1.Clinical guidelines for the diagnosis and treatment of osteoporotic thoracolumbar vertebral fracture with kyphotic deformity in the elderly (version 2024)
Jian CHEN ; Qingqing LI ; Jun GU ; Zhiyi HU ; Shujie ZHAO ; Zhenfei HUANG ; Tao JIANG ; Wei ZHOU ; Xiaojian CAO ; Yongxin REN ; Weihua CAI ; Lipeng YU ; Tao SUI ; Qian WANG ; Pengyu TANG ; Mengyuan WU ; Weihu MA ; Xuhua LU ; Hongjian LIU ; Zhongmin ZHANG ; Xiaozhong ZHOU ; Baorong HE ; Kainan LI ; Tengbo YU ; Xiaodong GUO ; Yongxiang WANG ; Yong HAI ; Jiangang SHI ; Baoshan XU ; Weishi LI ; Jinglong YAN ; Guangzhi NING ; Yongfei GUO ; Zhijun QIAO ; Feng ZHANG ; Fubing WANG ; Fuyang CHEN ; Yan JIA ; Xiaohua ZHOU ; Yuhui PENG ; Jin FAN ; Guoyong YIN
Chinese Journal of Trauma 2024;40(11):961-973
The incidence of osteoporotic thoracolumbar vertebral fracture (OTLVF) in the elderly is gradually increasing. The kyphotic deformity caused by various factors has become an important characteristic of OTLVF and has received increasing attention. Its clinical manifestations include pain, delayed nerve damage, sagittal imbalance, etc. Currently, the definition and diagnosis of OTLVF with kyphotic deformity in the elderly are still unclear. Although there are many treatment options, they are controversial. Existing guidelines or consensuses pay little attention to this type of fracture with kyphotic deformity. To this end, the Lumbar Education Working Group of the Spine Branch of the Chinese Medicine Education Association and Editorial Committee of Chinese Journal of Trauma organized the experts in the relevant fields to jointly develop Clinical guidelines for the diagnosis and treatment of osteoporotic thoracolumbar vertebral fractures with kyphotic deformity in the elderly ( version 2024), based on evidence-based medical advancements and the principles of scientificity, practicality, and advanced nature, which provided 18 recommendations to standardize the clinical diagnosis and treatment.
2.Analysis of the risk factors for 30-day unplanned reoperation after laparoscopic pancreatoduodenectomy
Shiwei ZHANG ; Yin JIANG ; Xinhua ZHOU ; Haibiao WANG ; Hong LI ; Yongfei HUA
Chinese Journal of Hepatobiliary Surgery 2024;30(9):672-677
Objective:To study the risk factors of unplanned reoperation within 30 days after laparoscopic pancreaticoduodenectomy (LPD).Methods:The clinical data of 207 patients who underwent LPD in the Lihuili Hospital Affiliated to Ningbo University from February 2017 to October 2022 were retrospectively analyzed. There were enrolled 118 males and 89 females, aged (65.1±11.1) years old. Patients were divided into the reoperation group ( n=15) and non-reoperation group ( n=192) based on whether unplanned reoperation was performed within 30 days after LPD. The risk factors of unplanned reoperation were analyzed with univariate and multivariate logistic regression analysis. Results:The rate of unplanned reoperation within 30 days after LPD was 7.2%(15/207). The unplanned reoperation group exhibited a higher incidence of complications 80% (12/15), mortality 13.3% (2/15), and extended hospital stay (32.9±20.1)d compared to the non-reoperation group, which incidences of complications, mortality and extended hospital stay were 40.1% (77/192)( χ2=9.04, P=0.003), 0.5%(1/192)( χ2=8.28, P=0.004), and (17.9±8.6)d ( t=-2.79, P=0.014), respectively. Unplanned reoperation was associated with diabetes, intraoperative bleeding >130 ml, preoperative serum prealbumin <0.15 g/L, pancreatic texture and pancreatic duct diameter (all P<0.05). Multivariate logistic regression analysis identified diabetes ( OR=4.991, 95% CI: 1.431-17.415), preoperative serum prealbumin <0.15 g/L ( OR=4.06, 95% CI: 1.178-14.043), soft pancreatic texture ( OR=3.900, 95% CI: 1.146-13.272) and pancreatic duct diameter ≤3 mm ( OR=3.449, 95% CI: 1.009-11.789) as independent risk factors for unplanned reoperation within 30 days. Conclusion:Preoperative diabetes, preoperative serum prealbumin levels <0.15 g/L, soft pancreatic texture and pancreatic duct diameter ≤3 mm were independent risk factors for unplanned reoperation within 30 days after LPD.
3.Management of adult Langerhans cell histiocytosis in the hypothalamic-pituitary region—Experiences from Huashan Hospital
Qian WANG ; Quanya SUN ; Min HE ; Li PAN ; Yongfei WANG ; Haixia CHENG ; Yue WU ; Tianling DING ; Hongying YE ; Wei WU
Chinese Journal of Endocrinology and Metabolism 2024;40(5):386-392
Objective:To summarize experience of managing adult Langerhans cell histiocytosis(LCH) in hypothalamic-pituitary region(HPR) from Shanghai Huashan Hospital.Methods:Adult HPR-LCH patients diagnosed at oar endocrinology department from January 2013 to February 2022 were included. Clinical characteristics and treatment response were retrospectively analyzed.Results:A total of 27 adult HPR-LCH patients were included, with 14 cases involving the hypothalamus(H group) and 13 cases without(group NH). The common radiological findings included thickening of the pituitary stalk(25/27, 92.6%). At the time of diagnosis, 14 cases(51.9%) presented with panhypopituitarism, and 19 cases(70.4%) exhibited metabolic abnormalities. The group H had higher proportions of adrenal insufficiency, central hypothyroidism, panhypopituitarism, and diabetes compared to group NH(78.6% vs 23.1%; 78.6% vs 23.1%; 92.9% vs 30.8%, 35.7% vs 0%, respectively, all P<0.05). Hypothalamus syndrome was identified in 71.4%(10/14) of group H. The inital diagnosis rate was 79.2%(19/24), with 48.1% and 51.9% through biopsy of sellar and extrasellar lesions, respectively. Repeated biopsies confirmed the diagnosis in 25.9%(7/27) of cases. The peripheral lesions included bone, thyroid, lung, lymph node, thymus and liver. Out of 20 cases treated with chemotherapy, the objective response rate was 85% at 12 weeks. Four cases received local therapy, one case received traditional Chinese medicine treatment, one case abandoned treatment, and one case was lost to follow-up. The median follow-up time was 28(range 15 to 54) months. During this period, there were 3 deaths in group H and 1 death in group NH. Conclusion:Adult HPR-LCH patients presented with diabetes insipidus and high prevalences of hypopituitarism, hypothalamus syndrome and metabolic abnormalities. Typical imaging features were pituitary stalk thickening. A solitary mass in the HPR was usually very small, posing a great challenge for early diagnosis. Systemic evaluation would help to clarify the diagnosis. Patients with hypothalamus involvement had a higher mortality rate, suggesting the hypothalamus as a risk organ with poor prognosis.
4.Risk factors and development of a risk assessment model for postoperative venous thromboembolism in Cushing′s disease
Wenjuan LIU ; Dan LIU ; Min HE ; Qing MIAO ; Lijin JI ; Lili CHEN ; Yifei YU ; Zengyi MA ; Xuefei SHOU ; Shuo ZHANG ; Yutao WANG ; Zhiyuan WU ; Chaoyun ZHANG ; Yao ZHAO ; Yiming LI ; Yongfei WANG ; Hongying YE
Chinese Journal of Endocrinology and Metabolism 2024;40(6):487-493
Objective:To investigate the incidence and prothrombotic risk factors of postoperative venous thromboembolism(VTE) in Cushing′s disease and to further develop an assessment model to identify those at high risk of postoperative VTE events.Methods:A retrospective study was performed in 82 patients who were admitted to Huashan Hospital, Fudan University during January 2019 and January 2020 and diagnosed with Cushing′s disease. These patients underwent the evaluation about their clinical, hormonal, and coagulation parameters, as well as ultrasonography and pulmonary angio-CT when necessary. The least absolute shrinkage and selection operator(LASSO) regression analysis was used to screen independent risk factors, and a nomogram model for postsurgical VTE risk assessment in Cushing′s disease was initially established, and Bootstrap method was used for internal verification. Finally, the predictive model was evaluated for calibration and clinical applicability in the study cohort.Results:Nineteen patients(23.17%) developed VTE events, with 14 cases occurring after endoscopic transsphenoidal surgery. Compared to patients without VTE, those in the VTE group were older( P<0.001), had longer postoperative bed rest, higher rates of current infection, higher HbA 1C levels, and more severe glucose tolerance impairment(all P<0.05). Through LASSO regression analysis, two independent risk factors for postoperative VTE were identified: Age and current infection. Then a VTE risk assessment nomogram model was established to predict the patients at high risk of VTE. In the nomogram model for VTE risk assessment, the area under the receiver operating characteristic curve was 0.868(95% CI 0.787-0.949), with the calibration curve closely aligning with the ideal diagonal line and the clinical decision curve exceeding the two extreme curves. Conclusions:Advanced perioperative assessment needs to be taken to screen those with high VTE risks in patients diagnosed with Cushing′s disease. Additionally, during the perioperative period, patients with Cushing′s disease should undergo mandatory physical activity or prophylactic anticoagulant therapy.
5.Intracranial pressure changes at perioperative period in patients with large hemispheric infarction after standard large bone flap decompression
Yulong GUO ; Fandong MENG ; Yongfei LI ; Yuanyuan MA ; Yushe WANG
Chinese Journal of Neuromedicine 2024;23(6):578-584
Objective:To explore the correlations of neurological function recovery and intraoperative bone window parameters with intracranial pressure (ICP) changes at perioperative period in patients with large hemispheric infarction (LHI) after standard large bone flap decompression.Methods:Forty LHI patients accepted standard large bone flap decompression in Department of Neurosurgery, People's Hospital of Zhengzhou University from December 2020 to December 2023 were enrolled. ICP was measured before decompression, at the time of bone flap removal, during dural opening, and 24 h after decompression. Correlations of National Institutes of Health Stroke Scale (NIHSS), Extended Glasgow Outcome Scale (GOSE) and Glasgow Coma Scale (GCS) score changes, length and area of the bone window, bone window area/cranial bone area, infarct brain tissue volume/brain tissue volume with ICP changes were analyzed by Pearson's correlation. Length and area of bone window in patients with good neurological function recovery (NIHSS score decreased by≥5, GOSE score increased by≥3, or GCS score increased by≥3 before and after decompression) were calculated.Results:ICP at the time of bone flap removal, during dural opening, and 24 h after decompression was significantly lower than that before decompression ( P<0.05); ICP at the time of bone flap removal was higher than that at 24 h after decompression and during dural opening. Reduction between ICP before decompression and that during dural opening was more obvious than ICP reduction before and 24 h after decompression and ICP reduction before decompression and at the time of bone flap removal, with significant differences ( P<0.05). Postoperative NIHSS scores were significantly lower than preoperative ones ( P<0.05), and both postoperative GOSE and GCS scores were significantly higher than preoperative ones ( P<0.05). Decrease of NIHSS score, increase of GOSE and GCS scores before and after decompression were positively correlated with ICP reduction before and 24 h after decompression ( r=0.386, P=0.018; r=0.411, P=0.033; r=0.319, P=0.037); length and area of the bone window were positively correlated with ICP reduction before and 24 h after decompression ( r=0.461, P=0.028; r=0.536, P=0.034); bone window area/cranial bone area was positively correlated with ICP reduction before and 24 h after decompression ( r=0.438, P=0.027), while infarct brain tissue volume/brain tissue volume was negatively correlated with ICP reduction before and 24 h after decompression ( r=-0.371, P=0.031). Of the 40 patients, 25 had good neurological function recovery after decompression, with length of the bone window ranged 12.3-16.7 cm and area of the bone window ranged 54.5-91.9 cm 2. Conclusion:Standard large bone flap decompression can reduce ICP and improve prognosis in LHI patients; intraoperative bone window parameters are obviously correlated with ICP reduction before and 24 h after decompression; length of the bone window ranged 12.3-16.7 cm and area of the bone window ranged 54.5-91.9 cm 2 are suggested for decompression.
6.Analysis of the causal relationship between human immune cells and hypertrophic scar using two-sample bidirectional Mendelian randomization method
Honglin WU ; Yongfei CHEN ; Shuting LI ; Hao YANG ; Xiaohui LI ; Bing TANG ; Jiayuan ZHU ; Zhicheng HU
Chinese Journal of Burns 2024;40(6):572-578
Objective:To explore the causal relationship between human immune cells and hypertrophic scar (HS) using two-sample bidirectional Mendelian randomization (MR) method.Methods:This study was based on two-sample MR method, and the datasets of 731 immune cells and HS were obtained from the genome-wide association study (GWAS) catalog database and Finngen database, respectively. A significance threshold was established to discern single nucleotide polymorphism (SNP) significantly correlated with immune cells or HS, thereby eliminating the impact of weak instrumental variable bias. The inverse variance weighted (IVW) method (meanwhile, the Benjamini-Hochberg (BH) procedure of false discovery rate (FDR) to adjust P values) was used for preliminary detection of the causal relationship between immune cells and HS and screen the immune cells that had a significant causal relationship with HS. Further, the causal relationship between the selected immune cells and HS was detected through five two-sample MR methods: IVW method, weighted median method, simple mode method, weighted mode method, and MR-Egger method, and the scatter plot was drawn. SNPs conformed to the hypothesis were subjected to Cochran Q test for heterogeneity assessment, MR-Egger regression coupled with MR-PRESSO to eliminate horizontal pleiotropic effects, and a leave-one-out analysis was also conducted to determine if significant results were driven by individual SNP. Finally, the IVW method contained in the two-sample MR analysis was utilized to inversely examine the causal relationship between HS and immune cells. Results:The number of SNPs in 731 immune cells reaching the significance threshold varied from 7 to 1 786, while in HS, 119 SNPs met the significance threshold, with the F values of all SNPs being greater than 10, suggesting a low likelihood of bias from weak instrumental variables. The IVW method revealed that 60 types of immune cells potentially had a causal relationship with HS (with all P values <0.05), and after adjustment using the BH method, only CD45RA and CD39 positive regulatory T cell (Treg) maintained a potentially strong causal relationship with HS ( PFDR<0.05). The IVW method (with odds ratio of 1.16 and 95% confidence interval of 1.08-1.24, P<0.05, PFDR<0.05), weighted median method (with odds ratio of 1.16 and 95% confidence interval of 1.05-1.28, P<0.05), weighted mode method (with odds ratio of 1.14 and 95% confidence interval of 1.02-1.27, P<0.05), and MR-Egger method (with odds ratio of 1.18 and 95% confidence interval of 1.07-1.30, P<0.05) of scatter plot all suggested a causal relationship between the 14 SNPs of CD45RA and CD39 positive Treg and risk of HS, only simple mode method of scatter plot suggested a not obvious relationship between the 14 SNPs of CD45RA and CD39 positive Treg and risk of HS ( P>0.05). Cochran Q test indicated no heterogeneity in the causal relationship between CD45RA on CD39 positive Treg and HS ( P>0.05). MR-Egger regression and MR-PRESSO analyses showed that there was no horizontal pleiotropy in the significant causal relationship between CD45RA and CD39 positive Treg and HS ( P>0.05). Leave-one-out analysis confirmed that the significant causal relationship between CD45RA and CD39 positive Treg and HS remained stable after sequentially removing individual SNP. Reverse two-sample MR analysis showed that HS had no potential causal relationship with any of the 731 types of immune cells ( P>0.05). Conclusions:From the perspective of genetics, it is revealed that immune cells CD45RA and CD39 positive Treg may increase the risk of HS.
7.Application effect of acellular allogeneic dermal matrix combined with autologous razor-thin scalp grafts in scar rehabilitation
Jiangbo KUANG ; Yongfei WANG ; Xisheng XU ; Botong LI
Chinese Journal of Plastic Surgery 2024;40(6):641-650
Objective:To investigate the efficacy of acellular allogeneic dermal matrix (ADM) combined with autologous razor-thin scalp grafts in scar rehabilitation.Methods:A retrospective study was conducted on patients who underwent skin grafts transplantation to repair scar in the Department of Burns and Plastic Surgery of the First People’s Hospital of Chenzhou from July 2015 to December 2021. All the patients were divided into the observation group and the control group according to surgical methods. The observation group was treated with ADM combined with autologous razor-thin scalp grafts to repair the wound after scar resection, and the control group was treated with split-thickness skin grafts (STSGs) to repair the wound. Efficacy evaluation: On the 1st, 7th and 14th day after surgery, the patients in the two groups scored the pain degree of the donor sites through the visual analogue scale (VAS), with a score of 0 indicating no pain and a score of 10 indicating severe pain. The grid method was used to measure the surviving area of the skin and calculate the surviving proportion of the skin grafts. The wound healing time in donor and recipient sites were recorded. The postoperative complication was recorded, and the incidence of complications was calculated. Scars in donor and recipient sites were observed at the 3rd, 6th, 9th and 12th month after surgery, and the scars in recipient sites were scored by the Vancouver scar scale (VSS), with a total score of 0-13 points, and the higher the score, the more serious the scars were. SPSS 22.0 software was used for statistical analysis of the data. The normally distributed continuous data were represented as Mean±SD, and analyzed by t-test, and the non-normally distributed continuous data were represented as M ( Q1, Q3), and the Wilcoxon rank-sum test was used for comparison between groups. Enumeration data were expressed as examples and (or) percentages, and chi-square test was used for comparison between groups. The differences were considered statistically significant for probability values P<0.05. Results:A total of 50 patients, including 28 males and 22 females, aged (38.5±13.9) years, were enrolled in the observation group, and the wound area caused by scar resection and release was (70.4±17.7) cm 2. The scars were on upper limb in 16 cases, lower limb in 15 cases, trunk in 11 cases, neck in 8 cases. The control group included 50 patients, 30 males and 20 females, aged (34.8±14.6) years, and the wound area caused by scar resection and release was (66.2±16.5) cm 2. The scars were on upper limb in 15 cases, lower limb in 11 cases, trunk in 13 cases, neck in 11 cases. There was no significant difference in gender composition, age, skin graft site and the wound area caused by scar resection and release between these two groups ( P > 0.05). On the 1st, 7th and 14th day after surgery, the VAS scores of the observation group were 6.35 (5.11, 7.67) points, 4.95 (3.63, 6.46) points and 0.73 (0.18, 1.39) points, while the control group were 8.25 (7.14, 9.19) points, 7.00 (5.45, 8.06) points and 0.80(0.20, 1.55)points, respectively. The VAS score of the observation group was lower than that of the control group on the 1st and 7th day after surgery ( Z=-4.53, -3.86, both P < 0.001), and there was no significant difference in VAS score between the two groups on the 14th day after surgery ( P > 0.05). There was no significant difference between the two groups in terms of the survival ratio of skin grafts [(95.6±2.1) % vs. (95.8±2.3) %] ( P>0.05) and the postoperative incidence of complications [18% (9/50) vs. 10% (5/50)] ( P>0.05). The wound healing time in the donor sites in both groups were (6.80±0.88) days, (13.30±1.83) days ( t=-22.70, P<0.001), while the wound healing time in the recipient sites in both groups were 14.33 (12.73, 15.76) days and 8.91 (7.76, 10.67) days ( Z=-7.31, P<0.001). The average follow-up time was 21.8 months, the observation group had no scar formation at the donor site, while the control group had different degrees of scar hyperplasia. There was no significant difference in VSS scores between the two groups at the 3rd and 6th month after surgery ( P>0.05), while the VSS scores of the observation group at 9th and 12th month after surgery were 5.96 (4.81, 7.15) points and 5.85 (4.81, 6.75) points, which were significantly lower than those of in the control group [7.04(5.93, 8.14)points, 6.92(5.81, 8.06)points] ( Z=-2.82, P=0.005; Z=-3.54, P<0.001). Conclusion:The use of ADM combined with autologous razor-thin scalp graft to repair the wound after scar resection can effectively improve the appearance and function of the repair area, and reduce the pain and avoid scar hyperplasia in the donor sites.
8.Application effect of acellular allogeneic dermal matrix combined with autologous razor-thin scalp grafts in scar rehabilitation
Jiangbo KUANG ; Yongfei WANG ; Xisheng XU ; Botong LI
Chinese Journal of Plastic Surgery 2024;40(6):641-650
Objective:To investigate the efficacy of acellular allogeneic dermal matrix (ADM) combined with autologous razor-thin scalp grafts in scar rehabilitation.Methods:A retrospective study was conducted on patients who underwent skin grafts transplantation to repair scar in the Department of Burns and Plastic Surgery of the First People’s Hospital of Chenzhou from July 2015 to December 2021. All the patients were divided into the observation group and the control group according to surgical methods. The observation group was treated with ADM combined with autologous razor-thin scalp grafts to repair the wound after scar resection, and the control group was treated with split-thickness skin grafts (STSGs) to repair the wound. Efficacy evaluation: On the 1st, 7th and 14th day after surgery, the patients in the two groups scored the pain degree of the donor sites through the visual analogue scale (VAS), with a score of 0 indicating no pain and a score of 10 indicating severe pain. The grid method was used to measure the surviving area of the skin and calculate the surviving proportion of the skin grafts. The wound healing time in donor and recipient sites were recorded. The postoperative complication was recorded, and the incidence of complications was calculated. Scars in donor and recipient sites were observed at the 3rd, 6th, 9th and 12th month after surgery, and the scars in recipient sites were scored by the Vancouver scar scale (VSS), with a total score of 0-13 points, and the higher the score, the more serious the scars were. SPSS 22.0 software was used for statistical analysis of the data. The normally distributed continuous data were represented as Mean±SD, and analyzed by t-test, and the non-normally distributed continuous data were represented as M ( Q1, Q3), and the Wilcoxon rank-sum test was used for comparison between groups. Enumeration data were expressed as examples and (or) percentages, and chi-square test was used for comparison between groups. The differences were considered statistically significant for probability values P<0.05. Results:A total of 50 patients, including 28 males and 22 females, aged (38.5±13.9) years, were enrolled in the observation group, and the wound area caused by scar resection and release was (70.4±17.7) cm 2. The scars were on upper limb in 16 cases, lower limb in 15 cases, trunk in 11 cases, neck in 8 cases. The control group included 50 patients, 30 males and 20 females, aged (34.8±14.6) years, and the wound area caused by scar resection and release was (66.2±16.5) cm 2. The scars were on upper limb in 15 cases, lower limb in 11 cases, trunk in 13 cases, neck in 11 cases. There was no significant difference in gender composition, age, skin graft site and the wound area caused by scar resection and release between these two groups ( P > 0.05). On the 1st, 7th and 14th day after surgery, the VAS scores of the observation group were 6.35 (5.11, 7.67) points, 4.95 (3.63, 6.46) points and 0.73 (0.18, 1.39) points, while the control group were 8.25 (7.14, 9.19) points, 7.00 (5.45, 8.06) points and 0.80(0.20, 1.55)points, respectively. The VAS score of the observation group was lower than that of the control group on the 1st and 7th day after surgery ( Z=-4.53, -3.86, both P < 0.001), and there was no significant difference in VAS score between the two groups on the 14th day after surgery ( P > 0.05). There was no significant difference between the two groups in terms of the survival ratio of skin grafts [(95.6±2.1) % vs. (95.8±2.3) %] ( P>0.05) and the postoperative incidence of complications [18% (9/50) vs. 10% (5/50)] ( P>0.05). The wound healing time in the donor sites in both groups were (6.80±0.88) days, (13.30±1.83) days ( t=-22.70, P<0.001), while the wound healing time in the recipient sites in both groups were 14.33 (12.73, 15.76) days and 8.91 (7.76, 10.67) days ( Z=-7.31, P<0.001). The average follow-up time was 21.8 months, the observation group had no scar formation at the donor site, while the control group had different degrees of scar hyperplasia. There was no significant difference in VSS scores between the two groups at the 3rd and 6th month after surgery ( P>0.05), while the VSS scores of the observation group at 9th and 12th month after surgery were 5.96 (4.81, 7.15) points and 5.85 (4.81, 6.75) points, which were significantly lower than those of in the control group [7.04(5.93, 8.14)points, 6.92(5.81, 8.06)points] ( Z=-2.82, P=0.005; Z=-3.54, P<0.001). Conclusion:The use of ADM combined with autologous razor-thin scalp graft to repair the wound after scar resection can effectively improve the appearance and function of the repair area, and reduce the pain and avoid scar hyperplasia in the donor sites.
9.Chloroplast genomic characterization and phylogenetic analysis of Pellionia scabra.
Li YAN ; Xuelian YANG ; Yongfei WU ; Xia WANG ; Xiaojing HU
Chinese Journal of Biotechnology 2023;39(7):2914-2925
Pellionia scabra belongs to the genus Pellionia in the family of Urticaceae, and is a high-quality wild vegetables with high nutritional value. In this study, high-throughput techniques were used to sequence, assemble and annotate the chloroplast genome. We also analyzed its structure, and construct the phylogenetic trees from the P. scabra to further study the chloroplast genome characteristics. The results showed that the chloroplast genome size was 153 220 bp, and the GC content was 36.4%, which belonged to the typical tetrad structure in P. scabra. The chloroplast genome encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes in P. scabra. Among them, 15 genes contained 1 intron, 2 genes contained 2 introns, and rps12 had trans-splicing, respectively. In P. scabra, chloroplast genomes could be divided into four categories, including 43 photosynthesis, 64 self-replication, other 7 coding proteins, and 4 unknown functions. A total of 51 073 codons were detected in the chloroplast genome, among which the codon encoding leucine (Leu) accounted for the largest proportion, and the codon preferred to use A and U bases. There were 72 simple sequence repeats (SSRs) in the chloroplast genome of P. scabra, containing 58 single nucleotides, 12 dinucleotides, 1 trinucleotide, and 1 tetranucleotide. The ycf1 gene expansion was present at the IRb/SSC boundary. The phylogenetic trees showed that P. scabra (OL800583) was most closely related to Elatostema stewardii (MZ292972), Elatostema dissectum (MK227819) and Elatostema laevissimum var. laevissimum (MN189961). Taken together, our results provide worthwhile information for understanding the identification, genetic evolution, and genomics research of P. scabra species.
Phylogeny
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Genome, Chloroplast/genetics*
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Genomics
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Chloroplasts/genetics*
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Codon
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Urticaceae/genetics*
10.Characteristics and phylogenetic analysis of chloroplast genome of a new type of fruit Rubus rosaefolius.
Yongfei WU ; Xuelian YANG ; Xia WANG ; Li YAN ; Wanping ZHANG
Chinese Journal of Biotechnology 2023;39(7):2939-2953
The genomic DNA of Rubus rosaefolius was extracted and sequenced by Illumina NovaSeq platform to obtain the complete chloroplast genome sequence, and the sequence characteristics and phylogenetic analysis of chloroplast genes were carried out. The results showed that the complete chloroplast genome of the R. rosaefolius was 155 650 bp in length and had a typical tetrad structure, including two reverse repeats (25 748 bp each), a large copy region (85 443 bp) and a small copy region (18 711 bp). A total of 131 genes were identified in the whole genome of R. rosaefolius chloroplast, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The GC content of the whole genome was 36.9%. The genome of R. rosaefolius chloroplast contains 47 scattered repeats and 72 simple sequence repeating (SSR) loci. The codon preference is leucine codon, and the codon at the end of A/U is preferred. Phylogenetic analysis showed that R. rosaefolius had the closest relationship with R. taiwanicola, followed by R. rubraangustifolius and R. glandulosopunctatus. The chloroplast genome characteristics and phylogenetic analysis of R. rosaefolius provide a theoretical basis for its genetic diversity research and chloroplast development and utilization.
Phylogeny
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Rubus/genetics*
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Genome, Chloroplast
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Fruit/genetics*
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Codon/genetics*

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