Adaptive functions of structural variants in human brain development.

Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.

Origin of functional de novo genes in humans from "hopeful monsters".

For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.

Fabrication, structure, characterization and emulsion application of citrate agar.

In this study, citric acid successfully reacted with agar through the dry heat method, and citrate agar (CA) gel was used to stabilize O/W emulsions. The mechanisms of the CA structure and emulsion pH that affected emulsion stabilization were analyzed, and the application of CA gel emulsion (CAGE) was explored. Compared with native agar (NA), CA showed lower gel strength, higher transparency, and higher water contact angle. These changes indicate that a cross-linking reaction occurred, and it was demonstrated via FTIR and NMR. The emulsion properties were evaluated using particle size, ζ-potential, and the emulsification activity index. Results showed that CAGEs had a smaller particle size and lower ζ-potential than the native agar gel emulsion (NAGE). Meanwhile, confocal laser scanning microscopy confirmed that the CA gels stabilized the emulsions by forming a protective film around the oil droplets. Stability experiments revealed that CAGE (prepared with CA gel [DS = 0.145]) exhibited better stability than NAGE in the pH range of 3-11, and the rheological results further confirmed that the stability of the emulsions was influenced by the network structure and oil droplet interaction forces. Afterward, the application prospect of CAGE was evaluated by encapsulating vitamin D3 and curcumin.

Interferon-α induces differentiation of cancer stem cells and immunosuppression in hepatocellular carcinoma by upregulating CXCL8 secretion.

Interferon-alpha (IFN-α) is widely used in the clinical treatment of patients with chronic hepatitis B and hepatocellular carcinoma (HCC). However, high levels of CXCL8 are associated with resistance to IFN-α therapy and poorer prognosis in advanced cancers. In this study, we investigated whether IFN-α could directly induce the production of CXCL8 in HCC cells and whether CXCL8 could antagonize the antitumor activity of IFN-α. We found that IFN-α not only upregulated the expression of the inducible genes CXCL9, CXCL10, CXCL11 and PD-L1, but also significantly stimulated CXCL8 secretion in HCC cells. Mechanically, IFN-α induces CXCL8 expression by activating the AKT and JNK pathways. In addition, our results demonstrate that IFN-α exposure significantly increases the differentiation of HCC stem cells, but this effect is reversed by the addition of the CXCL8 receptor CXCR1/2 inhibitor Reparixin and STAT3 inhibitor Stattic. Besides, our study reveals that the cytokine CXCL8 secreted by IFN-α-induced HCC cells inhibits T-cell function. Conversely, inhibition of CXCL8 promotes TNF-α and IFN-γ secretion by T cells. Finally, liver cancer patients who received anti-PD-1/PD-L1 immunotherapy with high CXCL8 expression had a lower immunotherapy efficacy. Overall, our findings clarify that IFN-α triggers immunosuppression and cancer stem cell differentiation in hepatocellular carcinoma by upregulating CXCL8 secretion. This discovery provides a novel approach to enhance the effectiveness of HCC treatment in the future.

Dibromoacetonitrile induced autophagy by mediating the PERK signalling pathway and ROS interaction in HT22 cell.

Dibromoacetonitrile (DBAN) is a high-risk haloacetonitrile (HAN) generated as a byproduct of chloramine disinfection in drinking water. DBAN-induced neurotoxicity in mouse hippocampal neuronal cells (HT22) and mammals was observed to be related to reactive oxygen species (ROS). ROS, endoplasmic reticulum stress (ERS) and autophagy play crucial roles in regulating a variety of cellular processes. However, whether ERS and autophagy are associated with HAN-responsive apoptosis remains unclear. This study indicated that DBAN (10 µM, 24 h) activated the ERS protein kinase like endoplasmic reticulum kinase (PERK) signaling pathway. The ERS inhibitor 4-phenylbutyric acid (4-PBA) reversed DBAN-inhibited cell viability and alleviated DBAN-induced apoptosis in HT22 cell, indicating that activation of the ERS PERK pathway mediates DBAN induced cytotoxicity. Moreover, DBAN activated autophagy. The autophagy inhibitor 3-methyladenine(3-MA) reversed DBAN-inhibited cell viability and alleviated DBAN-induced apoptosis in HT22 cell, suggesting that autophagy activation mediates DBAN-induced cell toxicity. Notably, the results showed that 4-PBA inhibited DBAN-activated autophagy, demonstrating that ERS-PERK promotes DBAN-induced cellular autophagy. Pretreatment with antioxidant N-acetylcysteine (NAC) inhibited the increase in ROS production and the activation of ERS, and protected cells from toxicity. Furthermore, 4-PBA pretreatment reduced the increase in ROS production, indicating that the ROS and PERK promote each other and form a positive feedback loop. ROS also promoted DBAN-induced autophagy. In summary, our findings indicate that DBAN induced autophagy by mediating the PERK signalling pathway and ROS interaction, leading to HT22 cell damage. Accordingly, targeting these pathogenic mechanisms may provide a potential target and theoretical basis for preventing and improving HAN-induced neurotoxicity.

Cephalopod-inspired polymer composites with mechanically tunable infrared properties.

Cephalopods have evolved an all-soft skin that can rapidly display colors for protection, predation, or communication. Development of synthetic analogs to mimic such color-changing abilities in the infrared (IR) region is pivotal to a variety of technologies ranging from soft robotics, flexible displays, dynamic thermoregulatory systems, to adaptive IR disguise platforms. However, the integration of tissue-like mechanical properties and rapid IR modulation ability into smart materials remains challenging. Here, by drawing inspiration from cephalopod skin, we develop an all-soft adaptive IR composite that can dynamically change its IR appearance upon equiaxial stretching. The biomimetic composite is built entirely from soft materials of liquid metal droplets and elastic elastomer, which are analogs of chromatophores and dermal layer of cephalopod skin, respectively. Driven by externally applied strains, the liquid metal inclusions transition between a contracted droplet state with corrugated surface and an expanded platelet state with relatively smooth surface, enabling dynamic variations in the IR reflectance/emissivity of the composite and ultimately resulting in reversible IR adaption. Strain-actuated flexible IR displays and pneumatically-driven soft devices that can dynamically manipulate their IR appearance are demonstrated as examples of the applicability of this material in emerging adaptive soft electronics.

Associations of ITPA gene polymorphisms with outcomes among chronic hepatitis C patients treated with Peg-interferon/ribavirin: A 5-year follow-up study.

To investigate associations between inosine triphosphatase (ITPA) gene polymorphisms and long-term outcomes among chronic hepatitis C (CHC) patients in Northeast China treated with Peg-interferon (IFN)/ribavirin (RBV). CHC patients who received Peg-IFN-2a/RBV treatment during between 2011 and 2013 at 5 hepatitis centers in Northeast China were enrolled. ITPA single nucleotide polymorphisms rs1127354 and rs7270101 from all patients were detected and their associations with 5-year outcomes were analyzed. A total of 635 patients, including 421 infected with hepatitis C virus (HCV) genotype 1 and 214 infected with non-genotype 1 were included. No significant differences were observed in the distribution frequencies of ITPA rs1127354 variants and ITPase activity between patients with HCV genotype 1 and non-genotype 1. In patients who received more than 80% of the planned RBV dose, the 5-year virological response rate and the improvement in liver fibrosis were higher in those with ITPA rs1127354 non-CC with ITPase activity <25% compared with these outcomes in patients with ITPA rs1127354 CC with 100% ITPase activity. Multiple regression analysis revealed that HCV genotype non-1, low baseline HCV ribose nucleic acid (RNA) levels (≤4 × 105 IU/mL), interleukin-28B rs12979860 CC genotype, low baseline liver fibrosis (Fibroscan 0-2), and ITPA rs1127354 non-CC genotype were independent predictors for a high long-term virological response rate, whereas interleukin-28B rs12979860 CC genotype, ITPA rs1127354 non-CC genotype, and low baseline liver fibrosis were independent predictors for improvement of liver fibrosis. ITPA rs1127354 polymorphisms is predictors of long-term outcomes in CHC patients treated with Peg-IFN/RBV.

6mA-Sniper: Quantifying 6mA sites in eukaryotes at single-nucleotide resolution.

While N6-methyldeoxyadenine (6mA) modification is a fundamental regulation in prokaryotes, its prevalence and functions in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution, and delineate a 6mA profile in Caenorhabditis elegans with 2034 sites. Twenty-six of 39 events with Mnl I restriction endonuclease sites were verified, demonstrating the feasibility of this method. The levels of 6mA sites pinpointed by 6mA-Sniper are generally increased after Pseudomonas aeruginosa infection, but decreased in strains with the removal of METL-9, the dominant 6mA methyltransferase. The enrichment of these sites on specific motif of [GC]GAG, the selective constrains on them, and their coordinated changes with METL-9 levels thus support an active shaping of the 6mA profile by methyltransferase. Moreover, for regions marked by 6mA sites that emerged after infection, an enrichment of up-regulated genes was detected, possibly mediated through a mutual exclusive cross-talk between 6mA and H3K27me3 modification. We thus highlight 6mA regulation as a previously neglected regulator in eukaryotes.

Resveratrol alleviates DSS-induced IBD in mice by regulating the intestinal microbiota-macrophage-arginine metabolism axis.

BACKGROUND: Inflammatory bowel disease (IBD) is a global disease with a growing public health concern and is associated with a complex interplay of factors, including the microbiota and immune system. Resveratrol, a natural anti-inflammatory and antioxidant agent, is known to relieve IBD but the mechanism involved is largely unexplored. METHODS: This study examines the modulatory effect of resveratrol on intestinal immunity, microbiota, metabolites, and related functions and pathways in the BALB/c mice model of IBD. Mouse RAW264.7 macrophage cell line was used to further explore the involvement of the macrophage-arginine metabolism axis. The treatment outcome was assessed through qRT-PCR, western blot, immunofluorescence, immunohistochemistry, and fecal 16S rDNA sequencing and UHPLC/Q-TOF-MS. RESULTS: Results showed that resveratrol treatment significantly reduced disease activity index (DAI), retained mice weight, repaired colon and spleen tissues, upregulated IL-10 and the tight junction proteins Occludin and Claudin 1, and decreased pro-inflammatory cytokines IL-1ß, IL-6, and TNF-α. Resveratrol reduced the number of dysregulated metabolites and improved the gut microbial community structure and diversity, including reversing changes in the phyla Bacteroidetes, Proteobacteria, and Firmicutes, increasing 'beneficial' genera, and decreasing potential pathogens such as Lachnoclostridium, Acinobacter, and Serratia. Arginine-proline metabolism was significantly different between the colitis-treated and untreated groups. In the colon mucosa and RAW264.7 macrophage, resveratrol regulated arginine metabolism towards colon protection by increasing Arg1 and Slc6a8 and decreasing iNOS. CONCLUSION: This uncovers a previously unknown mechanism of resveratrol treatment in IBD and provides the microbiota-macrophage-arginine metabolism axis as a potential therapeutic target for intestinal inflammation.

Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality, local adaptation and demographic history.

Clonal propagation and extensive dispersal of seeds and asexual propagules are two important features of aquatic plants that help them adapt to aquatic environments. Accurate measurements of clonality and effective clonal dispersal are essential for understanding the evolution of aquatic plants. Here, we first assembled a high-quality chromosome-level genome of a widespread emergent aquatic plant Sparganium stoloniferum to provide a reference for its population genomic study. We then performed high-depth resequencing of 173 individuals from 20 populations covering different basins across its range in China. Population genomic analyses revealed three genetic lineages reflecting the northeast (NE), southwest (SW) and northwest (NW) of its geographical distribution. The NE lineage diverged in the middle Pleistocene while the SW and NW lineages diverged until about 2400 years ago. Clonal relationship analyses identified nine populations as monoclonal population. Dispersal of vegetative propagules was identified between five populations covering three basins in the NE lineage, and dispersal distance was up to 1041 km, indicating high dispersibility in emergent aquatic plant species. We also identified lineage-specific positively selected genes that are likely to be involved in adaptations to saline wetlands and high-altitude environments. Our findings accurately measure the clonality, determine the dispersal range and frequency of vegetative propagules, and detect genetic signatures of local adaptation in a widespread emergent aquatic plant species, providing new perspectives on the evolution of aquatic plants.

Extraction, Modification and Biomedical Application of Agarose Hydrogels: A Review.

Numerous compounds present in the ocean are contributing to the development of the biomedical field. Agarose, a polysaccharide derived from marine red algae, plays a vital role in biomedical applications because of its reversible temperature-sensitive gelling behavior, excellent mechanical properties, and high biological activity. Natural agarose hydrogel has a single structural composition that prevents it from adapting to complex biological environments. Therefore, agarose can be developed into different forms through physical, biological, and chemical modifications, enabling it to perform optimally in different environments. Agarose biomaterials are being increasingly used for isolation, purification, drug delivery, and tissue engineering, but most are still far from clinical approval. This review classifies and discusses the preparation, modification, and biomedical applications of agarose, focusing on its applications in isolation and purification, wound dressings, drug delivery, tissue engineering, and 3D printing. In addition, it attempts to address the opportunities and challenges associated with the future development of agarose-based biomaterials in the biomedical field. It should help to rationalize the selection of the most suitable functionalized agarose hydrogels for specific applications in the biomedical industry.

STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data.

Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression heterogeneities in diverse cell types underlying homeostasis, development and pathological states. However, the loss of spatial information hinders its applications in deciphering spatially related features, such as cell-cell interactions in a spatial context. Here, we present STellaris (https://spatial.rhesusbase.com), a web server aimed to rapidly assign spatial information to scRNA-seq data based on their transcriptomic similarity with public spatial transcriptomics (ST) data. STellaris is founded on 101 manually curated ST datasets comprising 823 sections across different organs, developmental stages and pathological states from humans and mice. STellaris accepts raw count matrix and cell type annotation of scRNA-seq data as the input, and maps single cells to spatial locations in the tissue architecture of properly matched ST section. Spatially resolved information for intercellular communications, such as spatial distance and ligand-receptor interactions (LRIs), are further characterized between annotated cell types. Moreover, we also expanded the application of STellaris in spatial annotation of multiple regulatory levels with single-cell multiomics data, using the transcriptome as a bridge. STellaris was applied to several case studies to showcase its utility of adding value to the ever-growing scRNA-seq data from a spatial perspective.

The complete chloroplast genome sequence of Zannichellia palustris (Potamogetonaceae).

Zannichellia palustris Linnaeus 1753 is a cosmopolitan submerged species capable of rapidly responding to environmental changes, with potential applications in the ecological treatment of heavy metal pollution in water bodies. This study aimed to characterize the complete chloroplast genome of Z. palustris, which has not been reported previously. The chloroplast genome of Z. palustris displays a quadripartite structure with a length of 155,262 base pairs (bp), comprising a large single copy (LSC) region of 85,397 bp, a small single copy (SSC) region of 18,057 bp, and a pair of inverted repeat (IR) regions of 25,904 bp. The GC content of the genome is 35.8%, with corresponding values of 33.4% for the LSC, 28.2% for the SSC, and 42.5% for the IR regions. The genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis within the order Alismatales revealed that Z. palustris clusters with the clade of Potamogeton perfoliatus, P. crispus and Stuckenia pectinata.

Ruppia mongolica (Ruppiaceae), a new species from Inner Mongolia (China), based on morphological and genetic data.

Ruppia mongolica Y. Zou & X.W. Xu, a new species from Inner Mongolia, China, is described and illustrated. The phylogenetic position of the new species within the genus was analyzed based on eight chloroplast DNA fragments and an ingroup sampling of all Eurasian species of Ruppia. The results showed that R. mongolica formed a separate branch between R. sinensis and the clade of R. maritima, R. brevipedunculata, R. drepanensis, and R. cirrhosa. Based on molecular and geographical evidence, our study reveals that R. mongolica is closely related to R. sinensis and R. brevipedunculata but differs from the former in the length and shape of the peduncle and seed size, and from the latter in the length of the peduncle, number of carpels per flower, and seed size. In addition, the karyotype analysis revealed that R. mongolica is octoploid, which is first reported within Ruppia, further supporting R. mongolica as a new species.

Scalable Polyimide-Organosilicate Hybrid Films for High-Temperature Capacitive Energy Storage.

High-temperature polymer dielectrics have broad application prospects in next-generation microelectronics and electrical power systems. However, the capacitive energy densities of dielectric polymers at elevated temperatures are severely limited by carrier excitation and transport. Herein, a molecular engineering strategy is presented to regulate the bulk-limited conduction in the polymer by bonding amino polyhedral oligomeric silsesquioxane (NH2 -POSS) with the chain ends of polyimide (PI). Experimental studies and density functional theory (DFT) calculations demonstrate that the terminal group NH2 -POSS with a wide-bandgap of Eg ≈ 6.6 eV increases the band energy levels of the PI and induces the formation of local deep traps in the hybrid films, which significantly restrains carrier transport. At 200 °C, the hybrid film exhibits concurrently an ultrahigh discharged energy density of 3.45 J cm-3 and a high gravimetric energy density of 2.74 J g-1 , with the charge-discharge efficiency >90%, far exceeding those achieved in the dielectric polymers and nearly all other polymer nanocomposites. Moreover, the NH2 -POSS terminated PI film exhibits excellent charge-discharge cyclability (>50000) and power density (0.39 MW cm-3 ) at 200 °C, making it a promising candidate for high-temperature high-energy-density capacitors. This work represents a novel strategy to scalable polymer dielectrics with superior capacitive performance operating in harsh environments.

Inhibition of TERC inhibits neural apoptosis and inflammation in spinal cord injury through Akt activation and p-38 inhibition via the miR-34a-5p/XBP-1 axis.

This study investigated the function of telomerase RNA component (TERC) in spinal cord injury (SCI). SCI models were established in rats via laminectomy and PC-12 cells were treated with lipopolysaccharide (LPS). TERC and miR-34a-5p expressions in cells and rat spinal cords were detected by quantitative reverse transcription polymerase chain reaction, followed by overexpression/knockdown of TERC/miR-34a-5p. Spinal cord histopathological changes were examined via hematoxylin-eosin staining. miR-34a-5p' relation with TERC and XBP-1 was predicted by TargetScan and checked by dual-luciferase reporter/RNA immunoprecipitation assays. Cell biological behaviors were assessed by Cell counting kit-8, wound healing, Transwell, and flow cytometry assays. XBP-1 and inflammation/apoptosis-related protein expressions were analyzed by western blot. TERC was upregulated and miR-34a-5p was low-expressed in SCI tissues and LPS-induced PC-12 cells. TERC-knockdown alleviated histopathological abnormalities yet upregulated miR-34a-5p in SCI tissues. In LPS-induced PC-12 cells, TERC knockdown promoted cell viability, migration, invasion, and inhibited apoptosis, while TERC overexpression ran oppositely. TERC knockdown downregulated the XBP-1, IL-6, TNF-α, Bax, p-p38/t-p38, and cleaved caspase-9/-3, but upregulated Bcl-2 and p-Akt/t-Akt. TERC targeted miR-34a-5p, which further targeted XBP-1. miR-34a-5p downregulation exerted effects opposite to and offset TERC knockdown-induced effects. TERC knockdown facilitated the regeneration of neuron tissues yet inhibited inflammation in SCI through Akt activation and p-38 inhibition via the miR-34a-5p/XBP-1 axis.

Tailoring Poly(Styrene-co-maleic anhydride) Networks for All-Polymer Dielectrics Exhibiting Ultrahigh Energy Density and Charge-Discharge Efficiency at Elevated Temperatures.

Polymer film capacitors have been widely used in electronics and electrical power systems due to their advantages of high power densities, fast charge-discharge speed, and great stability. However, the exponential increase of electrical conduction with temperature and applied electric field substantially degrades the capacitive performance of dielectric polymers at elevated temperatures. Here, the first example of controlling the energy level of charge traps in all-organic crosslinked polymers by tailoring molecular structures that significantly inhibit high-field high-temperature conduction loss, which largely differs from current approaches based on the introduction of inorganic fillers, is reported. The polymer network with optimized crosslinking structures exhibits an ultrahigh discharged energy density of 7.02 J cm-3 with charge/discharge efficiencies of >90% at 150 °C, far outperforming current dielectric polymers and composites. The charge-trapping effects in different crosslinked structures, as the origins of the marked improvements in the high-temperature capacitive performance, are comprehensively investigated experimentally and confirmed computationally. Moreover, excellent cyclability and self-healing features are demonstrated in the polymer film capacitors. This work offers a promising pathway of molecular structure design to scalable high-energy-density polymer dielectrics capable of operating under harsh environments.

Electrostatic Adhesion Clutch with Superhigh Force Density Achieved by MXene-Poly(Vinylidene Fluoride-Trifluoroethylene-Chlorotrifluoroethylene) Composites.

Electrostatic adhesion (EA) clutches are widely applied in robots, wearable devices, and virtual reality, due to their compliance, lightweight, ultrathin profile, and low power consumption. Higher force density has been constantly perpetuated in the past decades since EA was initially proposed. In this study, by composing terpolymer poly(vinylidene fluoride-trifluoroethylene-chlorotrifluoroethylene) [P(VDF-TrFE-CTFE)] and two-dimensional Ti3C2Tx nanosheets (MXene), nanocomposite films with high dielectric constant (δr' > 2300) and low loss tangent are achieved. The force representative index δr'Ebd2 (the relative dielectric constant times the square of breakdown electric field) is enhanced by 5.91 times due to the charge accumulation at matrix-filler interfaces. Superhigh shear stress (85.61 N cm-2) is generated, 408% higher than the previous maximum value. One of the EA clutches fabricated in this study is only 160 µm thin and 0.4 g heavy. Owing to the low current (<1 µA), the power consumption is <60 mW/cm2. It can hold a 2.5 kg weight by only 0.32 cm2 area and support an adult (45 kg) (Clinical Trial Registration number: 20210090). With this technology, a dexterous robotic hand is displayed to grasp and release a ball, showing extensive applications of this technique.

Clear phylogeographical structures shed light on the origin and dispersal of the aquatic boreal plant Hippuris vulgaris.

Aquatic plants are an important ecological group in the arctic flora; however, their evolutionary histories remain largely unknown. In order to deepen our understanding of the evolution of these plants, we explored the phylogeographical structure of an aquatic boreal plant Hippuris vulgaris in a broad geographical sampling from Eurasia and North America using the chloroplast intergenic spacer psbA-trnH and seven nuclear microsatellite loci. Two closely-related species H. lanceolata and H. tetraphylla were also included because of their taxonomic controversy. Both chloroplast DNA sequences and nuclear microsatellite data revealed three genetic lineages with distinct distribution ranges. Incongruence between nuclear and chloroplast DNA lineages occurred in 14 samples from Russian Far East and Europe caused by inter-lineage hybridization. No private haplotypes or independent genetic clusters were evident in H. lanceolata or H. tetraphylla, suggesting that these two species should be considered conspecific ecotypes of H. vulgaris. Analysis using Approximate Bayesian Computation-Random Forest approach suggests that Hippuris vulgaris originated in China, followed by dispersal into Russia plus Northeast China, then successively westwards into Europe and North America, and finally into the Russian Far East from both North America and Russia plus Northeast China. This study is the first to elucidate the historical dispersal processes of a circumarctic aquatic plant across the entirety of its range.

A reappraisal of the phylogeny and historical biogeography of Sparganium (Typhaceae) using complete chloroplast genomes.

BACKGROUND: Sparganium (Typhaceae) is a widespread temperate genus of ecologically important aquatic plants. Previous reconstructions of the phylogenetic relationships among Sparganium species are incompletely resolved partly because they were based on molecular markers comprising < 7,000 bp. Here, we sequenced and assembled the complete chloroplast genomes from 19 Sparganium samples representing 15 putative species and three putative subspecies in order to explore chloroplast genome evolution in this genus, clarify taxonomic lineages, estimate the divergence times of Sparganium species, and reconstruct aspects of the biogeographic history of the genus. RESULTS: The 19 chloroplast genomes shared a conserved genome structure, gene content, and gene order. Our phylogenomic analysis presented a well-resolved phylogeny with robust support for most clades. Non-monophyly was revealed in three species: S. erectum, S. eurycarpum, and S. stoloniferum. Divergence time estimates suggest that the two subgenera of Sparganium split from each other ca. 30.67 Ma in the middle Oligocene. The subgenus Xanthosparganium diversified in the late Oligocene and Miocene, while the subgenus Sparganium diversified in the late Pliocene and Pleistocene. Ancestral area reconstruction suggested that the two subgenera may have originated in East Eurasia and North America. CONCLUSION: The non-monophyletic nature of three putative species underscores the necessity of taxonomic revision for Sparganium: S. stoloniferum subsp. choui may be more appropriately identified as S. choui, and subspecies of S. erectum may be in fact distinct species. The estimated diversification times of the two subgenera correspond to their species and nucleotide diversities. The likely ancestral area for most of subgenus Xanthosparganium was East Eurasia and North America from where it dispersed into West Eurasia and Australia. Most of subgenus Sparganium likely originated in North America and then dispersed into Eurasia. Our study demonstrates some of the ways in which complete chloroplast genome sequences can provide new insights into the evolution, phylogeny, and biogeography of the genus Sparganium.