Integration of large and diverse angiosperm DNA fragments into Asian Gnetum mitogenomes.

BACKGROUND: Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus. RESULTS: We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots-mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT. CONCLUSIONS: Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.

The mitochondrial energy metabolism pathway-related signature predicts prognosis and indicates immune microenvironment infiltration in osteosarcoma.

BACKGROUND: Abnormalities in the mitochondrial energy metabolism pathways are closely related to the occurrence and development of many cancers. Furthermore, abnormal genes in mitochondrial energy metabolism pathways may be novel targets and biomarkers for the diagnosis and treatment of osteosarcoma. In this study, we aimed to establish a mitochondrial energy metabolism-related gene signature for osteosarcoma prognosis. METHODS: We first obtained differentially expressed genes based on the metastatic status of 84 patients with osteosarcoma from the TARGET database. After Venn analysis of differentially expressed genes and mitochondrial energy metabolism pathway-related genes (MMRGs), 2 key genes were obtained using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analysis. Next, we used these 2 genes to establish a prognostic signature. Subsequent analyses elucidated the correlation between these 2 key genes with clinical features and 28 types of immune cells. Pathway changes in osteosarcoma pathogenesis under different metastatic states were clarified using gene set enrichment analysis (GSEA) of differentially expressed genes. RESULTS: A gene signature composed of 2 key prognosis-related genes (KCNJ5 and PFKFB2) was identified. A risk score was calculated based on the gene signature, which divided osteosarcoma patients into low- or high-risk groups that showed good and poor prognosis, respectively. High expression of these 2 key genes is associated with low-risk group in patients with osteosarcoma. We constructed an accurate nomogram to help clinicians assess the survival time of patients with osteosarcoma. The results of immune cell infiltration level showed that the high-risk group had lower levels of immune cell infiltration. GSEA revealed changes in immune regulation and hypoxia stress pathways in osteosarcoma under different metastatic states. CONCLUSION: Our study identified an excellent gene signature that could be helpful in improving the prognosis of patients with osteosarcoma.

Hedyotislongiramulis (Rubiaceae), a new species from south China.

Hedyotislongiramulissp. nov. (Rubiaceae) is described from Guangdong Province, China. It is similar to H.caudatifolia but differs in having puberulent, more or less tetragonal and decussately sulcate juvenile stems, waxy leaf surface, short inflorescence peduncles, high length ratio of corolla lobe to tube, and subglobose capsules. The phylogenetic analysis reveals that H.longiramulis is sister to H.pubirachis. Dimorphism concerning pollen size was observed in the heterostylous flowers. The complete chloroplast genome of the new species comprises a typical quadripartite structure of 153,616 bp in length, with two inverted repeats of 25,457 bp, a large single-copy of 85,050 bp and a small single-copy of 17,652 bp. It contains 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes, the GC content of the chloroplast genome is 32.4%. The new species is provisionally evaluated as "Least Concern" because it is common and well-protected in two Provincial Nature Reserves.

Biomechanical analysis of internal fixation system stability for tibial plateau fractures.

Background: Complex bone plateau fractures have been treated with bilateral plate fixation, but previous research has overemphasized evaluating the effects of internal fixation design, plate position, and screw orientation on fracture fixation stability, neglecting the internal fixation system's biomechanical properties in postoperative rehabilitation exercises. This study aimed to investigate the mechanical properties of tibial plateau fractures after internal fixation, explore the biomechanical mechanism of the interaction between internal fixation and bone, and make suggestions for early postoperative rehabilitation and postoperative weight-bearing rehabilitation. Methods: By establishing the postoperative tibia model, the standing, walking and running conditions were simulated under three axial loads of 500 N, 1000 N, and 1500 N. Accordingly, finite element analysis (FEA) was performed to analyze the model stiffness, displacement of fractured bone fragments, titanium alloy plate, screw stress distribution, and fatigue properties of the tibia and the internal fixation system under various conditions. Results: The stiffness of the model increased significantly after internal fixation. The anteromedial plate was the most stressed, followed by the posteromedial plate. The screws at the distal end of the lateral plate, the screws at the anteromedial plate platform and the screws at the distal end of the posteromedial plate are under greater stress, but at a safe stress level. The relative displacement of the two medial condylar fracture fragments varied from 0.002-0.072 mm. Fatigue damage does not occur in the internal fixation system. Fatigue injuries develop in the tibia when subjected to cyclic loading, especially when running. Conclusion: The results of this study indicate that the internal fixation system tolerates some of the body's typical actions and may sustain all or part of the weight early in the postoperative period. In other words, early rehabilitative exercise is recommended, but avoid strenuous exercise such as running.

Risk factors and strategies for recovery quality, postoperative pain, and recurrent fractures between percutaneous kyphoplasty and percutaneous vertebroplasty in elderly patients with thoracolumbar compression fractures: a retrospective comparative cohort study.

Background: With the increase of clinical cases and the improvement of operation, we found that recurrent fracture of the adjacent vertebral body is a common long-term complication of percutaneous kyphoplasty (PKP). However, the mechanism of re-fracture of adjacent vertebrae after PKP has not been unified. Therefore, through retrospective study, this paper discussed the risk factors and countermeasures affecting the quality of rehabilitation, postoperative pain and recurrent fracture in elderly PKP patients. Methods: From December 2019 to May 2021, 313 patients with osteoporotic spinal fractures were analyzed retrospectively. Cases were allocated to percutaneous vertebroplasty (PVP; n=130) and PKP (n=183) groups according to the modes of operation. Visual analogue scale (VAS), Cobb angle, and Oswestry disability index (ODI) were evaluated. Based on the occurrence of new fractures, the PKP cohort (n=15) and control cohort (n=32) were classified. Questionnaires analyzed the postoperative re-fractures of people with different characteristics, and the influencing factors of postoperative re-fracture were measured by multivariate logistic regression analysis. Results: The postoperative VAS scores were significantly lower in the PKP group. The ODI scores in the PKP group were considerably lower than those in the PVP group after surgery. Univariate analysis indicated that age, number of injured vertebrae, history of complicated fracture, number of operative vertebrae, and bone mineral density (BMD) were remarkably correlated with recurrent fracture after PKP. Logistic regression analysis indicated that age, operative vertebral body, BMD, and the number of injured vertebrae were independent risk factors for recurrent fracture after PKP. BMI, BMD, low back soft tissue injury, postoperative vertebral height recovery rate, sagittal Cobb angle improvement rate, total diffusion coefficient of bone cement, short-term complications, non-union, and recurrent fracture were the main risk factors of residual low back pain after PKP. Conclusions: The clinical efficacy of PKP in elderly patients with thoracolumbar vertebral compression fracture is superior to that of PVP. Clinical attention should be paid to identifying high-risk factors for complications after PKP, and preventive measures should be implemented to help reduce the occurrence of recurrent fractures and postoperative residual pain.

Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil.

Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Our data consistently suggest that Matoniales, as a monophyletic lineage including Matoniaceae and Dipteridaceae, should be redefined as an ordinal rank. Furthermore, we have identified and located at least 11 whole-genome duplication events within the evolutionary history of four leptosporangiates lineages, and associated polyploidization with higher speciation rates and mass extinction events. We hypothesize that paleopolyploidization may have enabled leptosporangiate ferns to survive during mass extinction events at the end Permian period and then flourish throughout the Mesozoic era, which is supported by extensive fossil records. Our results highlight how ancient polyploidy can result in rapid species radiation, thus causing phylogenetic conflicts yet allowing plants to survive and thrive during mass extinction events.

Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants.

Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.

Dryopteriswulingshanensis (Dryopteridaceae), a new species from Hunan, China.

Dryopteriswulingshanensis, a new species growing on limestone in the Wulingshan Mountains, Hunan, China, is described and illustrated. This species is most similar to D.jishouensis and D.gymnophylla on general morphological traits, such as the form of scales, rhizome and sori, but differs by the number of vascular bundles at the base of the petiole, length to width ratio of lamina, stalk length of basal pinnae, division of the lamina, apex form of the pinnule and habitat. Moreover, molecular phylogenetic analysis using the chloroplast rbcL gene suggested that D.wulingshanensis, as the sister group of D.jishouensis, is a monophyletic clade. According to its restricted geographic range, small populations and few individuals, D.wulingshanensis should be considered endangered, according to the IUCN Red List criteria.

Morphology and molecules support the new monotypic genus Parainvolucrella (Rubiaceae) from Asia.

Parainvolucrella R.J. Wang, a new monotypic genus for P.scabra (Wall. ex Kurz) M.D.Yuan & R.J.Wang, new combination, is segregated from the Hedyotis-Oldenlandia complex, based on morphological and molecular evidence. Phylogenetically, the new genus is sister to Scleromitrion, from which it differs by a combination of morphological characters: herbaceous habit, terminal inflorescence with subtended leaves, heterostylous flowers, indehiscent fruits and pollen with double microreticulate tectum. A key to the genera of the Hedyotis-Oldenlandia complex in China is provided for further identification.

Chromosomal-level assembly of the Leptodermis oblonga (Rubiaceae) genome and its phylogenetic implications.

Rubiaceae is the fourth largest and a taxonomically complex family of angiosperms. Many species in this family harbor low reproductive isolation and frequently exhibit inconsistent phenotypic characteristics. Therefore, taxonomic classification and their phylogenetic relationships in the Rubiaceae family is challenging, especially in the genus Leptodermis. Considering the low taxonomic confusion and wide distribution, Leptodermis oblonga is selected as a representative Leptodermis for genome sequencing. The assemblies resulted in 497 Mbp nuclear and 155,100 bp chloroplast genomes, respectively. Using the nuclear genome as a reference, SNPs were called from 37 Leptodermis species or varieties. The phylogenetic tree based on SNPs exhibited high resolution for species delimitation of the complex and well-resolved phylogenetic relationships in the genus. Moreover, 28,987 genes were predicted in the nuclear genome and used for comparative genomics study. As the first chromosomal-level genome of the subfamily Rubioideae in Rubiaceae, it will provide fruitfully evolutionary understanding in the family.

Complete chloroplast genomes of Leptodermis scabrida complex: Comparative genomic analyses and phylogenetic relationships.

Leptodermis scabrida complex is one of the important components of genus Leptodermis, which is mainly distributed in the Himalaya Mountains. It includes species of L. gracilis, L. hirsutiflora, L. hirsutiflora var. ciliata, L. kumaonensis, L. pilosa var. acanthoclada and L. scabrida. However, species boundaries and relationships within this complex are unclear based on current morphological and molecular evidence. We sequenced 13 complete chloroplast (cp) genomes representing seven taxa of the complex and two non-Leptodermis scabrida complex taxa. After de novo assembly and annotation, we performed comparative genomic analysis. All cp genomes showed highly conserved structures, and the genome sizes ranged from 154,369 bp to 154,885 bp and possessed the same GC content (37.5%). A total of 113 unique genes were identified in each cp sample, including 79 protein coding genes, 30 tRNAs, and four rRNAs. Repeat sequences and SSRs were detected, showing great similarity among all taxa in this complex. Six highly variable regions, including trnS-trnG, rps2-rpoC2, ndhF, rpl32-ccsA, ccsA-ndhD, and ndhA, were screened as potential molecular markers for phylogenetic reconstruction. Based on a total of 27 complete cp genome sequences, the consistent and robust phylogenetic relationships were firstly constructed and the same species within L. scabrida complex clustered into a group. The divergence time of Leptodermis from ancestral taxa occurred at the middle Eocene, which might be due to geological and climatic changes. The 13 complete cp genome sequences reported will provide new clues for phylogeny elucidation, species identification and evolutionary history speculation of Leptodermis, as well as in Rubiaceae.

The complete chloroplast genome of Foonchewia coriacea (Rubioideae: Rubiaceae): a monotypic species endemic to Guangdong, China.

Foonchewia coriacea, a monotypic genus of the Rubiaceae, is endemic to China. Its complete chloroplast genome was determined to be 153,114 bp in length and the GC content was 37.90%. The sequence includes a large single-copy region of 83,978 bp, a small single-copy region of 18,290 bp, and the inverted region is 25,423 bp in length. It contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood (ML) and Bayesian inference (BI) analyses revealed F. coriacea was closely related to Dunnia sinensis with strong bootstrap values, belonging to the subfamily Rubioideae.

Morphology and molecules support the new monotypic genus Fenghwaia (Rhamnaceae) from south China.

Fenghwaia, a new monotypic genus, along with the new species Fenghwaia gardeniicarpa, is described from Guangdong Province, China. The combined features of inferior ovary, cylindrical drupaceous fruits and orbicular and dorsiventrally-compressed seeds with an elongate and pronounced basal appendage make the new genus significantly different from other genera of the family. In addition, its pollen morphology also showed great similarity to other species of this stenopalynous family. The molecular phylogenetic analysis, based on nuclear ribosomal internal transcribed spacer (ITS) and plastid trnL-F intron spacer (trnL-F) DNA sequence data from the new genus and the other 375 species representing 58 genera of Rhamnaceae, indicates that Fenghwaia is nested within the 'rhamnoid' group and sister to the tribe Rhamneae and then both sister to the tribe Maesopsideae. A taxonomic classification key to the 'rhamnoid' group is provided, based on morphological characters. A global conservation assessment is also performed and classifies Fenghwaia gardeniicarpa as Near Threatened (NT).

The complete chloroplast genome of Eleutherococcus trifoliatus (Araliaceae): a wild edible plant in the coastal region of South China.

Eleutherococcus trifoliatus (L.) S. Y. Hu is a wild edible plant and widely used in the coastal region of South China. Here, we report the complete chloroplast genome of E. trifoliatus. The length of the cp genome was determined to be 156751 bp with a small single copy (SSC) region of 18316 bp, a large single copy (LSC) region of 86747 bp and two separated inverted region of 25844 bp, respectively. Totally, 132 unique genes were identified of this genome, including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. The GC contents of this genome is 38%. Chloroplast phylogenomics analysis indicates that E. trifoliatus is closely related to E. gracilistylus (W.W. Sm.) S.Y. Hu.

The complete chloroplast genome of Dunnia sinensis (Rubiaceae): a monotypic species endemic to Guangdong, China.

Dunnia sinensis, a monotypic genus of the Rubiaceae, is an Endangered species endemic to China. Its complete chloroplast genome was determined to be 154,909 bp in length and the GC content was 37.80%. The sequence includes a large single-copy region of 84,894 bp, a small single-copy region of 16,973 bp, and the inverted region of 26,521 bp in length. It contains 130 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ML and BI analyses revealed D. sinensis was closely related to Galium mollugo and Leptodermis scabrida with strong bootstrap values belonging to the subfamily Rubioideae.

Nutritional and Functional Properties of Wild Food-Medicine Plants From the Coastal Region of South China.

Food-medicine plants play an important role in providing nutrition and treating chronic diseases, especially in many minority communities and developing regions. The coastal region of South China has abundant resources of medicinal plants. A long history of cross-cultural medicinal practices among different minority groups has facilitated the development of a remarkable dietary culture by using food-medicine plants. However, integrative ethnobotanical research on both nutritional and functional properties of the food-medicine plants in this region is still limited. In this study, 27 commonly used wild food-medicine plants were recorded and analyzed from the coastal region of South China. Most of them are good sources for calcium (47.83-1099.89 mg/100 g fresh weight), dietary fiber (3.00-31.87 mg/100 g fresh weight), iron (1.17-24.73 mg/100 g fresh weight), and vitamin C (0.44-68.32 mg/100 g fresh weight). Solanum americanum has the highest average nutritive value and is also considered to be good sources for proteins (7.90 g/100 g fresh weight). Medicinal properties of the studied species can be classified into 8 categories: treatment of the damp-heat syndrome, digestive diseases, urologic diseases, arthropathy, respiratory diseases, gynecological diseases, snake or insect bites, and uses as a tonic. Treating the damp-heat syndrome or expelling warm pathogenic factors is the most commonly used ethnomedicinal practice in the study area. The present study highlights that the local ethnomedicinal practices are deeply influenced by local natural conditions and customs. Food-medicine plants with superior key nutrients have been used regularly in the diet as medicinal food to alleviate common endemic diseases.

Development of microsatellite markers for a monotypic and globally endangered species, Glyptostrobus pensilis (Cupressaceae).

PREMISE OF THE STUDY: Microsatellite markers were developed to facilitate studies of genetic diversity and structure in Glyptostrobus pensilis, a critically endangered and monotypic conifer species. METHODS AND RESULTS: Using restriction site-associated DNA sequencing (RAD-Seq), we developed 10 polymorphic and 27 monomorphic microsatellite markers. Polymorphism was characterized using 333 individuals from nine populations. The number of alleles per locus ranged from one to 14 at the population level. The levels of observed and unbiased expected heterozygosities varied from 0.058 to 0.844 and 0.219 to 0.583, respectively. Nine of these 10 polymorphic markers were successfully cross-amplified in Taxodium distichum, the species most closely related to G. pensilis. CONCLUSIONS: These microsatellite markers can be used to reveal the genetic diversity in existing populations of G. pensilis, enabling its conservation and restoration.

The complete chloroplast genome of Leptodermis scabrida (Rubiaceae): an endemic shrub in Himalaya-Hengduan Mountains.

Leptodermis scabrida is an important endemic species in Himalaya-Hengduan Mountains. Here, we report the complete chloroplast genome of L. scabrida. The cp genome was determined to be 154783 bp in length and the GC content was 37.5%. The sequence included a large single copy (LSC) region of 84190 bp, a small single copy (SSC) region of 17183 bp and two separated inverted regions of 26705 bp, respectively. It contained 132 genes, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. This complete genome of L. scabrida will provide valuable information to resolve the complex phylogeny relationship and to elucidate the mechanism of speciation of Leptodermis, as well as for the phylogenetic studies of Rubiaceae.

Endangered but genetically stable-Erythrophleum fordii within Feng Shui woodlands in suburbanized villages.

Feng Shui woodlands are naturally or artificially formed green areas in southern China. They are precious for maintaining ecosystem balance in modern semiurban environments. However, they are generally small and geographically isolated from each other, and the status of genetic diversity of the plant species within them has been almost neglected. Therefore, we studied the genetic diversity of the endangered Erythrophleum fordii in eight Feng Shui woodlands (a total of 1,061 individuals) in Guangzhou, a large city in southern China, using microsatellites. For comparison, one population with 33 individuals sampled in a nature reserve was also studied. Although our results indicate that significant demographic declines occurred historically in E. fordii, such declines have not resulted in consistent reductions in genetic variation over generations in Feng Shui populations in the recent past, and the levels of genetic variation in these populations were higher than or comparable to the genetic variation of the population in the nature reserve. In addition, our parentage and paternity analyses indicated widespread and potential long-distance pollen flow within one Feng Shui woodland, indicating the presence of an unbroken pollination network, which would at least partially alleviate the genetic erosion due to habitat fragmentation and the unequal gene contributions of E. fordii parents to their progenies when favorable recruitment habitats are absent under most of the parent trees. Overall, our results suggest that E. fordii in Feng Shui woodlands may not be driven to extinction in the near future. Nevertheless, uncontrolled fast urban development with a lack of awareness of Feng Shui woodlands will cause the local extinction of E. fordii, which has already happened in some Feng Shui woodlands.

Spiradiclis pengshuiensis (Ophiorrhizeae, Rubioideae), a new species from Chongqing, China.

Spiradiclis pengshuiensis Bo Pan & R. J. Wang (Rubiaceae) is described as a new species from Chongqing in SW China. It is morphologically compared with Spiradiclis pauciflora L. Wu & Q. R. Liu because of their similarities in habit, pubescent surface, small leaf laminas and subglobose capsules. Its conservation status is evaluated as "VU" according to the IUCN categories and criteria.