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Sun L, Zhang S, Yu Z, Zheng X, Liang S, Ren H, Qi X. Transcription-Associated Metabolomic Analysis Reveals the Mechanism of Fruit Ripening during the Development of Chinese Bayberry. Int J Mol Sci 2024; 25:8654. [PMID: 39201345 PMCID: PMC11355050 DOI: 10.3390/ijms25168654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/04/2024] [Accepted: 08/04/2024] [Indexed: 09/02/2024] Open
Abstract
The ripening process of Chinese bayberries (Myrica rubra) is intricate, involving a multitude of molecular interactions. Here, we integrated transcriptomic and metabolomic analysis across three developmental stages of the Myrica rubra (M. rubra) to elucidate these processes. A differential gene expression analysis categorized the genes into four distinct groups based on their expression patterns. Gene ontology and pathway analyses highlighted processes such as cellular and metabolic processes, including protein and sucrose metabolism. A metabolomic analysis revealed significant variations in metabolite profiles, underscoring the dynamic interplay between genes and metabolites during ripening. Flavonoid biosynthesis and starch and sucrose metabolism were identified as key pathways, with specific genes and metabolites playing crucial roles. Our findings provide insights into the molecular mechanisms governing fruit ripening in M. rubra and offer potential targets for breeding strategies aimed at enhancing fruit quality.
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Affiliation(s)
- Li Sun
- Institute of Horticulture, State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.S.); (S.Z.); (Z.Y.); (X.Z.); (S.L.); (H.R.)
| | - Shuwen Zhang
- Institute of Horticulture, State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.S.); (S.Z.); (Z.Y.); (X.Z.); (S.L.); (H.R.)
| | - Zheping Yu
- Institute of Horticulture, State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.S.); (S.Z.); (Z.Y.); (X.Z.); (S.L.); (H.R.)
| | - Xiliang Zheng
- Institute of Horticulture, State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.S.); (S.Z.); (Z.Y.); (X.Z.); (S.L.); (H.R.)
| | - Senmiao Liang
- Institute of Horticulture, State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.S.); (S.Z.); (Z.Y.); (X.Z.); (S.L.); (H.R.)
| | - Haiying Ren
- Institute of Horticulture, State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.S.); (S.Z.); (Z.Y.); (X.Z.); (S.L.); (H.R.)
| | - Xingjiang Qi
- Institute of Horticulture, State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (L.S.); (S.Z.); (Z.Y.); (X.Z.); (S.L.); (H.R.)
- Xianghu Laboratory, Hangzhou 311231, China
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Liu Y, Wu W, Xiao Y, Zou H, Hao S, Jiang Y. Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients. Front Cell Infect Microbiol 2024; 14:1439472. [PMID: 39165919 PMCID: PMC11333343 DOI: 10.3389/fcimb.2024.1439472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/09/2024] [Indexed: 08/22/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale. Methods From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections. Results Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280). Conclusions Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.
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Affiliation(s)
- Yong Liu
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Wencai Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yunping Xiao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Hongyan Zou
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Sijia Hao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
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Han B, Li XM, Li R, Ning W, Zhang YY, Tang YF, Zhang Y, Hu L, Li JD, Liu G, Zhang D, Gu L, Xia H, Wang X, Jiang RM. Epidemiological surveillance of acute respiratory infections based on targeted metagenomic next generation sequencing during the flu season after COVID-19 pandemic in Beijing. J Infect 2024; 89:106188. [PMID: 38789013 DOI: 10.1016/j.jinf.2024.106188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/16/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Affiliation(s)
- Bing Han
- Diagnosis and Treatment Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xu-Ming Li
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Bejing 100176, China
| | - Ran Li
- Department of Infectious and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-yang Hospital, Capital Medical University, Beijing 100043, China
| | - Wu Ning
- Department of Infectious Diseases, Peking University Shougang Hospital, Beijing 100144, China
| | - Yuan-Yuan Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Yan-Fen Tang
- Diagnosis and Treatment Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Department of Respiratory, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Ye Zhang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Bejing 100176, China
| | - Long Hu
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Bejing 100176, China
| | - Jian-Dong Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Gang Liu
- Department of Infectious Diseases, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing 100045, China
| | - Dan Zhang
- Department of Infectious Diseases, Peking University Shougang Hospital, Beijing 100144, China
| | - Li Gu
- Department of Infectious and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-yang Hospital, Capital Medical University, Beijing 100043, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Bejing 100176, China
| | - Xi Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Institute of Infectious Diseases, Beijing 100015, China; National Center for Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
| | - Rong-Meng Jiang
- Diagnosis and Treatment Center of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China.
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Han D, Zhao X, Zhang D, Wang Z, Zhu Z, Sun H, Qu Z, Wang L, Liu Z, Zhu X, Yuan M. Genome-wide association studies reveal novel QTLs for agronomic traits in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1375646. [PMID: 38807775 PMCID: PMC11132100 DOI: 10.3389/fpls.2024.1375646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
Introduction Soybean, as a globally significant crop, has garnered substantial attention due to its agricultural importance. The utilization of molecular approaches to enhance grain yield in soybean has gained popularity. Methods In this study, we conducted a genome-wide association study (GWAS) using 156 Chinese soybean accessions over a two-year period. We employed the general linear model (GLM) and the mixed linear model (MLM) to analyze three agronomic traits: pod number, grain number, and grain weight. Results Our findings revealed significant associations between qgPNpP-98, qgGNpP-89 and qgHGW-85 QTLs and pod number, grain number, and grain weight, respectively. These QTLs were identified on chromosome 16, a region spanning 413171bp exhibited associations with all three traits. Discussion These QTL markers identified in this study hold potential for improving yield and agronomic traits through marker-assisted selection and genomic selection in breeding programs.
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Affiliation(s)
- Dongwei Han
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
- Heilongjiang Chinese Academy of Sciences Qiuying Zhang Soybean Scientist Studio, Qiqihar, Heilongjiang, China
| | - Xi Zhao
- Biotechnology Institute, Heilongjiang Academy of Agricultural Science, Harbin, Heilongjiang, China
| | - Di Zhang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhen Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhijia Zhu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Haoyue Sun
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhongcheng Qu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Lianxia Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhangxiong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu Zhu
- Department of Research and Development, Ruibiotech Co., Ltd, Beijing, China
| | - Ming Yuan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
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Bi M, Li M, Wei J, Meng Z, Wang Z, Ying M, Yang X, Huang L. Genome-scale cis-acting catabolite-responsive element editing confers Bacillus pumilus LG3145 plant-beneficial functions. iScience 2024; 27:108983. [PMID: 38357660 PMCID: PMC10864199 DOI: 10.1016/j.isci.2024.108983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/26/2023] [Accepted: 01/17/2024] [Indexed: 02/16/2024] Open
Abstract
Rhizosphere dwelling microorganism such as Bacillus spp. are helpful for crop growth. However, these functions are adversely affected by long-term synthetic fertilizer application. We developed a modified CRISPR/Cas9 system using non-specific single-guide RNAs to disrupt the genome-wide cis-acting catabolite-responsive elements (cres) in a wild-type Bacillus pumilus strain, which conferred dual plant-benefit properties. Most of the mutations occurred around imperfectly matched cis-acting elements (cre-like sites) in genes that are mainly involved in carbon and secondary metabolism pathways. The comparative metabolomics and transcriptome results revealed that carbon is likely transferred to some pigments, such as riboflavin, carotenoid, and lycopene, or non-ribosomal peptides, such as siderophore, surfactin, myxochelin, and bacilysin, through the pentose phosphate and amino acid metabolism pathways. Collectively, these findings suggested that the mutation of global cre-like sequences in the genome might alter carbon flow, thereby allowing beneficial biological interactions between the rhizobacteria and plants.
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Affiliation(s)
- Meiying Bi
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Mingkun Li
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Jiaxun Wei
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Ziwen Meng
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Zhaoyang Wang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Ming Ying
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
| | - Xiurong Yang
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300384, People’s Republic of China
| | - Lei Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, People’s Republic of China
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Gao Y, Zhang G, Jiang S, Liu Y. Wekemo Bioincloud: A user-friendly platform for meta-omics data analyses. IMETA 2024; 3:e175. [PMID: 38868508 PMCID: PMC10989175 DOI: 10.1002/imt2.175] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 06/14/2024]
Abstract
The increasing application of meta-omics approaches to investigate the structure, function, and intercellular interactions of microbial communities has led to a surge in available data. However, this abundance of human and environmental microbiome data has exposed new scalability challenges for existing bioinformatics tools. In response, we introduce Wekemo Bioincloud-a specialized platform for -omics studies. This platform offers a comprehensive analysis solution, specifically designed to alleviate the challenges of tool selection for users in the face of expanding data sets. As of now, Wekemo Bioincloud has been regularly equipped with 22 workflows and 65 visualization tools, establishing itself as a user-friendly and widely embraced platform for studying diverse data sets. Additionally, the platform enables the online modification of vector outputs, and the registration-independent personalized dashboard system ensures privacy and traceability. Wekemo Bioincloud is freely available at https://www.bioincloud.tech/.
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Affiliation(s)
- Yunyun Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Guoxing Zhang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Shunyao Jiang
- Shenzhen Wekemo Technology Group Co., Ltd.ShenzhenChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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