Identification of clinically relevant subsets CD39+PD-1+CD8+ T cells and CD39+ regulatory T cells in intrahepatic cholangiocarcinoma using single-cell CyTOF.

Intrahepatic cholangiocarcinoma (iCCA) is an aggressive liver malignancy with limited treatment options and a dismal prognosis. The tumor immune microenvironment (TIME) is crucial for iCCA progression, yet its comprehensive characterization remains incomplete. This study utilized mass cytometry by time of flight (CyTOF) to comprehensively analyze immune cell populations in fresh iCCA tumor samples and adjacent peritumor liver tissues. Notably, NK cell percentages significantly decreased in iCCA lesions compared to peritumor liver tissues. Conversely, an enrichment of immunosuppressive CD39+Foxp3+CD4+ regulatory T cells (CD39+T-regs) and exhausted-like CD8+T cells (with pronounced CD39 and PD-1 expression) within TIME was identified and confirmed by multiplex immunofluorescence staining in an independent patient cohort (n = 140). Crucially, tumor-infiltrating CD39+T-regs and CD39+PD-1+CD8+T cells emerged as independent prognostic indicators associated with an unfavorable prognosis in iCCA. These findings unveil the intricate immune landscape within iCCA, offering valuable insights for disease management and novel cancer immunotherapies.

Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae).

Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigate phylogenetic conflict analyses within and between plastid and mitochondrial genomes using Potentilla as a case study. We generated three plastid datasets (coding, noncoding, and all-region) and one mitochondrial dataset (coding regions) to infer phylogenies based on concatenated and multispecies coalescent (MSC) methods. Conflict analyses were then performed using PhyParts and Quartet Sampling (QS). Both plastid and mitochondrial genomes divided the Potentilla into eight highly supported clades, two of which were newly identified in this study. While most organellar loci were uninformative for the majority of nodes (bootstrap value < 70%), PhyParts and QS detected conflicting signals within the two organellar genomes. Regression analyses revealed that conflict signals mainly occurred among shorter loci, whereas longer loci tended to be more concordant with the species tree. In addition, two significant disagreements between the two organellar genomes were detected, likely attributed to hybridization and/or incomplete lineage sorting. Our results demonstrate that mitochondrial genes can fully resolve the phylogenetic relationships among eight major clades of Potentilla and are not always linked with plastome in evolutionary history. Stochastic inferences appear to be the primary source of observed conflicts among the gene trees. We recommend that the loci with short sequence length or containing limited informative sites should be used cautiously in MSC analysis, and suggest the joint application of concatenated and MSC methods for phylogenetic inference using organellar genomes.

Gas7 attenuates hepatocellular carcinoma progression and chemoresistance through the PI3K/Akt signaling pathway.

Growth arrest-specific gene 7 (Gas7) was involved in various cellular functions, although its specific roles and molecular mechanisms in hepatocellular carcinoma (HCC) remained unclear. So the current study was to investigate the role of Gas7 in HCC. Our findings revealed that Gas7 was downregulated in various HCC cell lines and low Gas7 expression was associated with decreased overall survival in patients with HCC. Additionally, our functional assays showed that Gas7 inhibited cell proliferation and migration, induced cell cycle arrest, apoptosis, and autophagy, and enhanced oxaliplatin sensitivity by inhibiting the PI3K/Akt signaling pathway. We also observed that transcription factorSp1 was responsible for inhibiting Gas7. These findings provide insights into the role and elucidated a potential mechanism of Gas7 in HCC progression and metastasis. It was also observed that the Sp1/Gas7/PI3K/Akt axis was critical for malignant phenotype and oxaliplatin sensitivity in HCC. Therefore, Gas7 can be considered as a prognostic predictor and therapeutic target for HCC.

Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era.

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. With a well-inferred phylogenetic backbone, we propose an updated generic delimitation of Stranvaesia and introduce a new genus, Weniomeles. This new genus is distinguished by its purple-black fruits, thorns trunk and/or branches, and a distinctive fruit core anatomy characterized by multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Through this study, we highlight a broadly-applicable workflow that underscores the significance of reticulate evolution analyses in shaping taxonomic revisions from phylogenomic data.

Malus includes Docynia (Maleae, Rosaceae): evidence from phylogenomics and morphology.

Docynia has been treated as a separate genus or merged into Cydonia or Docyniopsis. Our phylogenomic evidence from 797 single-copy nuclear genes and plastomes confirmed the sister relationship between Docynia and Docyniopsis. By integrating the phylogenomic and morphological evidence, we propose to accept a broad generic concept of Malus and merge Docynia into Malus. Three new combinations are also made here: Malusdelavayi (Franch.) B.B.Liu, M.indica (Wall.) B.B.Liu and M.longiunguis (Q.Luo & J.L.Liu) B.B.Liu.

Abnormal Systemic and Ocular Responses to the Valsalva Manoeuvre in Primary Open-Angle Glaucoma: A Case for Autonomic Failure?

OBJECTIVE: This study aimed to examine the association of primary open-angle glaucoma (POAG) with autonomic dysfunction by assessing the differences in systemic and ocular responses to an autonomic provocation test, the Valsalva manoeuvre (VM), between POAG patients and normal subjects. METHODS: Forty POAG and forty control subjects were subjected to the VM. Systemic and ocular parameters were measured at baseline, phase 2, and phase 4 of the VM (VM2 and VM4), where VM2 and VM4 are sympathetic and parasympathetic nervous activation states, respectively. Heart rate variability was used to assess the autonomic nervous activity, among which the high-frequency component (HF) and the low-frequency (LF)/HF ratio were used as indices of parasympathetic and sympathetic activation, respectively. RESULTS: POAG patients demonstrated higher sympathetic activation (LF/HF ratio median: 2.17 vs. 1.53, P=0.000) than controls at baseline and exhibited attenuated sympathetic and parasympathetic responses (a smaller change in LF/HF and HF values) during the VM than controls. During VM, the intraocular pressure (IOP), mean blood pressure (MAP), mean ocular perfusion pressure (MOPP), and the Schlemm's canal area (SCAR) increased from baseline to VM2 and then decreased from VM2 to VM4 in both the POAG and control groups (all P<0.05). However, when we compared the changes above, the fluctuations in IOP, MAP, and MOPP were more pronounced in POAG than in controls (all P<0.05), while the changes in amplitudes of SCAR were smaller in POAG (P<0.05). Furthermore, from VM2 to VM4, the choroid thickness (ChT) in the POAG group was significantly decreased, while it was unchanged in normal subjects (P=0.258). A regression analysis showed a significant correlation of the baseline LF/HF with IOP change values (ΔIOP) from baseline to VM2 in POAG (R2=0.147, P=0.014). CONCLUSION: Patients with POAG showed more pronounced fluctuations in IOP, MAP, MOPP and ChT during the VM than controls. These reactions could be associated with autonomic dysfunction in POAG.

Evaluating the diagnostic value of using metagenomic next-generation sequencing on bronchoalveolar lavage fluid and tissue in infectious pathogens located in the peripheral lung field.

BACKGROUND: Metagenomic next-generation sequencing (mNGS) exerts a vital part in accurately diagnosing pulmonary infection. However, the diagnostic value of different samples obtained by virtual bronchoscopic navigation (VBN) combined with mNGS for pathogen detection in infections located in the peripheral lung field (PLF) is still unclear. METHODS: Patients infected from July 2018 to February of the following year were carefully analyzed and divided into two parts, namely, non-infectious disease group and the infectious disease group. Then bronchial expansion tests were performed for each subject, collected liquid specimens and tissue standards, and conducted regular mNGS and microbiological detection and analysis. The value of mNGS and culture in pathogen detection was compared, at the same time, the performance of tissue mNGS and bronchoalveolar lavage fluid (BALF) mNGS in the diagnosis process was compared. When discrete variables were processed, Pearson χ2 and Fisher's exact test could be used to perform categorical variables analysis. Continuous variables were analyzed and compared by Mann-Whitney U test. RESULTS: After mNGS diagnosis, Acinetobacter baumannii, Pseudomonas aeruginosa and Rothia mucilaginosa were the bacterial species showing the highest abundances. In addition, mNGS achieved the sensitivities in the detection of pathogens in tissues and BALF of 72.9% and 81.4%, respectively, and it is higher than conventional culture. Bacterial diagnostic sensitivity was significantly different between BALF and tissue using mNGS (95.0% vs. 62.5%, P=0.03). The sensitivity and specificity of BALF in detecting fungal infections were not significantly different from those of mNGS. A consistency test showed that these two methods had some degree of consistency (k=0.673, P=0.000). CONCLUSIONS: This study showed that the mNGS in BALF samples and the mNGS in tissue samples which could be used to test for pathogens in the lungs. The sensitivity will increase when mNGS is combined with culture. Also, mNGS of BALF and tissues had some degree of consistency to detect fungal infections, whereas mNGS of BALF had better sensitivity to detect bacterial infection than mNGS of tissues.

A Correlational Study on Cardiopulmonary Endurance in Male Patients with New-Onset Type 2 Diabetes.

Background: Cardiopulmonary exercise tests (CPETs) are widely used non-invasive and reliable functional evaluation methods. This study investigated the correlation between cardiopulmonary endurance indices and plasma glucose levels and abdominal visceral fat in males with new-onset type 2 diabetes. Methods: A total of 136 male individuals, who had been treated in the First Hospital of Qinhuangdao City, were selected to form a new-onset type 2 diabetes group (66 cases) and a control group (70 cases); individuals were divided into three groups (Q1, Q2, and Q3) from low to high according to their anaerobic threshold (AT) oxygen uptake (VO2), AT VO2/kg (VO2 per kg of body weight), peak VO2, peak VO2/kg, AT heart rate (HR), peak HR, and HR recovery after 1 minute. A cardiopulmonary exercise test was used to determine the VO2 of each group of subjects for VO2 max and AT VO2/kg, HR, and HR recovery after 1 minute. The differences in fat areas and plasma glucose levels were compared under different cardiorespiratory endurance indicators. Results: Compared with the control group, the abdominal visceral fat (AVF) area, fasting plasma glucose (FPG), and postprandial plasma glucose (PPG) levels increased in the new-onset type 2 diabetes group. Concurrently, AT VO2, AT VO2/kg, peak VO2, peak VO2/kg, AT HR, peak HR, and 1-minute HR recovery all decreased, and the difference between the groups was statistically significant (P<0.05). The higher the AT VO2 and peak VO2 values, the lower the PPG level (P<0.05) and the smaller the area of abdominal visceral fat (P<0.05). The AT VO2/kg and peak VO2/kg values were negatively correlated with the abdominal visceral fat area, while other indicators had no obvious relationship with either plasma glucose levels or the area of fat. Conclusion: The levels of blood glucose and visceral fat are correlated with cardiopulmonary function. With the increase in blood glucose levels and visceral fat, the indices of cardiopulmonary function gradually decrease. The correlation between different cardiopulmonary function indices and blood glucose levels and visceral fat was different.

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere.

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

Phylogenomic and morphological evidence reveal a new species of spider lily, Lycorislongifolia (Amaryllidaceae) from China.

Lycorislongifolia, a new species from China, was described and illustrated here. Our phylogenomic evidence based on whole plastomes strongly supported the separate phylogenetic position of this new species, and morphologically it could also be distinguished by its long leaves with a distinct purplish-red midrib on the abaxial surface.

A comprehensive checklist of the deciduous photinia genus Pourthiaea (Maleae, Rosaceae), with emphasis on their validity and typification.

Due to the complicated evolutionary history in Pourthiaea, ninety-seven taxa have been described since 1784, and ninety-one of them are validly published taxa, five are naked names, and one is an invalid name. After a comprehensive and critical evaluation, 213 names have been published, including new combinations, new status, and new names; this may be due to the controversial taxonomic position of Pourthiaea in the apple tribe, Maleae. We herewith provide a taxonomic checklist of Pourthiaea for further taxonomic and evolutionary studies. We also lectotypify two taxa: Photiniaamphidoxavar.stylosa and P.glabravar.fokienensis.

Correlation between Insulin Resistance and Cardiopulmonary Function during Physical Exams for Male Patients.

Objective: In this study, we investigated the correlation between insulin resistance (IR) and cardiopulmonary function during physical exams for male patients. Methods: We selected 124 healthy male participants in the physical examination center of our hospital. They were divided into 3 groups according to the homeostasis model assessment of insulin resistance values. The oxygen uptake, peak oxygen uptake (VO2/kg), heart rate, systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured by a cardiopulmonary exercise function tester. We analyzed the correlation between the index of IR and cardiopulmonary function. Results: There were statistically significant differences in body mass index, waist circumference, fasting insulin level, anaerobic threshold SBP, maximum VO2/kg and maximum SBP among the 3 groups (p<.05). However, no significant difference was found in SBP, DBP, total cholesterol, low-density lipoprotein cholesterol and fasting blood glucose levels (p>.05). The anaerobic threshold SBP, maximum VO2/kg and maximum SBP were all negatively correlated with the IR index. Conclusion: Our results indicate that IR is associated with cardiopulmonary function and that there are different correlations between the various cardiopulmonary function indexes and IR.

On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology.

The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

Exosomal miR-3682-3p Suppresses Angiogenesis by Targeting ANGPT1 via the RAS-MEK1/2-ERK1/2 Pathway in Hepatocellular Carcinoma.

BACKGROUND: Angiogenesis is a crucial process in tumorigenesis and development. The role of exosomes derived from hepatocellular carcinoma (HCC) cells in angiogenesis has not been clearly elucidated. METHODS AND RESULTS: Exosomes were isolated from HCC cell lines (HCCLM3, MHCC97L, and PLC/RFP/5) by ultracentrifugation and identified by nano transmission electron microscopy (TEM), NanoSight analysis and western blotting, respectively. In vitro and in vivo analyses showed that exosomes isolated from highly metastatic HCC cells enhanced the migration, invasion and tube formation of human umbilical vein endothelial cells (HUVECs) compared to exosomes derived from poorly metastatic HCC cells. In addition, microarray analysis of HCC-Exos was conducted to identify potential functional molecules, and miR-3682-3p expression was found to be significantly downregulated in exosomes isolated from highly metastatic HCC cells. By in vitro gain-of-function experiments, we found that HCC cells secreted exosomal miR-3682-3p, which negatively regulates angiopoietin-1 (ANGPT1), and this led to inhibition of RAS-MEK1/2-ERK1/2 signaling in endothelial cells and eventually impaired angiogenesis. CONCLUSION: Our study elucidates that exosomal miR-3682-3p attenuates angiogenesis by targeting ANGPT1 through RAS-MEK1/2-ERK1/2 signaling and provides novel potential targets for liver cancer therapy.

A useful intraoperative technique for transiliac-transsacral screws: a point-to-point coaxial guide apparatus.

BACKGROUND: The transiliac-transsacral screw placement is a clinical challenge for surgeons. This study explored a point-to-point coaxial guide apparatus assisting the transiliac-transsacral screw insertion and aimed to investigate the feasibility and accuracy of the guide apparatus in the treatment of posterior ring unstable pelvic fracture compared with a free-hand technique. METHODS: A retrospective study was performed to evaluate patients treated with transiliac-transsacral screws assisted by the point-to-point coaxial guide apparatus or free-hand technique. The intraoperative data of operative time and radiation exposure times were recorded. Postoperative radiographs and CT scans were performed to scrutinize the accuracy of screws position. The quality of the postoperative fracture reduction was assessed according to Matta radiology criteria. The pelvic function was assessed according to the Majeed scoring criteria at 6 months postoperatively. RESULTS: From July 2017 to December 2019, a total of 38 patients were included in this study, 20 from the point-to-point guide apparatus group and 18 from the free-hand group. There were no significant differences between the two groups in gender, age, injury causes, pelvic fracture type, screws level, and follow-up time (P > 0.05). The average operative time of the guide apparatus group for each screw was significantly less than that in the free-hand group (25.8 ± 4.7 min vs 40.5 ± 5.1, P < 0.001). The radiation exposure times were significantly lower in the guide apparatus group than that in the free-hand group (24.4 ± 6.0 vs 51.6 ± 8.4, P < 0.001). The intraosseous and juxtacortical rate of screw placement (100%) higher than in the free-hand group (94.4%). CONCLUSION: The point-to-point coaxial guide apparatus is feasible for assisting the transiliac-transsacral screw in the treatment of posterior unstable pelvic fractures. It has the advantages of simple operation, reasonable design and no need for expensive equipment, and provides an additional surgical strategy for the insertion of the transiliac-transsacral screw.

Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae-Gillenieae Clade.

Plant biologists have debated the evolutionary origin of the apple tribe (Maleae; Rosaceae) for over a century. The "wide-hybridization hypothesis" posits that the pome-bearing members of Maleae (base chromosome number x = 17) resulted from a hybridization and/or allopolyploid event between progenitors of other tribes in the subfamily Amygdaloideae with x = 8 and x = 9, respectively. An alternative "spiraeoid hypothesis" proposed that the x = 17 of Maleae arose via the genome doubling of x = 9 ancestors to x = 18, and subsequent aneuploidy resulting in x = 17. We use publicly available genomic data-448 nuclear genes and complete plastomes-from 27 species representing all major tribes within the Amygdaloideae to investigate evolutionary relationships within the subfamily containing the apple tribe. Specifically, we use network analyses and multi-labeled trees to test the competing wide-hybridization and spiraeoid hypotheses. Hybridization occurred between an ancestor of the tribe Spiraeeae (x = 9) and an ancestor of the clade Sorbarieae (x = 9) + Exochordeae (x = 8) + Kerrieae (x = 9), giving rise to the clade Gillenieae (x = 9) + Maleae (x = 17). The ancestor of the Maleae + Gillenieae arose via hybridization between distantly related tribes in the Amygdaloideae (i.e., supporting the wide hybridization hypothesis). However, some evidence supports an aspect of the spiraeoid hypothesis-the ancestors involved in the hybridization event were likely both x = 9, so genome doubling was followed by aneuploidy to result in x = 17 observed in Maleae. By synthesizing existing genomic data with novel analyses, we resolve the nearly century-old mystery regarding the origin of the apple tribe. Our results also indicate that nuclear gene tree-species tree conflict and/or cytonuclear conflict are pervasive at several other nodes in subfamily Amygdaloideae of Rosaceae.

The complete chloroplast genome sequence of Magnolia mexicana DC. (Magnoliaceae) from Central America.

The chloroplast genome of the Magnolia species from Central America has never been reported. With its local use for food flavoring, medicine, and wood, M. mexicana has been of good economic importance. In the present study, the complete chloroplast genome of M. mexicana was assembled via the genome skimming data. As a typical quadripartite structure, the plastome of M. mexicana with 159,906 bp in length includes two inverted repeats (26,554 bp) separated by a small single copy region (18,761 bp) as well as a large single copy region (88,037 bp). This chloroplast genome consists of 131 different genes, including 86 protein coding genes (CDS), eight rRNA genes, and 37 tRNA genes. The maximum likelihood phylogenetic analysis showed that M. mexicana from Central America was closely related to an evergreen species, M. odoratissima from East Asia.

Modeling analysis of COVID-19 based on morbidity data in Anhui, China.

Since the first case of coronavirus disease (COVID-19) in Wuhan Hubei, China, was reported in December 2019, COVID-19 has spread rapidly across the country and overseas. The first case in Anhui, a province of China, was reported on January 10, 2020. In the field of infectious diseases, modeling, evaluating and predicting the rate of disease transmission is very important for epidemic prevention and control. Different intervention measures have been implemented starting from different time nodes in the country and Anhui, the epidemic may be divided into three stages for January 10 to February 11, 2020, namely. We adopted interrupted time series method and develop an SEI/QR model to analyse the data. Our results displayed that the lockdown of Wuhan implemented on January 23, 2020 reduced the contact rate of epidemic transmission in Anhui province by 48.37%, and centralized quarantine management policy for close contacts in Anhui reduced the contact rate by an additional 36.97%. At the same time, the estimated basic reproduction number gradually decreased from the initial 2.9764 to 0.8667 and then to 0.5725. We conclude that the Wuhan lockdown and the centralized quarantine management policy in Anhui played a crucial role in the timely and effective mitigation of the epidemic in Anhui. One merit of this work is the adoption of morbidity data which may reflect the epidemic more accurately and promptly. Our estimated parameters are largely in line with the World Health Organization estimates and previous studies.

A synopsis of the expanded Rhaphiolepis (Maleae, Rosaceae).

As part of the integrative systematic studies on the tribe Maleae, a synopsis of the expanded Rhaphiolepis is presented, recognizing 45 species. Three new forms were validated: R. bengalensis f. contracta B.B.Liu & J.Wen, R. bengalensis f. intermedia B.B.Liu & J.Wen, and R. bengalensis f. multinervata B.B.Liu & J.Wen, and four new combinations are made here: R. bengalensis f. angustifolia (Cardot) B.B.Liu & J.Wen, R. bengalensis f. gigantea (J.E.Vidal) B.B.Liu & J.Wen, R. laoshanica (W.B.Liao, Q.Fan & S.F.Chen) B.B.Liu & J.Wen, and R. latifolia (Hook.f.) B.B.Liu & J.Wen. Furthermore, one new name, Rhaphiolepis yui B.B.Liu & J.Wen is proposed here, and three taxa were reduced as new synonyms. We also provide lectotypification for 13 names: Crataegus bibas, Eriobotrya philippinensis, Mespilus spiralis, Opa integerrima, Photinia luzonensis, Rhaphiolepis brevipetiolata, R. ferruginea var. serrata, R. fragrans, R. gracilis, R. hainanensis, R. kerrii, R. indica subsp. umbellata var. liukiuensis, and R. parvibracteolata.

Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape.

Despite the commercial importance of the Concord grape, its origin has remained unresolved for over 150 years without a comprehensive phylogenetic analysis. In this study we aimed to reconstruct the evolutionary history of the Concord grape using sequence data from four nuclear markers (AT103, GAI1, PHYA, and SQD1), six plastid markers (matK, psbA-trnH, petN-trnC, ycf1, trnL-F, and trnS-G), and the plastid genome. We sampled extensively the Vitis species native to northeastern North America as well as representative species from Europe and Asia, including the commercially important Vitis vinifera (wine grape), a native European species with hermaphroditic flowers, and its wild progenitor, V. vinifera subsp. sylvestris. We also sequenced the plastid genome of one accession of the Concord grape and compared the plastid genome data to the recently published data set of Vitis plastomes. Phylogenetic analyses of the plastid and nuclear data using maximum likelihood and Bayesian inference support the hybrid origin of the Concord grape. The results clearly pinpoint the wine grape, V. vinifera, as the maternal donor and the fox grape, Vitis labrusca, which is common in northeastern North America, as the paternal donor. Moreover, we infer that the breeding history of the Concord grape must have involved the backcrossing of the F1 hybrid with the paternal parent V. labrusca. This backcrossing also explains the higher morphological similarity of the Concord grape to V. labrusca than to V. vinifera. This study provides concrete genetic evidence for the hybrid origin of a widespread Vitis cultivar and is, therefore, promising for similar future studies focused on resolving ambiguous origins of major crops or to create successful hybrid fruit crops.