1.Effect and mechanism of circular RNA SEC24A on proliferation and apoptosis of synovial fibroblasts in osteoarthritis
Lijun ZHOU ; Keyuan ZHANG ; Feihu XU ; Xi WANG ; Li YU ; Shiming DONG ; Junyu XU ; Yufeng GUO ; Hairong MA ; Hong DING
Chinese Journal of Tissue Engineering Research 2025;29(24):5086-5092
BACKGROUND:Synovitis is involved in all stages of osteoarthritis and is a key factor contributing to the development of osteoarthritis.Studies have shown that circular RNA(circRNA)plays an important role in the proliferation,apoptosis and extracellular matrix degradation of synovial cells and chondrocytes.OBJECTIVE:To observe the effects of circRNA SEC24A on the interleukin-1β-induced proliferation,apoptosis,and expression of inflammatory factors in human synovial fibroblasts.METHODS:Human synovial fibroblasts were divided into four groups,including control group,interleukin-1β group,empty vector group,and sh-circSEC24A group.Except for the control group,the other three groups were induced with 10 ng/mL interleukin-1β for 24 hours to establish inflammatory cell models;the empty vector group and sh-circSEC24A group were infected with empty vector virus and lentiviral vector knocking down circSEC24A.CCK-8 assay was used to detect cell proliferation.Flow cytometry was used to detect cell apoptosis.ELISA was used to detect the levels of matrix metalloproteinase-9,matrix metalloproteinase-13,interleukin-6,and tumor necrosis factor-α in cell supernatant.Western blot assay was used to detect the relative expression levels of Bax,Bcl-2,matrix metalloproteinase-9,matrix metalloproteinase-13,casepase3,cleaved-casepase3,casepase8,and cleaved-casepase8 proteins in cells.RESULTS AND CONCLUSION:(1)qRT-PCR results showed that compared with the normal group,the expression of circSEC24A in human synovial fibroblasts induced by interleukin 1β was significantly up-regulated.(2)The absorbance value of cells in the sh-circSEC24A group detected by CCK-8 assay was significantly higher than that of interleukin 1β group and empty vector group(P<0.05).The apoptosis rate of sh-circSEC24A group detected by flow cytometry was significantly lower than that of interleukin 1β group and empty vector group(P<0.05).(3)The levels of tumor necrosis factor α and interleukin 6 in the supernatant of human synovial fibroblasts in the sh-circSEC24A group detected by ELISA were significantly lower than those in the interleukin 1β group and the empty vector group(P<0.01,P<0.001).(4)Western blot assay results showed that compared with the interleukin 1β group and the empty vector group,the expression of the pro-apoptotic factor Bax protein in the sh-circSEC24A group significantly decreased,and the expression of the anti-apoptotic factor Bcl-2 protein increased significantly(P<0.05);apoptosis and related activating factors cleaved-casepase3 and cleaved-casepase8 protein expressions were both reduced(P<0.05).(5)ELISA and western blot assay results showed that compared with the interleukin 1β group and the empty vector group,the sh-circSEC24A group had lower levels of matrix metalloproteinase 9 and matrix metalloproteinase 13 protein(P<0.05).These findings indicated that the expression of circSEC24A was abnormally increased in human synovial fibroblasts induced by interleukin 1β.Knocking down circSEC24A expression could promote the proliferation of human synovial fibroblasts and inhibit apoptosis,inflammatory factor release,and extracellular matrix degradation,suggesting that circSEC24A may be an important intervention target for early osteoarthritis.
2.Clinical efficacy of "four-step" aortic valve anatomic repair for regurgitant bicuspid aortic valve
Jun LI ; Zheng ZUO ; Hao LAI ; Lili DONG ; Kai ZHU ; Junyu ZHAI ; Yongxin SUN ; Wenjun DING ; Tao HONG ; Chunsheng WANG
Chinese Journal of Thoracic and Cardiovascular Surgery 2025;41(6):334-340
Objective:To explore the clinical efficacy of "four-step" aortic valve anatomic repair for bicuspid aortic valve(BAV) with aortic regurgitation(AR).Methods:From August 2021 to November 2024, a total of 298 consecutive patients with BAV-AR underwent aortic valve anatomic repair(AVr) in Shanghai Zhongshan Hospital Fudan University, 266 males and 32 females, with age of 39(29.5, 48.5) years. All patients underwent " four-step" three-dimensional anatomic repair of the aortic annulus and leaflets, 129(43.3%) patients via upper mini-sternotomy and 169(56.7%) patients via conventional median sternotomy, with the main steps including: (1) deep dissecting and annuloplasty of the virtual basal ring(VBR); (2) symmetrical repairing of leaflets; (3) replacement or remodeling of the sinus of Valsalva; (4) annuloplasty of the sinotubular junction(STJ). Basal and perioperative data were retrospectively collected, and statistical analysis was performed in conjunction with follow-up data.Results:All patients successfully underwent anatomical repair without transferring to valve replacement during operation. Among them, 43 patients underwent aortic root reimplantation technique(Reimplantation group), while 255 patients underwent modified aortic root sleeve remodeling technique(Sleeve group). The median cardiopulmonary bypass time for the Reimplantation and Sleeve groups were 154(134, 169) minutes and 111(95, 129) minutes, respectively( P<0.05); the median aortic cross-clamp time were 112(100, 131) minutes and 80(67, 94) minutes, respectively( P<0.05). Preoperative TEE showed 35 patients(81.4%) and 229 patients(89.8%) with moderate and severe AR in Reimplantation and Sleeve groups, respectively. Postoperative TEE showed 41 patients(95.3%) with no/trace AR and 2 patients(4.7%) with central mild AR in Reimplantation group, while 212 patients(83.1%) with no/trace AR and 43 patients(16.9%) with central mild AR in Sleeve group. Follow-up was completed in all patients, with a median follow-up of 12.9(4.7, 21.2) months. Echocardiography was obtained in 271 patients(90.9%) at the latest follow-up, including no/trace AR in 167 patients(56.0%), mild AR in 89 patients(29.9%), moderate AR in 14 patients(4.7%), and severe AR in 1 patient(0.3%). Conclusion:Aortic valve anatomic repair by standardized "four-step" approach is safe and reproducible. Satisfied short- and mid-term outcome have obtained in selected BAV-AR patients.
3.Effect and mechanism of circular RNA SEC24A on proliferation and apoptosis of synovial fibroblasts in osteoarthritis
Lijun ZHOU ; Keyuan ZHANG ; Feihu XU ; Xi WANG ; Li YU ; Shiming DONG ; Junyu XU ; Yufeng GUO ; Hairong MA ; Hong DING
Chinese Journal of Tissue Engineering Research 2025;29(24):5086-5092
BACKGROUND:Synovitis is involved in all stages of osteoarthritis and is a key factor contributing to the development of osteoarthritis.Studies have shown that circular RNA(circRNA)plays an important role in the proliferation,apoptosis and extracellular matrix degradation of synovial cells and chondrocytes.OBJECTIVE:To observe the effects of circRNA SEC24A on the interleukin-1β-induced proliferation,apoptosis,and expression of inflammatory factors in human synovial fibroblasts.METHODS:Human synovial fibroblasts were divided into four groups,including control group,interleukin-1β group,empty vector group,and sh-circSEC24A group.Except for the control group,the other three groups were induced with 10 ng/mL interleukin-1β for 24 hours to establish inflammatory cell models;the empty vector group and sh-circSEC24A group were infected with empty vector virus and lentiviral vector knocking down circSEC24A.CCK-8 assay was used to detect cell proliferation.Flow cytometry was used to detect cell apoptosis.ELISA was used to detect the levels of matrix metalloproteinase-9,matrix metalloproteinase-13,interleukin-6,and tumor necrosis factor-α in cell supernatant.Western blot assay was used to detect the relative expression levels of Bax,Bcl-2,matrix metalloproteinase-9,matrix metalloproteinase-13,casepase3,cleaved-casepase3,casepase8,and cleaved-casepase8 proteins in cells.RESULTS AND CONCLUSION:(1)qRT-PCR results showed that compared with the normal group,the expression of circSEC24A in human synovial fibroblasts induced by interleukin 1β was significantly up-regulated.(2)The absorbance value of cells in the sh-circSEC24A group detected by CCK-8 assay was significantly higher than that of interleukin 1β group and empty vector group(P<0.05).The apoptosis rate of sh-circSEC24A group detected by flow cytometry was significantly lower than that of interleukin 1β group and empty vector group(P<0.05).(3)The levels of tumor necrosis factor α and interleukin 6 in the supernatant of human synovial fibroblasts in the sh-circSEC24A group detected by ELISA were significantly lower than those in the interleukin 1β group and the empty vector group(P<0.01,P<0.001).(4)Western blot assay results showed that compared with the interleukin 1β group and the empty vector group,the expression of the pro-apoptotic factor Bax protein in the sh-circSEC24A group significantly decreased,and the expression of the anti-apoptotic factor Bcl-2 protein increased significantly(P<0.05);apoptosis and related activating factors cleaved-casepase3 and cleaved-casepase8 protein expressions were both reduced(P<0.05).(5)ELISA and western blot assay results showed that compared with the interleukin 1β group and the empty vector group,the sh-circSEC24A group had lower levels of matrix metalloproteinase 9 and matrix metalloproteinase 13 protein(P<0.05).These findings indicated that the expression of circSEC24A was abnormally increased in human synovial fibroblasts induced by interleukin 1β.Knocking down circSEC24A expression could promote the proliferation of human synovial fibroblasts and inhibit apoptosis,inflammatory factor release,and extracellular matrix degradation,suggesting that circSEC24A may be an important intervention target for early osteoarthritis.
4.Clinical efficacy of "four-step" aortic valve anatomic repair for regurgitant bicuspid aortic valve
Jun LI ; Zheng ZUO ; Hao LAI ; Lili DONG ; Kai ZHU ; Junyu ZHAI ; Yongxin SUN ; Wenjun DING ; Tao HONG ; Chunsheng WANG
Chinese Journal of Thoracic and Cardiovascular Surgery 2025;41(6):334-340
Objective:To explore the clinical efficacy of "four-step" aortic valve anatomic repair for bicuspid aortic valve(BAV) with aortic regurgitation(AR).Methods:From August 2021 to November 2024, a total of 298 consecutive patients with BAV-AR underwent aortic valve anatomic repair(AVr) in Shanghai Zhongshan Hospital Fudan University, 266 males and 32 females, with age of 39(29.5, 48.5) years. All patients underwent " four-step" three-dimensional anatomic repair of the aortic annulus and leaflets, 129(43.3%) patients via upper mini-sternotomy and 169(56.7%) patients via conventional median sternotomy, with the main steps including: (1) deep dissecting and annuloplasty of the virtual basal ring(VBR); (2) symmetrical repairing of leaflets; (3) replacement or remodeling of the sinus of Valsalva; (4) annuloplasty of the sinotubular junction(STJ). Basal and perioperative data were retrospectively collected, and statistical analysis was performed in conjunction with follow-up data.Results:All patients successfully underwent anatomical repair without transferring to valve replacement during operation. Among them, 43 patients underwent aortic root reimplantation technique(Reimplantation group), while 255 patients underwent modified aortic root sleeve remodeling technique(Sleeve group). The median cardiopulmonary bypass time for the Reimplantation and Sleeve groups were 154(134, 169) minutes and 111(95, 129) minutes, respectively( P<0.05); the median aortic cross-clamp time were 112(100, 131) minutes and 80(67, 94) minutes, respectively( P<0.05). Preoperative TEE showed 35 patients(81.4%) and 229 patients(89.8%) with moderate and severe AR in Reimplantation and Sleeve groups, respectively. Postoperative TEE showed 41 patients(95.3%) with no/trace AR and 2 patients(4.7%) with central mild AR in Reimplantation group, while 212 patients(83.1%) with no/trace AR and 43 patients(16.9%) with central mild AR in Sleeve group. Follow-up was completed in all patients, with a median follow-up of 12.9(4.7, 21.2) months. Echocardiography was obtained in 271 patients(90.9%) at the latest follow-up, including no/trace AR in 167 patients(56.0%), mild AR in 89 patients(29.9%), moderate AR in 14 patients(4.7%), and severe AR in 1 patient(0.3%). Conclusion:Aortic valve anatomic repair by standardized "four-step" approach is safe and reproducible. Satisfied short- and mid-term outcome have obtained in selected BAV-AR patients.
5.Therapeutic results of three-dimensional aortic valve anatomic repair for regurgitant bicuspid aortic valve
Jun LI ; Chunsheng WANG ; Zheng ZUO ; Hao LAI ; Lili DONG ; Kai ZHU ; Junyu ZHAI ; Yongxin SUN ; Wenjun DING ; Tao HONG
Chinese Journal of Surgery 2024;62(11):1024-1031
Objective:To explore the surgical technique and results of three-dimensional aortic valve anatomic repair for bicuspid aortic valve (BAV) with aortic regurgitation (AR).Methods:This is a retrospective case series study. From August 2021 to December 2023, 130 consecutive patients with BAV-AR underwent aortic valve anatomic repair at the Department of Cardiothoracic Surgery, Zhongshan Hospital, Fudan University,and the data were retrospectively analyzed. There were 115 males and 15 females, aged (38.6±11.7) years (range: 15 to 67 years). All patients received modified aortic root reconstruction, to do three-dimensional root remodeling, including the basal ring, sinus of Valsalva and sino-tubular junction simultaneously. Perioperative and follow-up data were collected and analyzed. Comparisons between groups were performed using independent samples t-test, Wilcoxon paired signed-rank test, or χ2 test. Results:No patient transferred to valve replacement during the operation. The cardiopulmonary bypass time ( M(IQR)) was 109(34) minutes (range:67 to 247 minutes), and the aortic cross-clamp time was 76(26) minutes (range: 32 to 158 minutes). Preoperative transesophageal echocardiography showed 123 patients (94.6%) presented with moderate or severe regurgitation. Immediately postoperative transesophageal echocardiography showed no regurgitation in 22 patients (16.9%), trace regurgitation in 81 patients (62.3%) and mild regurgitation in 27 patients (20.8%). Follow up was completed in all patients, with a follow-up of 5.5(9.4) months (range: 0.1 to 27.6 months). No mortality was observed during follow-up. Echocardiography was obtained in 112 patients at the latest follow-up, including no regurgitation in 4 patients (3.6%), trace regurgitation in 58 patients (51.8%), mild regurgitation in 45 patients (40.2%), moderate regurgitation in 4 patients (3.6%), and severe regurgitation in 1 patient (0.9%). Conclusion:For patients with BAV-AR who have good valve quality and no severe aortic sinus dilation, the recent outcomes of three-dimensional anatomical repair technique, focusing on overall remodeling of the aortic root, are satisfactory.
6.Therapeutic results of three-dimensional aortic valve anatomic repair for regurgitant bicuspid aortic valve
Jun LI ; Chunsheng WANG ; Zheng ZUO ; Hao LAI ; Lili DONG ; Kai ZHU ; Junyu ZHAI ; Yongxin SUN ; Wenjun DING ; Tao HONG
Chinese Journal of Surgery 2024;62(11):1024-1031
Objective:To explore the surgical technique and results of three-dimensional aortic valve anatomic repair for bicuspid aortic valve (BAV) with aortic regurgitation (AR).Methods:This is a retrospective case series study. From August 2021 to December 2023, 130 consecutive patients with BAV-AR underwent aortic valve anatomic repair at the Department of Cardiothoracic Surgery, Zhongshan Hospital, Fudan University,and the data were retrospectively analyzed. There were 115 males and 15 females, aged (38.6±11.7) years (range: 15 to 67 years). All patients received modified aortic root reconstruction, to do three-dimensional root remodeling, including the basal ring, sinus of Valsalva and sino-tubular junction simultaneously. Perioperative and follow-up data were collected and analyzed. Comparisons between groups were performed using independent samples t-test, Wilcoxon paired signed-rank test, or χ2 test. Results:No patient transferred to valve replacement during the operation. The cardiopulmonary bypass time ( M(IQR)) was 109(34) minutes (range:67 to 247 minutes), and the aortic cross-clamp time was 76(26) minutes (range: 32 to 158 minutes). Preoperative transesophageal echocardiography showed 123 patients (94.6%) presented with moderate or severe regurgitation. Immediately postoperative transesophageal echocardiography showed no regurgitation in 22 patients (16.9%), trace regurgitation in 81 patients (62.3%) and mild regurgitation in 27 patients (20.8%). Follow up was completed in all patients, with a follow-up of 5.5(9.4) months (range: 0.1 to 27.6 months). No mortality was observed during follow-up. Echocardiography was obtained in 112 patients at the latest follow-up, including no regurgitation in 4 patients (3.6%), trace regurgitation in 58 patients (51.8%), mild regurgitation in 45 patients (40.2%), moderate regurgitation in 4 patients (3.6%), and severe regurgitation in 1 patient (0.9%). Conclusion:For patients with BAV-AR who have good valve quality and no severe aortic sinus dilation, the recent outcomes of three-dimensional anatomical repair technique, focusing on overall remodeling of the aortic root, are satisfactory.
7.Immunometabolic rewiring in macrophages for periodontitis treatment via nanoquercetin-mediated leverage of glycolysis and OXPHOS.
Yi ZHANG ; Junyu SHI ; Jie ZHU ; Xinxin DING ; Jianxu WEI ; Xue JIANG ; Yijie YANG ; Xiaomeng ZHANG ; Yongzhuo HUANG ; Hongchang LAI
Acta Pharmaceutica Sinica B 2024;14(11):5026-5036
Periodontitis is a chronic inflammatory disease marked by a dysregulated immune microenvironment, posing formidable challenges for effective treatment. The disease is characterized by an altered glucose metabolism in macrophages, specifically an increase in aerobic glycolysis, which is linked to heightened inflammatory responses. This suggests that targeting macrophage metabolism could offer a new therapeutic avenue. In this study, we developed an immunometabolic intervention using quercetin (Q) encapsulated in bioadhesive mesoporous polydopamine (Q@MPDA) to treat periodontitis. Our results demonstrated that Q@MPDA could reprogram inflammatory macrophages to an anti-inflammatory phenotype (i.e., from-M1-to-M2 repolarization). In a murine periodontitis model, locally administered Q@MPDA reduced the presence of inflammatory macrophages, and decreased the levels of inflammatory cytokines (IL-1β and TNF-α) and reactive oxygen species (ROS) in the periodontium. Consequently, it alleviated periodontitis symptoms, reduced alveolar bone loss, and promoted tissue repair. Furthermore, our study revealed that Q@MPDA could inhibit the glycolysis of inflammatory macrophages while enhancing oxidative phosphorylation (OXPHOS), facilitating the shift from M1 to M2 macrophage subtype. Our findings suggest that Q@MPDA is a promising treatment for periodontitis via immunometabolic rewiring.
8.Systematic Review and Meta-Analysis of Efficacy and Safety of Linggui Zhugantang Combined with Conventional Drugs in Delaying Course of Heart Failure
Rui DING ; Peichao ZHU ; Jinling HUANG ; Junyu XI
Chinese Journal of Experimental Traditional Medical Formulae 2022;28(21):212-220
ObjectiveTo evaluate the efficacy and safety of Linggui Zhugantang in the treatment of heart failure. MethodCNKI,Wanfang Data,VIP,CBM,PubMed,ClinicalKey,Cochrane Library ,Web of Science ,Medline and Embase were systematically searched to screen randomized controlled trials(RCT)of Linggui Zhugantang in the treatment of heart failure. Meta-analysis was performed on the included studies using RevMan 5.3 ResultTwenty-seven studies were included with a total sample size of 3 569 cases,including 1 816 in experimental group and 1 753 in control group. Meta-analysis showed that compared with conventional drugs alone,combination of Linggui Zhugantang and conventional drugs improved the marked effective rate [relative risk(RR)=1.41,95% confidence interval(CI)[1.29,1.54],P<0.000 01] and the total effective rate(RR=1.21,95%CI[1.17,1.25],P<0.000 01),decreased the levels of serum B-type brain natriuretic peptide (BNP)[mean difference(MD)=-390.08,95%CI[-538.84,-241.52],P<0.000 01] and serum N-terminal pro-brain natriuretic peptide(NT-proBNP)(MD=-713.83,95%CI[-828.41, -599.25],P<0.000 01), left ventricular end-diastolic diameter(LVDD)(MD=-5.23,95%CI[-7.18, -3.29],P<0.000 01), left ventricular end-systolic diameter(LVSD)(MD=-4.54,95%CI[-6.75,-2.33],P<0.000 01), tumor necrosis factor-α(TNF-α)(MD=-37.53,95%CI [-50.72,-24.34],P<0.000 01)and interleukin-6(IL-6)(MD=-23.64,95%CI [-47.40,0.11],P=0.05), increased left ventricular ejection fraction(LVEF)(MD=5.73,95%CI [3.33,8.14],P<0.000 01),and cardiac output [stroke volume (SV) ](MD=5.90,95%CI[4.56,7.25],P<0.000 01). In addition, the combination prolonged the 6 minute walking test distance(MD=51.08,95%CI [33.01,69.16],P<0.000 01),reduced the traditional Chinese medicine (TCM) syndrome score(MD=-3.50,95%CI [-4.92,-2.07],P<0.000 01),and improved quality of life(MD=-7.26,95%CI [-10.43,-4.09],P<0.000 01),with higher safety(RR=0.36,95%CI [0.17,0.79],P=0.01). ConclusionLinggui Zhugantang combined with conventional drug therapy could improve cardiac function,reduce cardiac fibrosis,and improve prognosis, with high safety.
9.Antibacterial treatment scheme and risk factors of bloodstream infection with carbapenem-resistant Klebsiella pneumoniae
Changxin LIU ; Lin MA ; Kan ZHANG ; Hua GUO ; Junyu DING ; Bo WANG ; Xingang ZHANG ; Jiyong YANG ; Xizhou GUAN
Clinical Medicine of China 2021;37(6):547-554
Objective:To investigate the relationship between antibacterial treatment scheme and prognosis, and to analyze the mortality risk factors of bloodstream infection with carbapenem-resistant Klebsiella pneumoniae(CRKP).Methods:A retrospective case-control study was conducted. The CRKP isolated from clinical venous blood samples in the First Medical Center, Chinese PLA General Hospital between January 1, 2013 and December 31, 2018(not included from January 1, 2016 to December 31, 2017) was collected. According to relevant standards, a total of 50 patients with bloodstream infection with CRKP were included. The patients were divided into death (19 cases) or survival (31 cases) group according to their hospitalization outcomes, and clinical data and antibacterial treatment scheme after infection were collected. The clinical features of the two groups and the correlation between different antibacterial treatment regimens and prognosis were compared. Logistics regression model was used to analyze the risk factors for death in CRKP-infected patients.Results:The all-cause mortality rate of patients with CRKP bloodstream infection during hospitalization was 38%(19/50). The age ((66.89±18.13) vs. (55.06±14.39) years old, t=2.555, P=0.014), charlson's comorbidity index ((6.11±2.87) vs. (3.19±1.97), t=4.256, P<0.001) of the death group was higher than that of the survival group. The proportion of patients with chronic obstructive pulmonary disease (42.1%(8/19) vs. 3.2%(1/31), χ2=9.574, P=0.002), Charlson's comorbidity index ≥5 (68.4%(13/19) vs. 22.6%(7/31), χ2=10.314, P=0.001), septic shock (36.8%(7/19) vs. 6.5%(2/31), χ2=5.456, P=0.020), source of lung infection (36.8%(7/19) vs. 9.7%(3/31), χ2=3.868, P=0.049) was higher in death group than those in survival group. Kaplan-meier survival curve showed that the 30-day mortality of appropriate targeted treatment was lower than that of inappropriate targeted treatment ( χ2=8.138, P=0.004). Multivariate analysis showed that septic shock ( OR=56.363, 95% CI: 4.309-737.273, P=0.002) and charlson's comorbidity index ≥5 ( OR=18.605,95% CI: 1.813-190.896, P=0.014) were independent risk factors for mortality in patients with bloodstream CRKP infection. Conclusion:Appropriate targeted therapy can reduce 30-day mortality in patients with CRKP bloodstream infection. In order to reduce the risk of mortality, we should prevent the occurrence of septic shock and strengthen the diagnosis and treatment of patients with Chalson's comorbidity index ≥5.
10.RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
Wanfei LIU ; Shuangyang WU ; Qiang LIN ; Shenghan GAO ; Feng DING ; Xiaowei ZHANG ; Hasan Awad ALJOHI ; Jun YU ; Songnian HU
Genomics, Proteomics & Bioinformatics 2018;16(5):373-381
The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.
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High-Throughput Nucleotide Sequencing
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Sequence Analysis, DNA
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