our well-designed randomized controlled trial will allow us to analyze the clinical efficacy of this novel Hebbian theory-based neuromodulation strategy regarding promoting the connection between the cortex and peripheral limb. The results may have significance for the development and implementation of effective neurorehabilitation treatments. CLINICAL TRIAL REGISTRATION: [www.ClinicalTrials.gov], identifier [ChiCTR2000039949].

The complete chloroplast genome of Geodorum eulophioides (Orchidaceae).

Geodorum eulophioides Schltr., is a critically Endangered orchid (IUCN). In this study, we report the first complete chloroplast (cp) genome of G. eulophioides to provide the underlying information for genetic breeding and conservation studies of this species. The cp genome sequence of G. eulophioides is 149,466 bp in length, which contains one large single-copy region (LSC, 85,436 bp), one small single-copy region (SSC, 14,086 bp), and two inverted repeat regions (IRs, 24,972 bp). The cp genome encoded 177 genes, of which 106 were unique genes (78 protein-coding genes, 24 tRNAs, and 4 rRNAs). Phylogenetic analysis showed that G. eulophioides is closely related to the genera Eulophia.

The complete chloroplast genome of Cymbidium eburneum (Orchidaceae).

Cymbidium eburneum Lindl. is an endangered species of Orchidaceae and distributed in Guangxi, Yunnan and Hainan of China, and India, Myanmar, Nepal, Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. eburneum. The complete chloroplast (cp) genome sequence of C. eburneum is 156,520 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 85,518 bp), one small single-copy region (SSC, 20,014 bp), and two inverted repeat regions (IRs, 25,471 bp). The cp genome encoded 135 genes, of which 106 were unique genes (78 protein-coding genes, 24 tRNAs, and 4 rRNAs). The phylogenetic relationships show that C. eburneum is closely related to other species in the genus Cymbidium, and is sister with C. tracyanum.

The complete chloroplast genome of Cymbidium erythraeum (Orchidaceae).

Cymbidium erythraeum Lindl. is an endangered species of Orchidaceae and distributed in China and Bhutan, India, Myanmar, Nepal, and Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. erythraeum. The complete chloroplast (cp) genome sequence of C. erythraeum is 156,327 bp in length and including one large single-copy region (LSC, 85,404 bp), one small single-copy region (SSC, 20,021 bp), and two inverted repeat regions (IRs, 25,426 bp). The cp genome encoded 136 genes, of which 107 were unique genes (80 protein-coding genes, 23 tRNAs, and four rRNAs). The phylogenetic relationships show that C. erythraeum is closely related to other species in the genus Cymbidium and is sister with C. tracyanum.

The complete chloroplast genome of Vanilla shenzhenica (Orchidaceae).

Vanilla shenzhenica Z.J.Liu & S.C.Chen is a new species of orchid found in Shenzhen, South China for the first time. Here we report the complete chloroplast (cp) genome sequence and the features of V. shenzhenica. Its cp genome sequence was 151,537 bp, including one large single-copy region (LSC, 87,487 bp), one small single-copy region (SSC, 19,172 bp), and two inverted repeat regions (IRs, 22,439 bp). It encoded 123 genes, of which 104 were unique genes (69 protein-coding genes, 31 tRNAs and 4 rRNAs). The phylogenetic relationships show that V. shenzhenica is sister with V. aphylla.

The complete chloroplast genome of Paphiopedilum malipoense (Orchidaceae).

Paphiopedilum malipoense S.C.Chen & Z.H.Tsi is a new orchid species found in Malipo county, Yunnan. Here we report the complete chloroplast (cp) genome sequence and the features of P. malipoense. Its cp genome sequence of P. malipoense is 158,708 bp, including one large single-copy region (LSC, 89,452 bp), one small single-copy region (SSC, 17,692 bp), and two inverted repeat regions (IRs, 25,782 bp). The cp genome encoded 132 genes, of which 112 were unique genes (79 protein-coding genes, 29 tRNAs, and 4 rRNAs). The phylogenetic relationships show that P. malipoense is sister with P. armeniacum-P. wardii.

Complete chloroplast genome of Dendrobium thyrsiflorum (Orchidaceae).

Dendrobium thyrsiflorum H. G. Reichenbach ex André is an endemic herb with ornamental and medicinal orchid value distributed in Southeast of Yunnan of China. Here, we report and characterize the complete chloroplast (cp) genome sequence of D. thyrsiflorum in order to provide genomic resources helpful for its identification, conservation and utilization. The complete cp genome of D. thyrsiflorum is 160,123 bp, including one large single-copy region (LSC, 88,001), one small single-copy region (SSC, 21,142), and two inverted repeat regions (IRs, 25,490). The cp genome contains 143 genes, consisting of 110 unique genes (80 protein-coding genes, 26 tRNAs, and 4 rRNAS). The phlyogenetic relationships show that D. thyrsiflorum is closely related to other species of Dendrobium.

The complete chloroplast genome of Pholidota imbricata (Orchidaceae).

Pholidota imbricata belongs to tribe Coelogninae in Orchidaceae distributed in Sichuan, Xizang, and Yunnan. Here, we report the first complete chloroplast (cp) genome and the cp genome features of P. imbricata. The complete cp genome sequence of P. imbricata is 159,292 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 87,515 bp), one small single-copy region (SSC, 20,999 bp), and two inverted repeat regions (IRs, 25,389 bp each). The cp genome encoded 141 genes, of which 108 were unique genes (80 protein-coding genes, 24 tRNAs, and 4 rRNAs). The phylogenetic relationships show that P. imbricata is sister to the species of the genus Pleione in tribe Coelogninae.