Co-Immobilization of ADH and GDH on Metal-Organic-Framework: An Effective Biocatalyst for Asymmetric Reduction of Ketones.

Chiral alcohols are not only important building blocks of various bioactive natural compounds and pharmaceuticals, but can serve as synthetic precursors for other valuable organic chemicals, thus the synthesis of these products is of great importance. Bio-catalysis represents one effective way to obtain these molecules, however, the weak stability and high cost of enzymes often hinder its broad application. In this work, we designed a biological nanoreactor by embedding alcohol dehydrogenase (ADH) and glucose dehydrogenase (GDH) in metal-organic-framework ZIF-8. The biocatalyst ADH&GDH@ZIF-8 could be applied to the asymmetric reduction of a series of ketones to give chiral alcohols in high yields (up to 99 %) and with excellent enantioselectivities (>99 %). In addition, the heterogeneous biocatalyst could be recycled and reused at least four times with slight activity decline. Moreover, E. coli containing ADH and GDH was immobilized by ZIF-8 to form biocatalyst E. coli@ZIF-8, which also exhibits good catalytic behaviours. Finally, the chiral alcohols are further converted to marketed drugs (R)-Fendiline, (S)-Rivastigmine and NPS R-568 respectively.

Pyrene-Based D-A Molecules as Efficient Heterogeneous Catalysts for Visible-Light-Induced Aerobic Organic Transformations.

In this work, an efficient visible light promoted aerobic dehydro-coupling of amines, oxidation of thioethers and hydroxylation of arylboronic acids under benign conditions by using pyrene-based donor-acceptor (D-A) conjugated organic molecules was described. Donor-acceptor structure influences their π-conjugation and band gap a lot, and thereby enhances their visible light absorption ability, single electron transfer and oxidative behaviors. Alkynyl units in PS-IV play a crucial role in the catalyst which could serve as electron transferring bridge to strengthen electron delocalization, thus facilitating the single electron transfer from photosensitizer to substrates, and making it an efficient ⋅O2 - generator. While PS-III without alkynyl units tends to produce 1 O2 . Therefore, these molecules can serve as efficient catalysts for different kinds of visible-light-induced aerobic organic reactions. More importantly, the simply structured molecule is insoluble and stable in various solvents, and thus could be recycled as heterogeneous catalyst for many rounds with slight catalytic activity degradation. Besides, large scale (1 mol) reaction of benzylamine coupling proceeded smoothly under the standard conditions.

Description of a Nonhuman Primate Model of Retinal Ischemia/Reperfusion Injury.

Purpose: To establish an inducible model of retinal ischemia/reperfusion injury (RI/RI) in nonhuman primates (NHPs) to improve our understanding of the disease conditions and evaluate treatment interventions in humans. Methods: We cannulated the right eye of rhesus macaques with a needle attached to a normal saline solution reservoir at up to 1.9 m above the eye level that resulted in high intraocular pressure of over 100 mm Hg for 90 minutes. Retinal morphology and function were monitored before and after RI/RI over two months by fundus photography, optical coherence tomography, electroretinography, and visual evoked potential. Terminal experiments involved immunostaining for retinal ganglion cell marker Brn3a, glial fibrillary acidic protein, and quantitative polymerase chain reaction to assess retinal inflammatory biomarkers. Results: We observed significant and progressive declines in retinal and retinal nerve fiber layer thickness in the affected eye after RI/RI. We noted significant reductions in amplitudes of electroretinography a-wave, b-wave, and visual evoked potential N2-P2, with minimal recovery at 63 days after injury. Terminal experiments conducted two months after injury revealed ∼73% loss of retinal ganglion cells and a fivefold increase in glial fibrillary acid protein immunofluorescence intensity compared to the uninjured eyes. We observed marked increases in tumor necrosis factor-alpha, interferon-gamma, interleukin-1beta, and inducible nitric oxide synthase in the injured retinas. Conclusions: The results demonstrated that the pathophysiology observed in the NHP model of RI/RI is comparable to that of human diseases and suggest that the NHP model may serve as a valuable tool for translating interventions into viable treatment approaches. Translational Relevance: The model serves as a useful platform to study potential interventions and treatments for RI/RI or blinding retinal diseases.

Effects of Tetrabasic Zinc Chloride on Growth Performance, Nutrient Digestibility and Fecal Microbial Community in Weaned Piglets.

The study was conducted to explore the effects of tetrabasic zinc chloride (TBZC), as an alternative to zinc oxide (ZnO), on growth performance, serum indexes, and fecal microbiota of weaned piglets. A total of 108 weaned piglets (average initial body weight of 7.84 ± 0.97 kg) were randomly allocated into one of three dietary treatments with six replicate pens and six piglets per pen. The dietary treatments included a control diet (CON, negative control), a ZnO diet (CON + 1,600 mg Zn/kg from ZnO, positive control), and a TBZC diet (CON + 1,000 mg Zn/kg from TBZC). The average daily gain of pigs in the TBZC group was greater (P < 0.05) than those in CON and ZnO groups during the whole period. Piglets fed the ZnO and TBZC diets showed lower (P < 0.05) diarrhea incidence than those fed the CON diet during d 1-14 and the whole period. Piglets fed the TBZC diet had higher (P < 0.05) digestibility of crude protein and gross energy than those fed the CON diet. Serum concentrations of IGF-I and GH, as well as ALP activity, were significantly elevated (P < 0.05) in the TBZC treatment group compared to the CON group on d 14. Piglets fed the ZnO diet had greater (P < 0.05) acetate and total short-chain fatty acids concentrations, while the TBZC diet had greater (P < 0.05) fecal acetate and propionate concentrations on d 28. Moreover, TBZC supplementation significantly increased (P < 0.05) microbial α-diversity compared with the CON group. The fecal microbiota of piglets in ZnO and TBZC treatment groups tended (P = 0.08) to have greater relative abundance of Prevotellaceae compared with the CON piglets. In conclusion, TBZC acted as a suitable alternative to ZnO to reduce zinc excretion, and improve growth performance of weaned piglets.

A new non-human primate model of desiccating stress-induced dry eye disease.

Dry eye disease (DED), a multifactorial ocular surface disease, is estimated to affect up to 34% of individuals over 50 years old. Although numerous animal models, including rodents and rabbits, have been developed to mimic the pathophysiologic mechanisms involved in dry eye, there is a lack of non-human primate (NHP) models, critical for translational drug studies. Here, we developed a novel desiccating stress-induced dry eye disease model using Rhesus macaque monkeys. The monkeys were housed in a controlled environment room for 21 to 36 days under humidity, temperature, and airflow regulation. Following desiccating stress, NHPs demonstrated clinical symptoms similar to those of humans, as shown by increased corneal fluorescein staining (CFS) and decreased tear-film breakup time (TFBUT). Moreover, corticosteroid treatment significantly reduced CFS scoring, restored TFBUT, and prevented upregulation of tear proinflammatory cytokines as observed in dry eye patients following steroid treatment. The close resemblance of clinical symptoms and treatment responses to those of human DED patients provides great translational value to the NHP model, which could serve as a clinically relevant animal model to study the efficacy of new potential treatments for DED.

Synthesis of bioactive fluoropyrrolidines via copper(i)-catalysed asymmetric 1,3-dipolar cycloaddition of azomethine ylides.

Chiral pyrrolidinyl units are important building blocks in biologically active natural products and drugs, and the development of efficient methods for the synthesis of diverse structured pyrrolidine derivatives is of great importance. Meanwhile, incorporating fluorine containing groups into small molecules often changes their activities to a great extent due to the special physicochemical properties of fluorine atoms. Herein, we report an efficient route to obtain enantioenriched 3,3-difluoro- and 3,3,4-trifluoropyrrolidinyl derivatives by Cu(i)-catalysed enantioselective 1,3-dipolar cycloaddition of azomethine ylides with less active 1,1-difluoro- and 1,1,2-trifluorostyrenes. A series of new fluorinated pyrrolidines have been prepared in high yields (up to 96%) and with excellent stereoselectivities (up to >20 : 1 dr and 97% ee), and these unique structural blocks could be readily introduced into some natural compounds and pharmaceuticals. Additionally, antifungal activity investigation against four common plant fungi showed that some products possess general and high biological activities; comparison with the low antifungal activities of corresponding nonfluorinated compounds revealed that the fluorine atoms at the pyrrolidinyl rings play a crucial role in the antifungal activity.

Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes.

Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.

The complete chloroplast genome of Polygonatum zanlanscianense (Pampanini, 1915) (Asparagaceae), an adulterants of Polygonati rhizoma.

Polygonatum zanlanscianense Pamp. is a plant species of the genus Polygonatum (Asparagaceae) distributed widely in China. The complete chloroplast genome of P. zanlanscianense was sequenced by Illumina sequencing technology. The plastome is 155,609 bp in length with a typical quadripartite structure, including one small single copy (SSC, 18,427 bp), one large copy (LSC, 84,438 bp), and two inverted repeat regions (IRs, 26,372 bp each). The cp genome encoded 132 genes, including 38 tRNA, 8 rRNA, and 86 protein-coding genes. The overall GC content is 37.7%. The ML phylogenetic analysis based on the cp genomes indicated that the genus Polygonatum is sister to the genus Heteropolygonatum within the tribe Polygonateae, P. zanlanscianense is sister to P. cirrhifolium within the genus Polygonatum. This study provides an important theoretical foundation for varieties identification, the phylogenetic relationship of P. zanlanscianense. Furthermore, this article takes a radical reform of Polygonati rhizoma.

Development of Primary Open Angle Glaucoma-Like Features in a Rhesus Macaque Colony From Southern China.

Purpose: To describe the ocular phenotype of spontaneous glaucoma in a non-human primate colony. Methods: In total, 722 Rhesus macaque monkeys aged 10 to 25 years underwent optical coherence tomography (OCT), fundus photography (FP), and intraocular pressure (IOP) measurements. Monkeys with baseline cup-to-disc ratio (CDR) <0.5 were used to establish baseline ocular features. A subset was followed longitudinally for three years and compared to glaucoma suspects on the basis of OCT/FP criteria. Results: The average IOP under ketamine sedation and average CDR for the entire colony was 13.0 ± 4.3 mm Hg and 0.38 ± 0.07, respectively. The mean baseline conscious IOP of glaucoma suspects (N = 18) versus controls (N = 108) was 16.2 ± 3.5 mm Hg and 13.9 ± 2.3 mm Hg, respectively (P = 0.001). All glaucoma suspects had unremarkable slit lamp examinations and open angles based on anterior segment OCT. Baseline global circumpapillary retinal nerve fiber layer (RNFL) thickness was 91.5 ± 11.0 µM versus 102.7 ± 8.5 µM in suspects and controls, respectively (P < 0.0001). All sectors on the baseline circumpapillary OCT showed a significant reduction in RNFL thickness versus controls (P ≤ 0.0022) except for the temporal sector (P ≥ 0.07). In three-year longitudinal analysis, neither CDR nor OCT parameters changed in controls (N = 40; P ≥ 0.16), whereas significant increase in CDR (P = 0.018) and nominally significant decreases in two OCT sectors (nasal, P = 0.023 and nasal inferior, P = 0.046) were noted in suspects. Conclusions: Members of a nonhuman primate colony exhibit important ophthalmic features of human primary open-angle glaucoma. Translational Relevance: Identification of a spontaneous model of glaucoma in nonhuman primates represents an unprecedented opportunity to elucidate the natural history, pathogenesis and effective therapeutic strategies for the disease.

Plastome phylogenomics of the East Asian endemic genus Dobinea.

Dobinea is a dioecious genus endemic to East Asia that consists of two extant species: Dobinea delavayi and Dobinea vulgaris. Although the genus is morphologically distinct, its phylogenetic position remains controversial. In this study, we investigated the phylogenetic relationships between Dobinea and related taxa by sequencing the whole plastome DNA sequences for both extant species of Dobinea and comparing them to published plastomes within Sapindales. The complete plastomes of D. vulgaris and D. delavayi were 160,683 and 160, 154 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 26,889 and 26,759 bp) divided by the large single-copy region (LSC, 87,962 and 87,555 bp) and small single-copy region (SSC, 18,943 and 19,081 bp), and identically encoded 113 unique genes (79 protein-coding genes, 30 tRNAs, and 4 rRNA genes). Plastid phylogenomic analyses showed that Dobinea was a well-supported monophyletic unit and sister to the clade including tribes Anacardieae and Rhoideae, which suggests that Dobinea is a member of Anacardiaceae. In addition, molecular dating inferred D. delavayi and D. vulgaris diverged approximately 10.76 Ma, suggesting the divergence between these two species may have been driven by the intensification of the Asian summer monsoon and the establishment of distinct monsoon regimes in East Asia.

Novel GLP-1 analog supaglutide improves glucose homeostasis in diabetic monkeys.

Glucagon-like peptide 1 (GLP-1) is an insulinotropic hormone and plays an important role in regulating glucose homeostasis. GLP-1 has a short half-life (t1/2 < 2 min) due to degrading enzyme dipeptidyl peptidase-IV and rapid kidney clearance, which limits its clinical application as a therapeutic reagent. We demonstrated recently that supaglutide, a novel GLP-1 mimetic generated by recombinant fusion protein techniques, exerted hypoglycemic and ß-cell trophic effects in type 2 diabetes db/db mice. In the present study, we examined supaglutide's therapeutic efficacy and pharmacokinetics in diabetic rhesus monkeys. We found that a single subcutaneous injection of supaglutide of tested doses transiently and significantly reduced blood glucose levels in a dose-dependent fashion in the diabetic monkeys. During a 4-week intervention period, treatment of supaglutide of weekly dosing dose-dependently decreased fasting and random blood glucose levels. This was associated with significantly declined plasma fructosamine levels. The repeated administration of supaglutide remarkably also decreased body weight in a dose-dependent fashion accompanied by decreased food intake. Intravenous glucose tolerance test results showed that supaglutide improved glucose tolerance. The intervention also showed enhanced glucose-stimulated insulin secretion and improved lipid profile in diabetic rhesus monkeys. These results reveal that supaglutide exerts beneficial effects in regulating blood glucose and lipid homeostasis in diabetic rhesus monkeys.

Ultra-Barcoding Discovers a Cryptic Species in Paris yunnanensis (Melanthiaceae), a Medicinally Important Plant.

Ultra-barcoding is a technique using whole plastomes and nuclear ribosomal DNA (nrDNA) sequences for plant species identification. Paris yunnanensis is a medicinal plant of great economic importance for the pharmaceutical industry. However, the alpha taxonomy of P. yunnanensis is still uncertain, hindering effective conservation and management of the germplasm. To resolve long-standing taxonomic disputes regarding this species, we newly generated the complete plastomes and nrDNA sequences from 22 P. yunnanensis accessions. Ultra-barcoding analyses suggest that P. yunnanensis as currently circumscribed is made up of two distinct genetic lineages, corresponding to the two phenotypes ("typical" and "high stem" form) identified early in our study. With distinct morphologies and distribution, the "high stem" form should be recognized as a previously unrecognized species; here it is described as a new species, P. liiana sp. nov. Moreover, the ultra-barcoding data do not support treatment of P. yunnanensis as a conspecific variety under Paris polyphylla. Our study represents a guiding practical application of ultra-barcoding for discovery of cryptic species in taxonomically challenging plant taxa. The findings highlight the great potential of ultra-barcoding as an effective tool for resolving perplexing problems in plant taxonomy.

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae).

BACKGROUND: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus. RESULTS: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary. CONCLUSIONS: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae).

BACKGROUND: Robust phylogenies for species with giant genomes and closely related taxa can build evolutionary frameworks for investigating the origin and evolution of these genomic gigantisms. Paris japonica (Melanthiaceae) has the largest genome that has been confirmed in eukaryotes to date; however, its phylogenetic position remains unresolved. As a result, the evolutionary history of the genomic gigantisms in P. japonica remains poorly understood. RESULTS: We used next-generation sequencing to generate complete plastomes of P. japonica, P. verticillata, Trillium govanianum, Ypsilandra thibetica and Y. yunnanensis. Together with published plastomes, the infra-familial relationships in Melanthiaceae and infra-generic phylogeny in Paris were investigated, and their divergence times were calculated. The results indicated that the expansion of the ancestral genome of extant Paris and Trillium occurred approximately from 59.16 Mya to 38.21 Mya. The sister relationship between P. japonica and the section Euthyra was recovered, and they diverged around the transition of the Oligocene/Miocene (20 Mya), when the Japan Islands were separated from the continent of Asia. CONCLUSIONS: The genome size expansion in the most recent common ancestor for Paris and Trillium was most possibly a gradual process that lasted for approximately 20 million years. The divergence of P. japonica (section Kinugasa) and other taxa with thick rhizome may have been triggered by the isolation of the Japan Islands from the continent of Asia. This long-term separation, since the Oligocene/Miocene boundary, would have played an important role in the formation and evolution of the genomic gigantism in P. japonica. Moreover, our results support the taxonomic treatment of Paris as a genus rather than dividing it into three genera, but do not support the recognition of T. govanianum as the separate genus Trillidium.

Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae).

Complete plastid genome (plastome) sequences and nuclear ribosomal DNA (nrDNA) regions have been proposed as candidates for the next generation of DNA barcodes for plant species discrimination. However, the efficacy of this approach still lacks comprehensive evaluation. We carried out a case study in the economically important but phylogenetically and taxonomically difficult genus Panax (Araliaceae). We generated a large data set of plastomes and nrDNA sequences from multiple accessions per species. Our data improved the phylogenetic resolution and levels of species discrimination in Panax, compared to any previous studies using standard DNA barcodes. This provides new insights into the speciation, lineage diversification and biogeography of the genus. However, both plastome and nrDNA failed to completely resolve the phylogenetic relationships in the Panax bipinnatifidus species complex, and only half of the species within it were recovered as monophyletic units. The results suggest that complete plastome and ribosomal DNA sequences can substantially increase species discriminatory power in plants, but they are not powerful enough to fully resolve phylogenetic relationships and discriminate all species, particularly in evolutionarily young and complex plant groups. To gain further resolving power for closely related species, the addition of substantial numbers of nuclear markers is likely to be required.

Transcriptome analyses of Paris polyphylla var. chinensis, Ypsilandra thibetica, and Polygonatum kingianum characterize their steroidal saponin biosynthesis pathway.

Steroidal saponins, one of the most diverse groups of plant-derived natural products, elicit biological and pharmacological activities; however, the genes involved in their biosynthesis and the corresponding biosynthetic pathway in monocotyledon plants remain unclear. This study aimed to identify genes involved in the biosynthesis of steroidal saponins by performing a comparative analysis among transcriptomes of Paris polyphylla var. chinensis (PPC), Ypsilandra thibetica (YT), and Polygonatum kingianum (PK). De novo transcriptome assemblies generated 57,537, 140,420, and 151,773 unigenes from PPC, YT, and PK, respectively, of which 56.54, 47.81, and 44.30% were successfully annotated, respectively. Among the transcriptomes for PPC, YT, and PK, we identified 194, 169, and 131; 17, 14, and 26; and, 80, 122, and 113 unigenes corresponding to terpenoid backbone biosynthesis; sesquiterpenoid and triterpenoid biosynthesis; and, steroid biosynthesis pathways, respectively. These genes are putatively involved in the biosynthesis of cholesterol that is the primary precursor of steroidal saponins. Phylogenetic analyses indicated that lanosterol synthase may be exclusive to dicotyledon plant species, and the cytochrome P450 unigenes were closely related to clusters CYP90B1 and CYP734A1, which are UDP-glycosyltransferases unigenes homologous with the UGT73 family. Thus, unigenes of ß-glucosidase may be candidate genes for catalysis of later period modifications of the steroidal saponin skeleton. Our data provide evidence to support the hypothesis that monocotyledons biosynthesize steroidal saponins from cholesterol via the cycloartenol pathway.

Characterization of the whole plastome of Dipentodon Sinicus (Dipentodontaceae).

In this study, we sequenced and assembled the whole plastome of Dipentodon sinicus. The plastome was 158,020 bp in length and consisted of a pair of inverted repeat regions (IRs, 26,551 bp), a large single-copy region (LSC, 86,624 bp) and a small single-copy region (SSC, 18,294 bp). It encoded 114 unique genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes). Phylogenetic analysis showed that Dipentodon sinicus was sister to Tapiscia sinensis.

The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae).

Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.

Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis.

The Arcto-Tertiary relict genera, Camptotheca, Davidia, and Nyssa represent deep lineages in the asterid order Cornales. Recent phylogenetic studies suggested that these genera should be placed in a newly circumscribed family, Nyssaceae. However, because these analyses were based upon a few genes, it is prudent and necessary to examine further evidence before adopting this taxonomic treatment. In this study, we determined the complete chloroplast (cp) genomes of Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Their cp genomes ranged from 156,672 to 158,409 bp, which included 115 genes, and their genome features were highly similar to those of other species within the order Cornales. The phylogenetic relationships among the genera Camptotheca, Davidia, Nyssa, and 23 related taxa in the asterids were analyzed based on 73 protein-coding genes from the cp genomes. All of the previously recognized major clades (namely Cornales, Ericales, Campanulids, and Lamiids) in the asterids, as well as their relationships, were recovered with robust support. A clade including the genera Davidia, Nyssa, Camptotheca, and Diplopanax, was resolved as a well-supported monophyletic group, which was fully separated from the family Cornaceae by the family Hydrangeaceae. Our results provide novel evidence to support the acceptance of the family Nyssaceae outlined by the updated Angiosperm Phylogeny Group.

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae).

The genus Paris in the broad concept is an economically important group in the monocotyledonous family Melanthiaceae (tribe Parideae). The phylogeny of Paris was controversial in previous morphology-based classification and molecular phylogeny. Here, the complete cp genomes of eleven Paris taxa were sequenced, to better understand the evolutionary relationships among these plants and the mutation patterns in their chloroplast (cp) genomes. Comparative analyses indicated that the overall cp genome structure among the Paris taxa is quite similar. The triplication of trnI-CAU was found only in the cp genomes of P. quadrifolia and P. verticillata. Phylogenetic analyses based on the complete cp genomes did not resolve Paris as a monophyletic group, instead providing evidence supporting division of the twelve taxa into two segregate genera: Paris sensu strict and Daiswa. The sister relationship between Daiswa and Trillium was well supported. We recovered two fully supported lineages with divergent distribution in Daiswa; however, none of the previously recognized sections in Daiswa was resolved as monophyletic using plastome data, suggesting that the infrageneric relationships and biogeography of Daiswa species require further investigation. Ten highly divergent DNA regions, suitable for species identification, were detected among the 12 cp genomes. This study is the first successful attempt to provide well-supported evolutionary relationships in Paris based on phylogenomic analyses. The findings highlight the potential of the whole cp genomes for improving resolution in phylogeny as well as species identification in phylogenetically and taxonomically difficult plant genera.