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He J, Yang Z, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Tian B, He Y, Wu Z, Cheng A, Zhu D. Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution. Virulence 2024; 15:2359467. [PMID: 38808732 PMCID: PMC11141479 DOI: 10.1080/21505594.2024.2359467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Pasteurella multocida (P. multocida) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in P. multocida and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced P. multocida genomes obtained by high-throughput sequencing together with 393 publicly available P. multocida genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in P. multocida, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICEHin1056 family, with the latter being widely prevalent in P. multocida and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene blaOXA-2 and the bleomycin gene bleO to P. multocida. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in P. multocida were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in P. multocida and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.
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Affiliation(s)
- Jiao He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Yu He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Zhen Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
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Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D'Costa VM. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter. Emerg Microbes Infect 2024; 13:2320929. [PMID: 38530969 DOI: 10.1080/22221751.2024.2320929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.
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Affiliation(s)
- Farah Nasser
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Avery Gaudreau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Shareefah Lubega
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
| | - Arvin Zaker
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Xuhua Xia
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Arvind S Mer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Vanessa M D'Costa
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, Canada
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3
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Zhao J, Pu D, Li Z, Zhang Y, Liu X, Zhuo X, Lu B, Cao B. Loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing K1-ST23 hypervirulent Klebsiella pneumoniae. Virulence 2024; 15:2348251. [PMID: 38697754 PMCID: PMC11067985 DOI: 10.1080/21505594.2024.2348251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVES This study aimed at revealing the underlying mechanisms of the loss and gain of ceftazidime-avibactam susceptibility in a non-carbapenemase-producing hypervirulent Klebsiella pneumoniae (hvKp). METHODS Here we longitudinally recovered 3 non-carbapenemase-producing K1-ST23 hvKp strains at a one-month interval (KP29105, KP29499 and KP30086) from an elderly male. Antimicrobial susceptibility testing, whole genome sequencing, transcriptomic sequencing, gene cloning, plasmid conjugation, quantitative real-time PCR (qRT-PCR), and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) were conducted. RESULTS Among the 3 hvKp strains, KP29105 was resistant to the third- and fourth-generation cephalosporins, KP29499 acquired resistance to both ceftazidime-avibactam and carbapenems, while KP30086 restored its susceptibility to ceftazidime-avibactam, imipenem and meropenem but retained low-level resistance to ertapenem. KP29105 and KP29499 carried plasmid-encoded genes blaCTX-M-15 and blaCTX-M-71, respectively, but KP30086 lost both. Cloning of gene blaCTX-M-71 and conjugation experiment of blaCTX-M-71-carrying plasmid showed that the transformant and transconjugant were susceptible to ceftazidime-avibactam but had a more than 8-fold increase in MICs. Supplementation with an outer membrane permeabilizer could reduce the MIC of ceftazidime-avibactam by 32 folds, indicating that porins play a key role in ceftazidime-avibactam resistance. The OmpK35 of the 3 isolates was not expressed, and the OmpK36 of KP29499 and KP30086 had a novel amino acid substitution (L359R). SDS-PAGE and qRT-PCR showed that the expression of porin OmpK36 of KP29499 and KP30086 was significantly down-regulated compared with KP29105. CONCLUSIONS In summary, we reported the rare ceftazidime-avibactam resistance in a non-carbapenemase-producing hvKp strain. Resistance plasmid carrying blaCTX-M-71 and mutated OmpK36 had a synergetic effect on the resistance.
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Affiliation(s)
- Jiankang Zhao
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Danni Pu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ziyao Li
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Yulin Zhang
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xinmeng Liu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xianxia Zhuo
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Department of Respiratory Medicine, Capital Medical University, Beijing, China
| | - Binghuai Lu
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Cao
- National Center for Respiratory Medicine, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Beijing, China
- National Clinical Research Center for Respiratory Diseases, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Department of Respiratory Medicine, Capital Medical University, Beijing, China
- Tsinghua University-Peaking University Joint Center for Life Sciences, Beijing, China
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4
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Jarocki VM, Li D, Bogema DR, Yam J, Jenkins C, Hai FI, Djordjevic SP. Comparative genomic analysis of ESBL-selected and non-selected Escherichia coli in Australian wastewater: Elucidating differences in diversity, antimicrobial resistance, and virulence profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175079. [PMID: 39094658 DOI: 10.1016/j.scitotenv.2024.175079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/07/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Extended-spectrum β-lactamases (ESBLs)-producing E. coli have been proposed as an indicator bacterium for antimicrobial resistance (AMR) surveillance within a OneHealth framework. However, it is important to understand the effects and potential biases ESBL-selection has on E. coli populations. Utilising whole genome sequencing, this study compared 80 ESBL-selected E. coli isolates with 201 non-selected isolates from Australian wastewater. The findings revealed significant variations between these cohorts in genetic diversity, AMR profiles, and carriage of virulence-associated genes (VAGs), plasmids, and the transmissible Locus of Stress Tolerance (tLST), a genomic island that imparts resistance to extreme heat and chlorination. The study highlights the predominance of certain sequence types (STs), particularly ST131 (75 % clade A), in ESBL-selected isolates (40 % vs 2 %) and overall the ESBL-selected isolates were largely multidrug-resistant (MDR), predominantly carrying genes for resistance to aminoglycosides, extended-spectrum β-lactams, fluoroquinolone, macrolides, sulphonamides/trimethoprim, and tetracyclines. The ESBLs identified were almost exclusively blaCTX-M genes, most commonly blaCTX-M-15 > blaCTX-M-27 > blaCTX-M-14. These were predominately carried on IncF plasmids or chromosomally (always ISEcp1 associated), in equal numbers. In contrast, 80 % of non-selected isolates carried no acquired ARGs, and none carried blaCTX-M genes. In both cohorts, extraintestinal pathogenic E. coli (ExPEC) was the dominate pathotype (35 % total) with few (4 % total) intestinal pathogenic E. coli pathotypes identified (aEPEC > ETEC > EAEC). Nevertheless, some clinically important genes were only identified in the non-selected group, namely tigecycline-resistance gene tet(X4) and AmpC ESBL blaCMY-2. Additionally, the presence of tLST, associated with higher metal resistance gene carriage (Ag, As, Cu, Hg, Ni), in a substantial portion of non-selected isolates (20 % vs 0 %), underscores environmental pressures shaping bacterial populations in wastewater ecosystems. These insights are important for developing comprehensive, less biased genomic surveillance strategies to understand and manage public health threats posed by pathogenic E. coli and AMR.
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Affiliation(s)
- Veronica M Jarocki
- Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia; Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food and Environment (CRC SAAFE), South Australia, Australia.
| | - Dmitriy Li
- Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Daniel R Bogema
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia; Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, NSW, Australia
| | - Jerald Yam
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, NSW, Australia
| | - Cheryl Jenkins
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia; Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, NSW, Australia
| | - Faisal I Hai
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, NSW, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia.
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5
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Wade KJ, Suseno R, Kizer K, Williams J, Boquett J, Caillier S, Pollock NR, Renschen A, Santaniello A, Oksenberg JR, Norman PJ, Augusto DG, Hollenbach JA. MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge. Genome Biol 2024; 25:274. [PMID: 39420419 DOI: 10.1186/s13059-024-03412-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 09/30/2024] [Indexed: 10/19/2024] Open
Abstract
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short-read, de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target capture short-read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short-read data. MHConstructor facilitates wide-spread access to high-quality, alignment-free MHC sequence analysis.
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Affiliation(s)
- Kristen J Wade
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Rayo Suseno
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Kerry Kizer
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline Williams
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Juliano Boquett
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Stacy Caillier
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas R Pollock
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
| | - Adam Renschen
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Adam Santaniello
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jorge R Oksenberg
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Paul J Norman
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
| | - Danillo G Augusto
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.
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6
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Tourrette E, Torres RC, Svensson SL, Matsumoto T, Miftahussurur M, Fauzia KA, Alfaray RI, Vilaichone RK, Tuan VP, Wang D, Yadegar A, Olsson LM, Zhou Z, Yamaoka Y, Thorell K, Falush D. An ancient ecospecies of Helicobacter pylori. Nature 2024:10.1038/s41586-024-07991-z. [PMID: 39415013 DOI: 10.1038/s41586-024-07991-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/23/2024] [Indexed: 10/18/2024]
Abstract
Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer1,2. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation1. Here we identify a 'Hardy' ecospecies of H. pylori that shares the ancestry of 'Ubiquitous' H. pylori from the same region in most of the genome but has nearly fixed single-nucleotide polymorphism differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. Most Hardy strains have a second urease, which uses iron as a cofactor rather than nickel3, and two additional copies of the vacuolating cytotoxin VacA. Hardy strains currently have a limited distribution, including in Indigenous populations in Siberia and the Americas and in lineages that have jumped from humans to other mammals. Analysis of polymorphism data implies that Hardy and Ubiquitous coexisted in the stomachs of modern humans since before we left Africa and that both were dispersed around the world by our migrations. Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains.
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Affiliation(s)
- Elise Tourrette
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Roberto C Torres
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Sarah L Svensson
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | | | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Universitas Airlangga, Surabaya, Indonesia
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Universitas Airlangga, Surabaya, Indonesia
| | - Ratha-Korn Vilaichone
- Gastroenterology Unit, Department of Medicine and Center of Excellence in Digestive Diseases, Thammasat University, Bangkok, Thailand
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
- Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Difei Wang
- Cancer Genomics Research Lab, Frederick National Lab for Cancer Research, Rockville, MD, USA
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Lisa M Olsson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Zhemin Zhou
- Pasteurien College, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan.
- Universitas Airlangga, Surabaya, Indonesia.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
- Research center for global and local infectious diseases, Oita University, Yufu, Japan.
| | - Kaisa Thorell
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden.
| | - Daniel Falush
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
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7
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Wennmann JT, Senger S, Ruoff B, Jehle JA, Suraporn S. Distribution and genetic diversity of Bombyx mori nucleopolyhedrovirus in mass-reared silkworms in Thailand. J Invertebr Pathol 2024:108221. [PMID: 39413965 DOI: 10.1016/j.jip.2024.108221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 10/07/2024] [Accepted: 10/10/2024] [Indexed: 10/18/2024]
Abstract
Silk is an economically and culturally important product of Thailand that is threatened by the outbreaks of the Bombyx mori nucleopolyhedrovirus (BmNPV) in silkworm rearings. BmNPV infects the larval stages of the silkworm Bombyx mori, causing fatal viral infection and preventing the larvae from reaching the pupal stage. Numerous BmNPV isolates have been described from silk producing countries from all over the world. In this study, the geographic distribution of BmNPV in Thailand was analyzed by collecting 18 samples from different regions. The BmNPV samples were analyzed by PCR and whole genome sequencing was performed for eight specimens. Their genome size ranged from 125,888 bp to 126,783 bp, comprising 138 open reading frames. Although the sequenced BmNPV genomes could be phylogenetically differentiated, a correlation between geographic and genetic distance was not observed indicating a close relationship between the BmNPV from Thailand.
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Affiliation(s)
- Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany.
| | - Sergei Senger
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Birgit Ruoff
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Siripuk Suraporn
- Department of Biology, Faculty of Science, Mahasarakham University, Kantharawichai District, Maha Sarakham 44150, Thailand.
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8
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Manikandan R, Rajagunalan S, Malmarugan S, Gupta C. First report on whole genome sequencing and comparative genomics of Salmonella enterica serovar Abortusequi isolated from Donkey in India. Sci Rep 2024; 14:23455. [PMID: 39379477 PMCID: PMC11461527 DOI: 10.1038/s41598-024-73904-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 09/23/2024] [Indexed: 10/10/2024] Open
Abstract
Salmonella enterica subspecies enterica serovar Abortusequi (S. Abortusequi) is a leading cause of abortion in equines that hinders the rapid growth of equine industry. S. Abortusequi infection in equids has re-emerged over last ten years. In the present study, S. Abortusequi was isolated and characterized from donkeys during an abortion storm in the southern peninsular region of India. Further, whole genome sequencing and phylogenomic analysis revealed that the present isolate was clustered among S. Abortusequi clade. The core genome MLST (cgMLST) analysis based on hierarchical clustering and single nucleotide polymorphism (SNP) core-genome dendrogram of the present isolate against 10 S. Abortusequi isolates revealed that the present isolate established a distinct clade compared to all previously reported isolates. A comparison of cgMLST and SNP analyses revealed the same clustering concordance between isolates. In addition, comparative genomics and phylogenetic analysis was carried out with six S. Abortusequi serovars showed a higher number of core genes than accessory genes. Further, comparative analysis of phenotype and genotype antimicrobial resistance revealed a concordance of 32% and discordance of 68% respectively.
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Affiliation(s)
- Rajendran Manikandan
- Tamil Nadu Veterinary and Animal Sciences University, Veterinary College and Research Institute, Tirunelveli, 627358, Tamil Nadu, India.
- Department of Veterinary Microbiology, Tamil Nadu Veterinary and Animal Sciences University, Veterinary College and Research Institute, Tirunelveli, 627358, Tamil Nadu, India.
| | - Sithanandam Rajagunalan
- Tamil Nadu Veterinary and Animal Sciences University, Veterinary College and Research Institute, Tirunelveli, 627358, Tamil Nadu, India
| | - Shanmugasamy Malmarugan
- Tamil Nadu Veterinary and Animal Sciences University, Veterinary College and Research Institute, Tirunelveli, 627358, Tamil Nadu, India
| | - Chhavi Gupta
- Tamil Nadu Veterinary and Animal Sciences University, Veterinary College and Research Institute, Tirunelveli, 627358, Tamil Nadu, India
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9
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Kosmopoulos JC, Klier KM, Langwig MV, Tran PQ, Anantharaman K. Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology. MICROBIOME 2024; 12:195. [PMID: 39375774 PMCID: PMC11460016 DOI: 10.1186/s40168-024-01905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 08/12/2024] [Indexed: 10/09/2024]
Abstract
BACKGROUND Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied. RESULTS Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. CONCLUSIONS Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract.
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Affiliation(s)
- James C Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine M Klier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Sciences Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Marguerite V Langwig
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Sciences Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Data Science and AI, Wadhwani School of Data Science and AI, Indian Institute of Technology Madras, Chennai, India.
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10
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Kawaichi S, Kotoky R, Fiutowski J, Rotaru AE. Adaptation of a methanogen to Fe 0 corrosion via direct contact. NPJ Biofilms Microbiomes 2024; 10:100. [PMID: 39366964 PMCID: PMC11452385 DOI: 10.1038/s41522-024-00574-w] [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: 03/16/2024] [Accepted: 09/22/2024] [Indexed: 10/06/2024] Open
Abstract
Due to unique genomic adaptations, Methanococcus maripaludis Mic1c10 is highly corrosive when in direct contact with Fe0. A critical adaptation involves increased glycosylation of an extracellular [NiFe]-hydrogenase, facilitating its anchoring to cell surface proteins. Corrosive strains adapt to the constructed environment via horizontal gene transfer while retaining ancestral genes important for intraspecies competition and surface attachment. This calls for a reevaluation of how the built environment impacts methane cycling.
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Affiliation(s)
- Satoshi Kawaichi
- Department of Biology, University of Southern Denmark, Odense, Denmark.
| | - Rhitu Kotoky
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Jacek Fiutowski
- NanoSYD, Mads Clausen Institute, University of Southern Denmark, Sønderborg, Denmark
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11
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Stark GF, Truchon AR, Wilhelm SW. Mobilome impacts on physiology in the widely used non-toxic mutant Microcystis aeruginosa PCC 7806 ΔmcyB and toxic wildtype. BMC Genomics 2024; 25:922. [PMID: 39363260 PMCID: PMC11448079 DOI: 10.1186/s12864-024-10839-5] [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: 05/21/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024] Open
Abstract
The Microcystis mobilome is a well-known but understudied component of this bloom-forming cyanobacterium. Through genomic and transcriptomic comparisons, we found five families of transposases that altered the expression of genes in the well-studied toxigenic type-strain, Microcystis aeruginosa PCC 7086, and a non-toxigenic genetic mutant, Microcystis aeruginosa PCC 7806 ΔmcyB. Since its creation in 1997, the ΔmcyB strain has been used in comparative physiology studies against the wildtype strain by research labs throughout the world. Some differences in gene expression between what were thought to be otherwise genetically identical strains have appeared due to insertion events in both intra- and intergenic regions. In our ΔmcyB isolate, a sulfate transporter gene cluster (sbp-cysTWA) showed differential expression from the wildtype, which may have been caused by the insertion of a miniature inverted repeat transposable element (MITE) in the sulfate-binding protein gene (sbp). Differences in growth in sulfate-limited media also were also observed between the two isolates. This paper highlights how Microcystis strains continue to "evolve" in lab conditions and illustrates the importance of insertion sequences / transposable elements in shaping genomic and physiological differences between Microcystis strains thought otherwise identical. This study forces the necessity of knowing the complete genetic background of isolates in comparative physiological experiments, to facilitate the correct conclusions (and caveats) from experiments.
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Affiliation(s)
- Gwendolyn F Stark
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Alexander R Truchon
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN, USA.
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12
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Luo Y, Payne M, Kaur S, Octavia S, Lan R. Genomic evidence of two-staged transmission of the early seventh cholera pandemic. Nat Commun 2024; 15:8504. [PMID: 39353924 PMCID: PMC11445481 DOI: 10.1038/s41467-024-52800-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 09/19/2024] [Indexed: 10/03/2024] Open
Abstract
The seventh cholera pandemic started in 1961 in Indonesia and spread across the world in three waves in the decades that followed. Here, we utilised genomic evidence to detail the first wave of the seventh pandemic. Genomes of 22 seventh pandemic Vibrio cholerae isolates from 1961 to 1979 were completely sequenced. Together with 152 publicly available genomes from the same period, they fell into seven phylogenetic clusters (CL1-CL7). By multilevel genome typing (MGT), all were assigned to MGT2 ST1 (Wave 1) except three isolates in CL7 which were typed as MGT2 ST2 (Wave 2). The Wave 1 seventh pandemic expanded in two stages, with Stage 1 (CL1-CL5) spread across Asia and Stage 2 (CL6 and CL7) spread to the Middle East and Africa. Three non-synonymous mutations, one each, in three regulatory genes, csrD (global regulator), acfB (chemotaxis), and luxO (quorum sensing) may have critically contributed to its pandemicity. The three MGT2 ST2 isolates in CL7 were the progenitors of Wave 2 and evolved from within Wave 1 with acquisition of a novel IncA/C plasmid. Our findings provide new insight into the evolution and transmission of the early seventh pandemic, which may aid future cholera prevention and control.
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Affiliation(s)
- Yun Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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13
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Bartlett KV, Luo TL, Ong AC, Maybank RA, Stribling W, Thompson B, Powell A, Kwak YI, Bennett JW, Lebreton F, Mc Gann PT. Tn 4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa. Microb Genom 2024; 10:001303. [PMID: 39412865 PMCID: PMC11482538 DOI: 10.1099/mgen.0.001303] [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: 07/02/2024] [Accepted: 09/11/2024] [Indexed: 10/18/2024] Open
Abstract
Carriage of CTX-M-type extended-spectrum β-lactamase (ESBL) is rare in Pseudomonas aeruginosa. During routine surveillance of an endemic ST-621 P. aeruginosa at a large hospital, isolate MRSN 100690 carrying bla CTX-M-15 was cultured from a patient (P2). This was the first detection of this ESBL in the endemic ST-621 lineage. All 1 488 bacterial isolates collected from the same facility in the 12 months prior to the incidence of 100 690 were screened for the presence of bla CTX-M-15. A set of 183 isolates was identified, in which corresponding patient metadata was evaluated for spatiotemporal overlaps with P2. The resulting three isolates, along with 100 690, were long-read sequenced using the Oxford Nanopore MinION platform to determine a potential donor of bla CTX-M-15. The screen revealed a single Klebsiella michiganensis isolate, MRSN 895358, which carried an IncA/C2 plasmid harbouring bla CTX-M-15. Notably, the patient harbouring 895358, P1, occupied the same hospital room as P2 9 months prior. Genomic alignment revealed that both isolates shared an identical 80.8 kb region containing the IncA/C2 plasmid replicon and bla CTX-M-15. This region was plasmid bound in 895 358, but chromosomally bound in 100 690 due to Tn4661-mediated transposition. ESBL bla CTX-M-15 was acquired and subsequently integrated into the chromosome of a ST-621 P. aeruginosa, likely initiated by plasmid transfer from a K. michiganensis strain.
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Affiliation(s)
- Katelyn V. Bartlett
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ting L. Luo
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ana C. Ong
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Rosslyn A. Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - William Stribling
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Bernadette Thompson
- Infection Prevention & Control, Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston, Texas, USA
| | - Aubrey Powell
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Department of Pathology, Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston, Texas, USA
| | - Yoon I. Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jason W. Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Patrick T. Mc Gann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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14
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Westerström P, Gabrielsen Ås C, Bak Dragsted U. Characterising virulence in a nontoxigenic non-O1/non-O139 Vibrio cholerae isolate imported from Vietnam. Heliyon 2024; 10:e37205. [PMID: 39309771 PMCID: PMC11416250 DOI: 10.1016/j.heliyon.2024.e37205] [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: 03/14/2023] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/25/2024] Open
Abstract
Vibrio cholerae is a major human pathogen that can cause life-threatening acute diarrhea. V. cholerae are classified according to O-antigen polysaccharide outer membrane properties, where the serotypes O1 and O139 are strains that cause pandemics and epidemics while non-O1/non-O139 usually cause mild disease. The dynamic evolution of V. cholerae involves acquisition of new virulence factors through horizontal gene transfer and formerly nontoxigenic serogroups are increasingly being reported to cause severe forms of human disease. In this study we have serotyped one isolate (ST588-CPH) of imported V. cholerae from Vietnam to Denmark and performed whole genome sequencing to identify known virulence genes and furthermore studied the pattern of virulence in closely related pathogenic strains of V. cholerae. ST558-CPH was found to be a non-O1/non-O139 strain. Initial analysis from the whole genome sequencing gave a 96,6 % match to the O139-specific wbfZ gene, but in a second analysis with a higher identification threshold, the wbfZ gene was absent. We suggest a "de novo" display of a database misannotation, which explains the conflicting results. The MLST analysis revealed that the isolate belongs to the nontoxigenic non-O1/non-O139 sequence type ST558. ST558 has recently been reported as a sequence type forming a cluster of ST's that should be monitored, as it has shown to have virulence causing moderate to severe illness. Our analysis of virulence genes identified MakA, a recently discovered toxin, which seems to be generally present in both toxigenic and nontoxigenic strains.
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Affiliation(s)
- Pontus Westerström
- Department of Medical Microbiology, Clinic of Laboratory Medicine, St. Olavs University Hospital, Trondheim, Norway
| | - Christina Gabrielsen Ås
- Department of Medical Microbiology, Clinic of Laboratory Medicine, St. Olavs University Hospital, Trondheim, Norway
| | - Ulrik Bak Dragsted
- Department for Multimorbidity, North Zealand Hospital, Hilleroed, Denmark
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15
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Cheng M, Xu Y, Cui X, Wei X, Chang Y, Xu J, Lei C, Xue L, Zheng Y, Wang Z, Huang L, Zheng M, Luo H, Leng Y, Jiang C. Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness. Nat Commun 2024; 15:8361. [PMID: 39333527 PMCID: PMC11436904 DOI: 10.1038/s41467-024-52713-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 09/18/2024] [Indexed: 09/29/2024] Open
Abstract
The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.
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Affiliation(s)
- Minghui Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Yingjie Xu
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Xiao Cui
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
| | - Yundi Chang
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Jun Xu
- Department of Critical Care Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Lei Xue
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China
| | - Yifan Zheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China
| | - Zhang Wang
- School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Lingtong Huang
- Department of Critical Care Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Yuxin Leng
- Department of Intensive Care Unit, Peking University Third Hospital, 49 North Garden Road, Haidian District, Beijing, 100191, China.
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310030, China.
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, 321000, China.
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Li H, Abdullah, Yang H, Guo H, Yuan Y, Ahmed I, Li G, Wang Y, Chang Y, Tian X. Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding. Gene 2024; 933:148959. [PMID: 39326472 DOI: 10.1016/j.gene.2024.148959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 09/07/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024]
Abstract
Berberidis Radix (Sankezhen), a typical multi-origin Chinese medicinal material, originates from the dried roots of plants of the Berberis genus and is used to treat various ailments. These species have similar morphologies, potentially leading to misidentifications that can impact medicine efficacy. Therefore, developing suitable molecular markers to identify medicinal species is imperative. Furthermore, discrepancies exist in the taxonomy of the Berberis genus. In the present study, we de novo assembled the chloroplast genomes of six Berberis species (Berberis woomungensis C. Y. Wu, Berberis pruinosa Franch., Berberis thunbergii DC., Berberis chinensis Poir., Berberis wilsoniae Hemsl., and Berberis sp.) that commonly constitute Berberidis Radix and compared them with previously reported genomes. Our comparative analysis revealed similarities in genome structure, relative synonymous codon usage, amino acid frequency, repeats, and substitutions. Higher synonymous substitutions, indicative of predominant purifying selection on protein-coding genes, were observed compared to non-synonymous substitutions. However, positive selection was identified in six genes across 29 Berberis species-accD, matK, ndhD, rbcL, ycf1, and ycf2-highlighting their potential roles in adaptive responses to specific environmental conditions within the genus. Inverted repeats expansion and contraction affected the rate of mutations and were associated with the phylogenetic classification of Berberis. Our phylogenetic analysis supported the division of the Berberis complex into four genera, which corroborates previous studies involving extensive sampling. We identified the ndhD-ccsA region as the most polymorphic region and applied this region to Chinese patent medicines containing Berberidis Radix through metabarcoding. The metabarcoding analysis confirmed that five Berberis species commonly constitute Berberidis Radix in Chinese patent medicines. In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, metabarcoding provides insight into the species composition of Berberidis Radix in Chinese patent medicines.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Abdullah
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Hongxia Yang
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Hua Guo
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Ye Yuan
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan; Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Guohui Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Wang
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Yanxu Chang
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Chinese Medicine Modernization, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
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17
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Edelmann MP, Couperus S, Rodríguez-Robles E, Rivollier J, Roberts TM, Panke S, Marlière P. Evolving Escherichia coli to use a tRNA with a non-canonical fold as an adaptor of the genetic code. Nucleic Acids Res 2024:gkae806. [PMID: 39315692 DOI: 10.1093/nar/gkae806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/08/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024] Open
Abstract
All known bacterial tRNAs adopt the canonical cloverleaf 2D and L-shaped 3D structures. We aimed to explore whether alternative tRNA structures could be introduced in bacterial translation. To this end, we crafted a vitamin-based genetic system to evolve Escherichia coli toward activity of structurally non-canonical tRNAs. The system reliably couples (escape frequency <10-12) growth with the activities of a novel orthogonal histidine suppressor tRNA (HisTUAC) and of the cognate ARS (HisS) via suppression of a GTA valine codon in the mRNA of an enzyme in thiamine biosynthesis (ThiN). Suppression results in the introduction of an essential histidine and thereby confers thiamine prototrophy. We then replaced HisTUAC in the system with non-canonical suppressor tRNAs and selected for growth. A strain evolved to utilize mini HisT, a tRNA lacking the D-arm, and we identified the responsible mutation in an RNase gene (pnp) involved in tRNA degradation. This indicated that HisS, the ribosome, and EF-Tu accept mini HisT ab initio, which we confirmed genetically and through in vitro translation experiments. Our results reveal a previously unknown flexibility of the bacterial translation machinery for the accepted fold of the adaptor of the genetic code and demonstrate the power of the vitamin-based suppression system.
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Affiliation(s)
- Martin P Edelmann
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Sietse Couperus
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Emilio Rodríguez-Robles
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Julie Rivollier
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 75002 Paris, France
| | - Tania M Roberts
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zurich, 4056 Basel, Switzerland
| | - Philippe Marlière
- TESSSI, The European Syndicate of Synthetic Scientists and Industrialists, 75002 Paris, France
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Zhang Y, Zhang J, Chen Z, Huang Y, Liu J, Liu Y, Yang Y, Jin X, Yang Y, Chen Y. Comparison of organelle genomes between endangered mangrove plant Dolichandrone spathacea to terrestrial relative provides insights into its origin and adaptative evolution. FRONTIERS IN PLANT SCIENCE 2024; 15:1442178. [PMID: 39376234 PMCID: PMC11457174 DOI: 10.3389/fpls.2024.1442178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 09/02/2024] [Indexed: 10/09/2024]
Abstract
Dolichandrone spathacea is a mangrove associate with high medicinal and ecological values. However, due to the dual-pressure of climate change and human activities, D. spathacea has become endangered in China. Moreover, misidentification between D. spathacea and its terrestrial relative D. cauda-felina poses further challenges to field protection and proper medicinal usage of D. spathacea. Thus, to address these problems, we sequenced and assembled mitochondrial (mt) and chloroplast (cp) genomes for both D. spathacea and D. cauda-felina. Comparative analysis revealed apparently different size and scaffold number between the two mt genomes, but a high similarity between the cp genomes. Eight regions with high sequence divergence were identified between the two cp genomes, which might be used for developing candidate DNA markers for distinguishing the two species. The splitting between D. spathacea and D. cauda-felina was inferred to occur at ~6.8 - 7.7 million years ago (Mya), which may be driven by the environment fluctuations in late Miocene. In the cp genome, 12 genes related to the expression of photosynthesis-associated proteins were detected with signatures of positive selection, which may contribute to the origin and evolutionary adaptation of Dolichandrone mangrove species. These new findings do not only enrich organelle genomic resources of Dolichandrone species, but also provide important genetic clues for improving the conservation and proper usage of endangered mangrove associate D. spathacea.
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Affiliation(s)
- Ying Zhang
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Zewei Chen
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Yanni Huang
- Mangrove Rare and Endangered Species Protection and Utilization Engineering Technology Research Center, Zhanjiang Key Laboratory of Mangrove Ecosystem Protection and Restoration, Lingnan Normal University, Zhanjiang, China
| | - Jiaxuan Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuqi Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yong Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Xiang Jin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yiqing Chen
- Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China
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19
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Martineau M, Ambroset C, Lefebvre S, Kokabi É, Léon A, Tardy F. Unravelling the main genomic features of Mycoplasma equirhinis. BMC Genomics 2024; 25:886. [PMID: 39304803 DOI: 10.1186/s12864-024-10789-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 09/10/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Mycoplasma spp. are wall-less bacteria with small genomes (usually 0.5-1.5 Mb). Many Mycoplasma (M.) species are known to colonize the respiratory tract of both humans and livestock animals, where they act as primary pathogens or opportunists. M. equirhinis was described for the first time in 1975 in horses but has been poorly studied since, despite regular reports of around 14% prevalence in equine respiratory disorders. We recently showed that M. equirhinis is not a primary pathogen but could play a role in co-infections of the respiratory tract. This study was a set up to propose the first genomic characterization to better our understanding of the M. equirhinis species. RESULTS Four circularized genomes, two of which were generated here, were compared in terms of synteny, gene content, and specific features associated with virulence or genome plasticity. An additional 20 scaffold-level genomes were used to analyse intra-species diversity through a pangenome phylogenetic approach. The M. equirhinis species showed consistent genomic homogeneity, pointing to potential clonality of isolates despite their varied geographical origins (UK, Japan and various places in France). Three different classes of mobile genetic elements have been detected: insertion sequences related to the IS1634 family, a putative prophage related to M. arthritidis and integrative conjugative elements related to M. arginini. The core genome harbours the typical putative virulence-associated genes of mycoplasmas mainly involved in cytoadherence and immune escape. CONCLUSION M. equirhinis is a highly syntenic, homogeneous species with a limited repertoire of mobile genetic elements and putative virulence genes.
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Affiliation(s)
- Matthieu Martineau
- Research Department, LABÉO, Saint-Contest, Caen, F-14000, France
- University of Caen Normandie, University of Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, Caen, F-14000, France
- University of Lyon, Anses, VetAgro Sup, UMR Animal Mycoplasmosis, Lyon, F-69007, France
| | - Chloé Ambroset
- University of Lyon, Anses, VetAgro Sup, UMR Animal Mycoplasmosis, Lyon, F-69007, France
| | - Stéphanie Lefebvre
- University of Lyon, Anses, VetAgro Sup, UMR Animal Mycoplasmosis, Lyon, F-69007, France
| | - Éléna Kokabi
- Research Department, LABÉO, Saint-Contest, Caen, F-14000, France
- University of Caen Normandie, University of Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - Albertine Léon
- Research Department, LABÉO, Saint-Contest, Caen, F-14000, France
- University of Caen Normandie, University of Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, Caen, F-14000, France
| | - Florence Tardy
- University of Lyon, Anses, VetAgro Sup, UMR Animal Mycoplasmosis, Lyon, F-69007, France.
- Anses, Ploufragan-Plouzané-Niort Laboratory-Mycoplasmology, Bacteriology and Antimicrobial, Resistance Unit, Ploufragan, F-22440, France.
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20
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Rana R, Nayak PK, Madhavan VN, Sonti RV, Patel HK, Patil PB. Comparative genomics-based insights into Xanthomonas indica, a non-pathogenic species of healthy rice microbiome with bioprotection function. Appl Environ Microbiol 2024; 90:e0084824. [PMID: 39158313 PMCID: PMC11409687 DOI: 10.1128/aem.00848-24] [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: 05/01/2024] [Accepted: 07/02/2024] [Indexed: 08/20/2024] Open
Abstract
Xanthomonas species are major pathogens of plants and have been studied extensively. There is increasing recognition of the importance of non-pathogenic species within the same genus. With this came the need to understand the genomic and functional diversity of non-pathogenic Xanthomonas (NPX) at the species and strain level. This study reports isolation and investigation into the genomic diversity and variation in NPX isolates, chiefly Xanthomonas indica, a newly discovered NPX species from rice. The study establishes the relationship of X. indica strains within clade I of Xanthomonads with another NPX species, X. sontii, also associated with rice seeds. Identification of highly diverse strains, open-pan genome, and systematic hyper-variation at the lipopolysaccharide biosynthetic locus when compared to pathogenic Xanthomonas indicates the acquisition of new functions for adaptation. Furthermore, comparative genomics studies established the absence of major virulence genes such as type III secretion system and effectors, which are present in the pathogens, and the presence of a known bacterial-killing type IV secretion system (X-T4SS). The diverse non-pathogenic strains of X. indica and X. sontii were found to protect rice from bacterial leaf blight pathogen, X. oryzae pv. oryzae (Xoo). The absence of phenotype of an X-T4SS mutant suggests redundancy in the genetic basis of the mechanisms involved in the bioprotection function, which may include multiple genetic loci, such as putative bacteriocin-encoding gene clusters and involvement of other factors such as nutrient and niche competition apart from induction of innate immunity through shared microbial-associated molecular patterns. The rice-NPX community and its pathogenic counterpart can be a promising model for understanding plant-microbe-microbiome interaction studies.IMPORTANCEThe Xanthomonas group of bacteria is known for its characteristic lifestyle as a phytopathogen. However, the discovery of non-pathogenic Xanthomonas (NPX) species is a major shift in understanding this group of bacteria. Multi-strain, in-depth genomic, evolutionary and functional studies on each of these NPX species are still lacking. This study on diverse non-pathogenic strains provides novel insights into genome diversity, dynamics, and evolutionary trends of NPX species from rice microbiome apart from its relationship with other relatives that form a sub-clade. Interestingly, we also uncovered that NPX species protect rice from pathogenic Xanthomonas species. The plant protection property shows their importance as a part of a healthy plant microbiome. Furthermore, finding an open pan-genome and large-scale variation at lipopolysaccharide biosynthetic locus indicates a significant role of the NPX community in host adaptation. The findings and high-quality genomic resources of NPX species and the strains will allow further systematic molecular and host-associated microbial community studies for plant health.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Praveen Kumar Nayak
- Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Ramesh V. Sonti
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Hitendra K. Patel
- Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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Senavirathna I, Jayasundara D, Warnasekara J, Agampodi S, Putz EJ, Nally JE, Bayles DO, Chaurasia R, Vinetz JM. Genomic Analysis of Human-infecting Leptospira borgpetersenii isolates in Sri Lanka: expanded PF07598 gene family repertoire, less overall genome reduction than bovine isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613401. [PMID: 39345489 PMCID: PMC11429935 DOI: 10.1101/2024.09.17.613401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Leptospira borgpetersenii commonly causes human leptospirosis, including severe disease. The first published analysis of L. borgpetersenii, performed on two strains of serovar Hardjo (L550 and JB197), concluded that the L. borgpetersenii genome is in the process of genome decay with functional consequences leading to a more obligately host-dependent life cycle. Yet whole genome analysis has only been carried out on few strains of L. borgpetersenii, with limited closed genomes and comprehensive analysis. Herein we report the complete, circularized genomes of seven non-Hardjo Leptospira borgpetersenii isolates from human leptospirosis patients in Sri Lanka. These isolates (all ST144) were found to be nearly identical by whole genome analysis; serotyping showed they are a novel serovar. We show that the L. borgpetersenii isolated from humans in Sri Lanka are less genomically decayed than previously reported isolates: fewer pseudogenes (N=141) and Insertion Sequence (IS) elements (N=46) compared to N=248, N=270, and N=400 pseudogenes, and N=121 and N=116 IS elements in published L. borgpetersenii Hardjo genomes (L550, JB197 and TC112). Compared to previously published L. borgpetersenii whole genome analyses showing two to three VM proteins in L. borgpetersenii isolates from cattle, rats and humans, we found that all of the human L. borgpetersenii isolates from Sri Lanka, including previously reported serovar Piyasena, have 4 encoded VM proteins, one ortholog of L. interrogans Copenhageni LIC12339 and 3 orthologs of LIC12844. Our findings of fewer pseudogenes, IS elements and expansion of the LIC12844 homologs of the PF07598 family in these human isolates suggests that this newly identified L. borgpetersenii serovar from Sri Lanka has unique pathogenicity. Comparative genome analysis and experimental studies of these L. borgpetersenii isolates will enable deeper insights into the molecular and cellular mechanisms of leptospirosis pathogenesis.
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Affiliation(s)
- Indika Senavirathna
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
- Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
| | - Dinesha Jayasundara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
- Department of Microbiology, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
| | - Janith Warnasekara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
- Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
| | - Suneth Agampodi
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
- Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
| | - Ellie J Putz
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA
| | - Jarlath E Nally
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA
| | - Darrell O Bayles
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA
| | - Reetika Chaurasia
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT
| | - Joseph M Vinetz
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT
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22
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Talkah NSM, Jasim JHM, Nordin FA, Othman AS. Complete chloroplast genome of a montane plant Spathoglottis aurea Lindl.: Comparative analyses and phylogenetic relationships among members of tribe collabieae. PLoS One 2024; 19:e0291888. [PMID: 39283891 PMCID: PMC11404822 DOI: 10.1371/journal.pone.0291888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 07/23/2024] [Indexed: 09/20/2024] Open
Abstract
The yellow-flowered Spathoglottis aurea (tribe Collabieae; family Orchidaceae) is native to the mountainous areas of Peninsular Malaysia. The species is well known as an ornamental plant and for its role in artificial hybrid breeding. There is an interesting evolutionary relationship between S. aurea and the geographically isolated S. microchilina from Borneo that has encouraged further study of the S. aurea populations, but the genomic resource for S. aurea has not yet been reported. The present study reports the first work to characterize a chloroplast (cp) genome among the Spathoglottis genus. The complete cp genome of S. aurea was assembled from a sequence generated by the Illumina platform and analysed in comparison with other Collabieae species available in the GenBank database. The cp genome of S. aurea is 157,957 base pairs (bp) in length with guanine-cytosine (GC) content of 37.3%. The genome possessed a typical quadripartite cp genome structure with large single-copy (LSC) (86,888 bp), small single-copy (SSC) (18,125 bp) and inverted repeat (IR) (26,472 bp) sequences. A total of 134 genes were annotated, with 88 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. Overall, 80 simple sequence repeats (SSR) or microsatellites were identified. Comparative analysis with other Collabieae species revealed high conservation in the cp genome arrangements with minimal difference in genome lengths. However, several mutational hotspots were also detected, with high potential to be developed as genetic markers for phylogenetic analysis. Characterization of the S. aurea cp genome revealed its conserved nature without gene loss or rearrangements when compared to other species of the Collabieae tribe. Phylogenetic analysis of Collabieae species also revealed that S. aurea has a distant evolutionary relationship to other members of the Collabieae species, despite the presence of problematic genera such as Phaius and Cephalantheropsis.
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Affiliation(s)
| | | | - Farah Alia Nordin
- School of Biological Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia
| | - Ahmad Sofiman Othman
- School of Biological Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia
- Center of Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
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23
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Yang JX, Ma GN, Li YT, Shi YP, Liang GW. Resistance and virulence genes characteristic of a South Asia Clade (I) Candida auris strain isolated from blood in Beijing. Clinics (Sao Paulo) 2024; 79:100497. [PMID: 39284275 PMCID: PMC11419799 DOI: 10.1016/j.clinsp.2024.100497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/24/2024] [Accepted: 08/25/2024] [Indexed: 09/27/2024] Open
Abstract
INTRODUCTION Candida auris is a globally disseminated invasive ascomycetous yeast, that imposes a substantial burden on healthcare systems. It has been documented to have spread to over 40 countries across six continents, necessitating in-depth comprehension through advanced techniques like Whole-Genome Sequencing. METHOD This study entailed the isolation and Whole-Genome Sequencing of a fluconazole-resistant C. auris strain (CA01) obtained from a patient's blood in Beijing. Genome analysis was conducted to classify the strain, and molecular docking was performed to understand the impact of mutations on drug resistance. RESULTS Genome analysis revealed that CA01 belongs to the South Asia Clade (I) and shares the closest genetic relationship with previously reported strains BJCA001 and BJCA002. Notably, unlike BJCA001, CA01 exhibits significant resistance to fluconazole primarily due to the A395T mutation in the ERG11 gene. Molecular docking studies demonstrated that this mutation leads to geometric changes in the active site where fluconazole binds, resulting in decreased binding affinity. Additionally, the present findings have identified several core virulence genes in C. auris, such as RBF1. DISCUSSION The findings from this study expand the understanding of the genetic diversity and adaptive mechanisms of C. auris within the South Asia Clade (I). The observed fluconazole resistance driven by the ERG11 mutation A395T highlights the need for heightened awareness and adaptation in clinical treatment strategies in China. This study provides critical insights into drug resistance and virulence profiles at a genetic level, which could guide future therapeutic and management strategies for C. auris infections.
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Affiliation(s)
- Jing-Xian Yang
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing, 100049 China
| | - Guan-Nan Ma
- Zhejiang Key Laboratory of Digital Technology in Medical Diagnostics, Hangzhou, 310000 China
| | - Ya-Tong Li
- Zhejiang Key Laboratory of Digital Technology in Medical Diagnostics, Hangzhou, 310000 China
| | - Yu-Peng Shi
- Zhejiang Key Laboratory of Digital Technology in Medical Diagnostics, Hangzhou, 310000 China
| | - Guo-Wei Liang
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing, 100049 China.
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24
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Fang J, Lin A, Yan H, Feng L, Lin S, Mason P, Zhou L, Xu X, Zhao K, Huang Y, Henry RJ. Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion. BMC PLANT BIOLOGY 2024; 24:861. [PMID: 39272034 PMCID: PMC11401388 DOI: 10.1186/s12870-024-05557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal ("SP"), double-petal ("DP"), and multi-petal ("MP"). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions. RESULTS Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, "SP", "DP", and "MP-hutou" ("HT"), with PacBio reads and the "HT" chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in "HT". We identified a 14.3 kb "HT"-specific insertion on Chr7 of the "HT" nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that "DP" and "HT" evolved from "SP", with "HT" being the most recent derivative of "DP". CONCLUSION The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.
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Affiliation(s)
- Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, China.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
| | - Aiting Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hansong Yan
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, China
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Patrick Mason
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Linwei Zhou
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Zhao
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China.
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
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25
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Bombardi L, Orlando M, Aulitto M, Fusco S. Thermophilic Hemicellulases Secreted by Microbial Consortia Selected from an Anaerobic Digester. Int J Mol Sci 2024; 25:9887. [PMID: 39337375 PMCID: PMC11432564 DOI: 10.3390/ijms25189887] [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: 07/24/2024] [Revised: 08/30/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
The rise of agro-industrial activities over recent decades has exponentially increased lignocellulose biomasses (LCB) production. LCB serves as a cost-effective source for fermentable sugars and other renewable chemicals. This study explores the use of microbial consortia, particularly thermophilic consortia, for LCB deconstruction. Thermophiles produce stable enzymes that retain activity under industrial conditions, presenting a promising approach for LCB conversion. This research focused on two microbial consortia (i.e., microbiomes) that were analyzed for enzyme production using a cheap medium, i.e., a mixture of spent mushroom substrate (SMS) and digestate. The secreted xylanolytic enzymes were characterized in terms of temperature and pH optima, thermal stability, and hydrolysis products from LCB-derived polysaccharides. These enzymes showed optimal activity aligning with common biorefinery conditions and outperformed a formulated enzyme mixture in thermostability tests in the digestate. Phylogenetic and genomic analyses highlighted the genetic diversity and metabolic potential of these microbiomes. Bacillus licheniformis was identified as a key species, with two distinct strains contributing to enzyme production. The presence of specific glycoside hydrolases involved in the cellulose and hemicellulose degradation underscores these consortia's capacity for efficient LCB conversion. These findings highlight the potential of thermophilic microbiomes, isolated from an industrial environment, as a robust source of robust enzymes, paving the way for more sustainable and cost-effective bioconversion processes in biofuel and biochemical production and other biotechnological applications.
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Affiliation(s)
- Luca Bombardi
- Biochemistry and Industrial Biotechnology (BIB) Laboratory, Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano Bicocca, 20126 Milano, Italy
| | - Martina Aulitto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Salvatore Fusco
- Biochemistry and Industrial Biotechnology (BIB) Laboratory, Department of Biotechnology, University of Verona, 37134 Verona, Italy
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26
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Li Z, Han Y, Li Y, Wu W, Lei J, Wang D, Lin Y, Wang X. Whole Mitochondrial Genome Sequencing and Phylogenetic Tree Construction for Procypris mera (Lin 1933). Animals (Basel) 2024; 14:2672. [PMID: 39335261 PMCID: PMC11428242 DOI: 10.3390/ani14182672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 09/04/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Procypris mera (Lin, 1933), also known as the Chinese ink carp, currently has a second-class protection status in China. Understanding the structure and characteristics of mitochondrial genes provides essential information for resource conservation and phylogenetic studies of P. mera. Here, we sequenced the mitochondrial genomes of three P. mera (WYL1-3) from three sites and performed phylogenetic analysis. The generated three genomes were 16,587 bp in length, comprising 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and two non-coding regions (control region (CR), D-loop, and light-stranded replication start OL), with a preference for codons ending in A or C. The mitochondrial genomes of WYL2 and WYL3 were identical, differing from that of WYL1 by only five single-nucleotide polymorphisms (SNPs). All mitochondrial PCGs had Ka/Ks ratios of less than one, suggesting purifying selection. Phylogenetic tree analysis based on amino acid sequences suggested that the genus Puntioplites is sister to all other genera of the subfamily Cyprinidae of China; the genus Procypris forms a monophyletic group; and the genera Carassioides, Carassius, and Cyprinus form a monophyletic group. This study contributes to our understanding of the phylogenetic relationships in subfamily Cyprininae in China and lays the foundation for resource conservation and management of P. mera.
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Affiliation(s)
- Zhe Li
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China;
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (Y.H.)
| | - Yaoquan Han
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (Y.H.)
| | - Yusen Li
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (Y.H.)
| | - Weijun Wu
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (Y.H.)
| | - Jianjun Lei
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (Y.H.)
| | - Dapeng Wang
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (Y.H.)
| | - Yong Lin
- ASEAN Key Laboratory of Comprehensive Exploitation and Utilization of Aquatic Germplasm Resources, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquaculture Genetic and Breeding and Healthy Aquaculture of Guangxi, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (Y.H.)
| | - Xiaoqing Wang
- College of Fisheries, Hunan Agricultural University, Changsha 410128, China;
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27
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Almeida-Silva MA, Braga-Ferreira RS, Targueta CP, Corvalán LCJ, Silva-Neto CM, Franceschinelli EV, Sobreiro MB, Nunes R, Telles MPC. Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales. Sci Rep 2024; 14:21358. [PMID: 39266625 PMCID: PMC11393331 DOI: 10.1038/s41598-024-71956-5] [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: 04/01/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024] Open
Abstract
Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions.
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Affiliation(s)
- Marla A Almeida-Silva
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Universidade Estadual do Piauí, Campus Prof. Ariston Dias Lima, São Raimundo Nonato, PI, Brazil
| | - Ramilla S Braga-Ferreira
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Universidade Federal de Rondonópolis, Rondonópolis, MT, Brazil
| | - Cíntia P Targueta
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Leonardo C J Corvalán
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Instituto Federal de Goiás-Polo de Inovação, Goiânia, GO, Brazil
| | - Carlos M Silva-Neto
- Instituto Federal de Goiás-Polo de Inovação, Goiânia, GO, Brazil
- Laboratório de Bioinformática e Biodiversidade (LBB), Universidade Estadual de Goiás, Instituto Acadêmico de Ciências da Saúde e Biológicas (IACSB), Campus Oeste, Unidade Universitária de Iporá, Iporá, GO, 76200-000, Brazil
| | | | - Mariane B Sobreiro
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Laboratório Estadual de Saúde Pública Dr. Giovanni Cysneiros - LACEN-GO, Goiânia, GO, Brazil
| | - Rhewter Nunes
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil.
- Laboratório de Bioinformática e Biodiversidade (LBB), Universidade Estadual de Goiás, Instituto Acadêmico de Ciências da Saúde e Biológicas (IACSB), Campus Oeste, Unidade Universitária de Iporá, Iporá, GO, 76200-000, Brazil.
| | - Mariana P C Telles
- Laboratório de Genética and Biodiversidade (LGBio), Universidade Federal de Goiás, Goiânia, GO, Brazil
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Goiânia, GO, Brazil
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28
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Smedile D, Iurescia M, Carfora V, Cocumelli C, Palmerini T, Diaconu EL, Congiu I, Donati V, Stravino F, Sorbara L, Romano E, Caprioli A, Battisti A. Genomics Insights into Mycolicibacterium Hassiacum Causing Infection in a Cat with Pyogranulomatous Dermatitis and Panniculitis. Pathogens 2024; 13:785. [PMID: 39338976 PMCID: PMC11435378 DOI: 10.3390/pathogens13090785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 08/29/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
Mycolicibacterium hassiacum (homotypic synonym: Mycobacterium hassiacum) represents an ungrouped thermotolerant rapidly growing mycobacteria (RGM) species occasionally associated with infections and disease in humans. In this report, we describe a case of pyogranulomatous dermatitis and panniculitis due to M. hassiacum in an immunocompetent adult cat. To the best of our knowledge, this represents the first report of M. hassiacum infection in animals. We also report the results of the in-depth genome characterization of the isolate using a combined short- and long-read whole-genome sequencing (WGS) approach. We observed the lack of acquired-resistance genes and no evidence of mutations in housekeeping genes associated with resistance to rifampicin and isoniazid. We detected some virulence factors in our isolate, such as some associated with the interaction of mycobacteria with host cells, and the presence of multiple copies of heavy metal resistance genes (arsB, arsR, and arsL/cadL). In conclusion, M. hassiacum should be included among the RGM species associated with feline subcutaneous atypical mycobacteriosis (SAM). A reliable and fast RGM laboratory identification and characterization is important not only for an accurate etiological diagnosis but also for a correct approach to SAM treatment options.
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Affiliation(s)
- Daniele Smedile
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Manuela Iurescia
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Virginia Carfora
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Cristiano Cocumelli
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Tiziana Palmerini
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Elena Lavinia Diaconu
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Ilaria Congiu
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Valentina Donati
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Fiorentino Stravino
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Luigi Sorbara
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | | | - Andrea Caprioli
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
| | - Antonio Battisti
- General Diagnostic Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", 00178 Rome, Italy
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29
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da Silva MERJ, Breyer GM, da Costa MM, Brenig B, Azevedo VADC, Cardoso MRDI, Siqueira FM. Genomic Analyses of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus pseudintermedius Strains Involved in Canine Infections: A Comprehensive Genotypic Characterization. Pathogens 2024; 13:760. [PMID: 39338951 PMCID: PMC11434867 DOI: 10.3390/pathogens13090760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Staphylococcus pseudintermedius is frequently associated with several bacterial infections in dogs, highlighting a One Health concern due to the zoonotic potential. Given the clinical significance of this pathogen, we performed comprehensive genomic analyses of 28 S. pseudintermedius strains isolated from canine infections throughout whole-genome sequencing using Illumina HiSeq, and compared the genetic features between S. pseudintermedius methicillin-resistant (MRSP) and methicillin-susceptible (MSSP) strains. Our analyses determined that MRSP genomes are larger than MSSP strains, with significant changes in antimicrobial resistance genes and virulent markers, suggesting differences in the pathogenicity of MRSP and MSSP strains. In addition, the pangenome analysis of S. pseudintermedius from canine and human origins identified core and accessory genomes with 1847 and 3037 genes, respectively, which indicates that most of the S. pseudintermedius genome is highly variable. Furthermore, phylogenomic analysis clearly separated MRSP from MSSP strains, despite their infection sites, showing phylogenetic differences according to methicillin susceptibility. Altogether our findings underscore the importance of studying the evolutionary dynamics of S. pseudintermedius, which is crucial for the development of effective prevention and control strategies of resistant S. pseudintermedius infections.
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Affiliation(s)
- Maria Eduarda Rocha Jacques da Silva
- Department of Veterinary Clinical Pathology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil
- Postgraduate Program in Veterinary Science, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil
| | - Gabriela Merker Breyer
- Department of Veterinary Clinical Pathology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil
- Postgraduate Program in Veterinary Science, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil
| | - Mateus Matiuzzi da Costa
- Department of Animal Science, Federal University of São Francisco Valley (UNIVASF), Petrolina 56300-000, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Division of Molecular Biology of Livestock and Molecular Diagnostics, Georg August University Göttingen, 37077 Göttingen, Germany
| | - Vasco Ariston de Carvalho Azevedo
- Molecular and Cellular Genetics Laboratory (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | | | - Franciele Maboni Siqueira
- Department of Veterinary Clinical Pathology, Faculty of Veterinary Medicine, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil
- Postgraduate Program in Veterinary Science, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil
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30
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Bertrand C, Martins R, Nunes F, Brandão P, Nascimento FX. Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50. Access Microbiol 2024; 6:000856.v3. [PMID: 39239567 PMCID: PMC11373566 DOI: 10.1099/acmi.0.000856.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/02/2024] [Indexed: 09/07/2024] Open
Abstract
Auxins, mainly in the form of indole-3-acetic acid (IAA), regulate several aspects of plant and algal growth and development. Consequently, plant and algae-associated bacteria developed the ability to modulate IAA levels, including IAA catabolism. In this work, we present and analyse the genome sequence of the IAA-degrading and marine algae-associated bacterium, Marinomonas sp. NFXS50, analyse its IAA catabolism gene cluster and study the prevalence of IAA catabolism genes in other Marinomonas genomes. Our findings revealed the presence of homologs of the Pseudomonas iac gene cluster, implicated in IAA catabolism, in the genome of strain NFXS50; however, differences were observed in the content and organization of the Marinomonas iac gene cluster when compared to that of the model iac-containing Pseudomonas putida 1290. These variations suggest potential adaptations in the IAA catabolism pathway, possibly influenced by substrate availability and evolutionary factors. The prevalence of iac genes across several Marinomonas species underscores the significance of IAA catabolism in marine environments, potentially influencing plant/algae-bacteria interactions. This study provides novel insights into the IAA catabolism in Marinomonas, laying the groundwork for future investigations into the role of iac genes in Marinomonas physiology and the regulation of marine plant/algae-bacteria interactions.
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Affiliation(s)
- Constança Bertrand
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Rodrigo Martins
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Francisco Nunes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Pedro Brandão
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Francisco X Nascimento
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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31
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Zhou YR, Li Y, Yang LH, Kozlowski G, Yi LT, Liu MH, Zheng SS, Song YG. The adaptive evolution of Quercus section Ilex using the chloroplast genomes of two threatened species. Sci Rep 2024; 14:20577. [PMID: 39232239 PMCID: PMC11375091 DOI: 10.1038/s41598-024-71838-w] [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: 03/20/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, introgression, and incomplete lineage sorting. Therefore, we wanted to gain a better understanding of this genus at the level of the maternally inherited chloroplast genome. Here, we sequenced, assembled, and annotated the cp genomes of the threatened Quercus marlipoensis (160,995 bp) and Q. kingiana (161,167 bp), and mined these genomes for repeat sequences and codon usage bias. Comparative genomic analyses, phylogenomics, and selection pressure analysis were also performed in these two threatened species along with other species of Quercus. We found that the guanine and cytosine content of the two cp genomes were similar. All 131 annotated genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes, had the same order in the two species. A strong A/T bias was detected in the base composition of simple sequence repeats. Among the 59 synonymous codons, the codon usage pattern of the cp genomes in these two species was more inclined toward the A/U ending. Comparative genomic analyses indicated that the cp genomes of Quercus section Ilex are highly conserved. We detected eight highly variable regions that could be used as molecular markers for species identification. The cp genome structure was consistent and different within and among the sections of Quercus. The phylogenetic analysis showed that section Ilex was not monophyletic and was divided into two groups, which were respectively nested with section Cerris and section Cyclobalanopsis. The two threatened species sequenced in this study were grouped into the section Cyclobalanopsis. In conclusion, the analyses of cp genomes of Q. marlipoensis and Q. kingiana promote further study of the taxonomy, phylogeny and evolution of these two threatened species and Quercus.
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Affiliation(s)
- Yu-Ren Zhou
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yu Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Liang-Hai Yang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Department of Biology and Botanic Garden, University of Fribourg, 1700, Fribourg, Switzerland
- Natural History Museum Fribourg, 1700, Fribourg, Switzerland
| | - Li-Ta Yi
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Mei-Hua Liu
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
| | - Si-Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Yi-Gang Song
- College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
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Dalla Costa TP, Silva MC, de Santana Lopes A, Pacheco TG, da Silva GM, de Oliveira JD, de Baura VA, Balsanelli E, de Souza EM, de Oliveira Pedrosa F, Rogalski M. The plastomes of Lepismium cruciforme (Vell.) Miq and Schlumbergera truncata (Haw.) Moran reveal tribe-specific rearrangements and the first loss of the trnT-GGU gene in Cactaceae. Mol Biol Rep 2024; 51:957. [PMID: 39230768 DOI: 10.1007/s11033-024-09871-1] [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: 05/23/2024] [Accepted: 08/19/2024] [Indexed: 09/05/2024]
Abstract
BACKGROUND Recent studies have revealed atypical features in the plastomes of the family Cactaceae, the largest lineage of succulent species adapted to arid and semi-arid regions. Most plastomes sequenced to date are from short-globose and cylindrical cacti, while little is known about plastomes of epiphytic cacti. Published cactus plastomes reveal reduction and complete loss of IRs, loss of genes, pseudogenization, and even degeneration of tRNA structures. Aiming to contribute with new insights into the plastid evolution of Cactaceae, particularly within the tribe Rhipsalideae, we de novo assembled and analyzed the plastomes of Lepismium cruciforme and Schlumbergera truncata, two South American epiphytic cacti. METHODS AND RESULTS Our data reveal many gene losses in both plastomes and the first loss of functionality of the trnT-GGU gene in Cactaceae. The trnT-GGU is a pseudogene in L. cruciforme plastome and appears to be degenerating in the tribe Rhipsalideae. Although the plastome structure is conserved among the species of the tribe Rhipsalideae, with tribe-specific rearrangements, we mapped around 200 simple sequence repeats and identified nine nucleotide polymorphism hotspots, useful to improve the phylogenetic resolutions of the Rhipsalideae. Furthermore, our analysis indicated high gene divergence and rapid evolution of RNA editing sites in plastid protein-coding genes in Cactaceae. CONCLUSIONS Our findings show that some characteristics of the Rhipsalideae tribe are conserved, such as plastome structure with IRs containing only the ycf2 and two tRNA genes, structural degeneration of the trnT-GGU gene and ndh complex, and lastly, pseudogenization of rpl33 and rpl23 genes, both plastid translation-related genes.
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Affiliation(s)
- Tanara P Dalla Costa
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Maria C Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - José D de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Valter A de Baura
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil.
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Hansen AK, Argondona JA, Miao S, Percy DM, Degnan PH. Rapid Loss of Nutritional Symbionts in an Endemic Hawaiian Herbivore Radiation Is Associated with Plant Galling Habit. Mol Biol Evol 2024; 41:msae190. [PMID: 39238368 PMCID: PMC11425488 DOI: 10.1093/molbev/msae190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/19/2024] [Accepted: 09/03/2024] [Indexed: 09/07/2024] Open
Abstract
Insect herbivores frequently cospeciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host-plant species, Metrosideros polymorpha within the last ∼5 MY. Using 16S rRNA sequencing, we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few millions of years, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with the loss of the Morganella-like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya-like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, and lysine) as well as B vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and, combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect-symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella-like and Dickeya-like symbionts.
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Affiliation(s)
- Allison K Hansen
- Department of Entomology, University of California, Riverside, CA, USA
| | - Jacob A Argondona
- Department of Entomology, University of California, Riverside, CA, USA
| | - Sen Miao
- Department of Entomology, University of California, Riverside, CA, USA
| | - Diana M Percy
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Patrick H Degnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
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Tao J, Wang X, Long Y, Gao Z, Zhang G, Guo Z, Wang G, Xu G, Wang Y, Liu H. Determining Gene Order Patterns in the Suillus and Boletales through Comparative Analysis of Their Mitogenomes. Int J Mol Sci 2024; 25:9597. [PMID: 39273542 PMCID: PMC11394714 DOI: 10.3390/ijms25179597] [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: 08/14/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Suillus is one of the most important genera of ectomycorrhizal fungi. As a model for studying host specificity, its molecular fragments and nuclear genome have been analyzed. However, its mitochondrial genome has not yet been reported. In this study, we assembled five mitogenomes of Suillus and analyzed and compared their basic characteristics. Owing to the large number of introns as well as intergenic regions, the mitogenomic lengths of species of Suillus were greater than those of other species of Boletales. We identified two main patterns of gene order arrangement in the members of the order Boletales. The Ka/Ks values of 15 protein-coding genes were <1 for the mitochondrial genes of 39 Boletales species, indicating their conserved evolution. Phylogenetic trees, reconstructed using the mitogenomes, indicated that the genus Suillus was monophyletic. Phylogenetic results based on the internal transcribed spacer region and mitogenome were used to confirm the distribution of Suillus placidus in China. The results showed that the mitogenome was superior in distinguishing species compared with a single molecular fragment. This is the first study to investigate the mitogenome of Suillus, enriching the mitogenome information and providing basic data for the phylogeny, resource conservation, and genetic diversity of this genus.
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Affiliation(s)
- Jiawei Tao
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Xianyi Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Yaohang Long
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Zexin Gao
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Gongyou Zhang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Zhongyao Guo
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Guoyu Wang
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, The Key Laboratory of Optimal Utilization of Natural Medicine Resources, School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang 561113, China
| | - Guangyin Xu
- School of Basic Medicine Science, Guizhou Medical University, Guiyang 561113, China
| | - Yaping Wang
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
| | - Hongmei Liu
- Engineering Research Center of Medical Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- Engineering Research Center of Health Medicine Biotechnology of Institution of Higher Education of Guizhou Province, Guizhou Medical University, Guiyang 561113, China
- Key Laboratory of Biology and Medical Engineering, Immune Cells and Antibody Engineering Research Center of Guizhou Province, School of Biology and Engineering, Guizhou Medical University, Guiyang 561113, China
- School of Basic Medicine Science, Guizhou Medical University, Guiyang 561113, China
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Shi Y, Chen Z, Jiang J, Wu W, Yu W, Zhang S, Zeng W. The assembly and comparative analysis of the first complete mitogenome of Lindera aggregata. FRONTIERS IN PLANT SCIENCE 2024; 15:1439245. [PMID: 39290737 PMCID: PMC11405213 DOI: 10.3389/fpls.2024.1439245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024]
Abstract
Lindera aggregata, a member belongs to the genus Lindera of Lauraceae family. Its roots and leaves have been used as traditional Chinese medicine or functional food for thousands of years. However, its mitochondrial genome has not been explored. Our aim is to sequence and assemble the mitogenome of L. aggregata to elucidate the genetic mechanism and evolutionary pathway. The results had shown that the mitogenome was extremely complex and had a unique multi-branched conformation with total size of 912,473 bp. Comprehensive analysis of protein coding genes of 7 related species showed that there were 40 common genes in their mitogenome. Interestingly, positive selection had become an important factor in the evolution of ccmB, ccmFC, rps10, rps11 and rps7 genes. Furthermore, our data highlighted the repeated trend of homologous fragment migrations between chloroplast and mitochondrial organelles, and 38 homologous fragments were identified. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Laurales species described in the APG IV system. To sum up, this study will be helpful to the study of population genetics and evolution of Lindera species.
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Affiliation(s)
- Yujie Shi
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Zhen Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Jingyong Jiang
- Institute of Horticulture, Taizhou Academy of Agricultural Sciences, Linhai, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry (A&F) University, Hangzhou, China
| | - Weifu Yu
- Zhejiang Hongshiliang Group Tiantai Mountain Wu-Yao Co., Ltd., RedRock Group, Taizhou, China
| | - Shumeng Zhang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
| | - Wei Zeng
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, College of Life Sciences, Taizhou University, Taizhou, China
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Wang X, Guo L, Ding L, Medina L, Wang R, Li P. Comparative plastome analyses and evolutionary relationships of 25 East Asian species within the medicinal plant genus Scrophularia (Scrophulariaceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1439206. [PMID: 39301164 PMCID: PMC11411265 DOI: 10.3389/fpls.2024.1439206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/19/2024] [Indexed: 09/22/2024]
Abstract
Backgroud Scrophularia L., a genus of the Scrophulariaceae, is a group of important medicinal plants used for eliminating heat and detoxifying. East Asia has an abundance of potentially medicinal Scrophularia species, and it serves as a secondary diversity center of the genus. However, the genomic resources available for germplasm identification and pharmaceutical exploration of East Asian Scrophularia are insufficient, hindering its commercial and industrial development. Additionally, the interspecific relationships of most East Asian Scrophularia species remain unclear. Methods In this study, we sequenced the leaves of 25 East Asian species of the genus Scrophularia, assembled and annotated the complete chloroplast genomes, and subsequently performed comparative and phylogenetic analyses on these genomes. Results and discussion The conserved plastome length of these 25 species ranged from 151,582 bp to 153,239 bp, containing a total of 132 coding genes, including 18 duplicated genes and 114 unique genes. Through genome alignment of these 25 species, 38-53 repeated sequences and 7 shared SSRs were identified, along with regions with high nucleotide polymorphism (Pi), which could potentially serve as molecular markers for species identification. The genome structure, gene content, and arrangement showed conservation, while variations were observed in the IR boundary regions and IGS. Phylogenetic inferences based on whole plastomes or on coding sequences (CDS) only yielded congruent results. We categorized the 25 East Asian Scrophularia species into six distinct clades and further explored their interspecies relationships using morphological characteristics, such as flower color, the relative position of stamens and corolla, and plant height. This could lay a genetic basis for future resource development of Scrophularia in East Asia.
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Affiliation(s)
- Xia Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lei Guo
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lulu Ding
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Leopoldo Medina
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ruihong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Pan Li
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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Benowitz KM, Allan CW, Jaworski CC, Sanderson MJ, Diaz F, Chen X, Matzkin LM. Fundamental Patterns of Structural Evolution Revealed by Chromosome-Length Genomes of Cactophilic Drosophila. Genome Biol Evol 2024; 16:evae191. [PMID: 39228294 PMCID: PMC11411373 DOI: 10.1093/gbe/evae191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/05/2024] Open
Abstract
A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila, a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis, Drosophila arizonae, and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa.
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Affiliation(s)
- Kyle M Benowitz
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Carson W Allan
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | | | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Fernando Diaz
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Xingsen Chen
- Department of Entomology, University of Arizona, Tucson, AZ, USA
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
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Wang Y, Xu C, Guo X, Wang Y, Chen Y, Shen J, He C, Yu Y, Wang Q. Phylogenomics analysis of Scutellaria (Lamiaceae) of the world. BMC Biol 2024; 22:185. [PMID: 39218872 PMCID: PMC11367873 DOI: 10.1186/s12915-024-01982-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Scutellaria, a sub-cosmopolitan genus, stands as one of the Lamiaceae family's largest genera, encompassing approximately 500 species found in both temperate and tropical montane regions. Recognized for its significant medicinal properties, this genus has garnered attention as a research focus, showcasing anti-cancer, anti-inflammatory, antioxidant, and hepatoprotective qualities. Additionally, it finds application in agriculture and horticulture. Comprehending Scutellaria's taxonomy is pivotal for its effective utilization and conservation. However, the current taxonomic frameworks, primarily based on morphological characteristics, are inadequate. Despite several phylogenetic studies, the species relationships and delimitations remain ambiguous, leaving the genus without a stable and reliable classification system. RESULTS This study analyzed 234 complete chloroplast genomes, comprising 220 new and 14 previously published sequences across 206 species, subspecies, and varieties worldwide. Phylogenetic analysis was conducted using six data matrices through Maximum Likelihood and Bayesian Inference, resulting in a robustly supported phylogenetic framework for Scutellaria. We propose three subgenera, recommending the elevation of Section Anaspis to subgeneric rank and the merging of Sections Lupulinaria and Apeltanthus. The circumscription of Subgenus Apeltanthus and Section Perilomia needs to be reconsidered. Comparative analysis of chloroplast genomes highlighted the IR/SC boundary feature as a significant taxonomic indicator. We identified a total of 758 SSRs, 558 longer repetitive sequences, and ten highly variable regions, including trnK-rps16, trnC-petN, petN-psbM, accD-psaI, petA-psbJ, rpl32-trnL, ccsA-ndhD, rps15-ycf1, ndhF, and ycf1. These findings serve as valuable references for future research on species identification, phylogeny, and population genetics. CONCLUSIONS The phylogeny of Scutellaria, based on the most comprehensive sample collection to date and complete chloroplast genome analysis, has significantly enhanced our understanding of its infrageneric relationships. The extensive examination of chloroplast genome characteristics establishes a solid foundation for the future development and utilization of Scutellaria, an important medicinal plant globally.
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Affiliation(s)
- Yinghui Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Wuhan, 430047, China
| | - Yan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyi Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Shen
- School of Medical Laboratory, Shandong Second Medical University, Weifang, 261053, China
| | - Chunnian He
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Sciences, Sichuan University, Chengdu, 610065, China
| | - Qiang Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Yong Y, Hu S, Zhong M, Wen Y, Zhou Y, Ma R, Jiang X, Zhang Q. Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas. Genomics 2024; 116:110940. [PMID: 39303860 DOI: 10.1016/j.ygeno.2024.110940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 09/13/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.
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Affiliation(s)
- Yushun Yong
- Ocean School, Yantai University, Yantai 264005, PR China
| | - Shunxin Hu
- Shandong Marine Resources and Environment Research Institute, Shandong Provincial Key Laboratory of Restoration for Marine Ecology, Yantai 264006, PR China
| | - Mingyu Zhong
- Ocean School, Yantai University, Yantai 264005, PR China
| | - Yun Wen
- Ocean School, Yantai University, Yantai 264005, PR China
| | - Yue Zhou
- Ocean School, Yantai University, Yantai 264005, PR China
| | - Ruixue Ma
- Ocean School, Yantai University, Yantai 264005, PR China
| | - Xiangyang Jiang
- Shandong Marine Resources and Environment Research Institute, Shandong Provincial Key Laboratory of Restoration for Marine Ecology, Yantai 264006, PR China
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Li Y, Zheng S, Wang T, Liu M, Kozlowski G, Yi L, Song Y. New insights on the phylogeny, evolutionary history, and ecological adaptation mechanism in cycle-cup oaks based on chloroplast genomes. Ecol Evol 2024; 14:e70318. [PMID: 39290669 PMCID: PMC11407850 DOI: 10.1002/ece3.70318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Cycle-cup oaks (Quercus section Cyclobalanopsis) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the evolutionary history and adaptive mechanisms at the chloroplast genome level in cycle-cup oaks remain largely unknown. Therefore, we studied this problem by conducting chloroplast genomics on 50 of the ca. 90 species. Comparative genomics and other analyses showed that Quercus section Cyclobalanopsis had a highly conserved chloroplast genome structure. Highly divergent regions, such as the ndhF and ycf1 gene regions and the petN-psbM and rpoB-trnC-GCA intergenic spacer regions, provided potential molecular markers for subsequent analysis. The chloroplast phylogenomic tree indicated that Quercus section Cyclobalanopsis was not monophyletic, which mixed with the other two sections of subgenus Cerris. The reconstruction of ancestral aera inferred that Palaeotropics was the most likely ancestral range of Quercus section Cyclobalanopsis, and then dispersed to Sino-Japan and Sino-Himalaya. Positive selection analysis showed that the photosystem genes had the lowest ω values among the seven functional gene groups. And nine protein-coding genes containing sites for positive selection: ndhA, ndhD, ndhF, ndhH, rbcL, rpl32, accD, ycf1, and ycf2. This series of analyses together revealed the phylogeny, evolutionary history, and ecological adaptation mechanism of the chloroplast genome of Quercus section Cyclobalanopsis in the long river of earth history. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus.
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Affiliation(s)
- Yu Li
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
- College of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Si‐Si Zheng
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
| | - Tian‐Rui Wang
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
| | - Mei‐Hua Liu
- College of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Gregor Kozlowski
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
- Department of Biology and Botanic GardenUniversity of FribourgFribourgSwitzerland
- Natural History Museum FribourgFribourgSwitzerland
| | - Li‐Ta Yi
- College of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Yi‐Gang Song
- Eastern China Conservation Centre for Wild Endangered Plant ResourcesShanghai Chenshan Botanical GardenShanghaiChina
- College of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
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Greene SE, Huang Y, Fischer K, Rosa BA, Martin J, Mitreva M, Yates D, Wanji S, Kamgno J, Budge PJ, Weil GJ, Fischer PU. A novel antigen biomarker for detection of high-level of Loa loa microfilaremia. PLoS Negl Trop Dis 2024; 18:e0012461. [PMID: 39226306 PMCID: PMC11398663 DOI: 10.1371/journal.pntd.0012461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 09/13/2024] [Accepted: 08/17/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Loiasis is a disease caused by the nematode Loa loa. Serious adverse events sometimes occur in people with heavy L. loa microfilaremia after ivermectin treatment. In regions of Central Africa where loiasis is endemic, this significantly impedes global elimination programs for lymphatic filariasis and onchocerciasis that use mass distribution of ivermectin. Improved diagnostic tests to identify individuals at increased risk of serious adverse events could facilitate efforts to eliminate lymphatic filariasis and onchocerciasis in this region. METHODS AND FINDINGS We previously identified the L. loa protein Ll-Bhp-1 in loiasis patient sera. Here, we further characterize Ll-Bhp-1 and report development of an antigen capture ELISA to detect this antigen. This assay detected Ll-Bhp-1 in 74 of 116 (63.8%) loiasis patient sera. Ll-Bhp-1 levels were significantly correlated with L. loa microfilarial counts, and the sensitivity of the assay was highest for samples from people with high counts, (94% and 100% in people with ≥20,000 and ≥50,000 microfilaria per milliliter of blood, respectively). The antigen was not detected in 112 sera from people with other filarial infections, or in 34 control sera from the USA. CONCLUSIONS This Ll-Bhp-1 antigen assay is specific for loiasis, and highly sensitive for identifying people with high L. loa microfilarial counts who are at increased risk for serious adverse events after ivermectin treatment. L. loa antigen detection has the potential to facilitate loiasis mapping efforts and programs to eliminate lymphatic filariasis and onchocerciasis in Central Africa.
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Affiliation(s)
- Sarah E Greene
- Infectious Diseases Division, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Yuefang Huang
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Bruce A Rosa
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - John Martin
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Devyn Yates
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Samuel Wanji
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Joseph Kamgno
- Higher Institute for Scientific and Medical Research (ISM), Yaoundé, Cameroon
- Department of Public Health, Faculty of Medicine and Biomedical Sciences, Department of Public Health, University of Yaoundé I, Yaoundé, Cameroon
| | - Philip J Budge
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Gary J Weil
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Peter U Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
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de Carvalho A, Giambiagi-deMarval M, Rossi CC. Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale. J Microbiol 2024; 62:775-784. [PMID: 39037483 DOI: 10.1007/s12275-024-00156-7] [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: 05/14/2024] [Revised: 06/12/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.
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Affiliation(s)
- Allan de Carvalho
- Department of Biochemistry and Molecular Biology, Federal University of Vicosa, Minas Gerais, 36570-000, Brazil
| | - Marcia Giambiagi-deMarval
- Paulo de Góes Microbiology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Ciro César Rossi
- Department of Biochemistry and Molecular Biology, Federal University of Vicosa, Minas Gerais, 36570-000, Brazil.
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Xu P, Xiao Y, Xiao Z, Li J. Exploitation and Application of a New Genetic Sex Marker Based on Intron Insertion Variation of erc2 Gene in Oplegnathus punctatus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10363-3. [PMID: 39212851 DOI: 10.1007/s10126-024-10363-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Spotted knifejaw (Oplegnathus punctatus), one of the most valuable mariculture species, grows with significant sexual dimorphism, with males growing significantly faster than females. O. punctatus not only has excellent growth characteristics and high food value, but also shows high economic value in aquaculture, which has become a hotspot in the field of aquaculture. The current insufficiency of sex marker identification in O. punctatus restricts the process of its unisexual breeding. Rapid identification of sex will help to study the mechanisms of sex determination and accelerate the development of sex-controlled breeding. With the completion of the sequencing of the male and female genomes of O. punctatus, the efficient and precise development of genetic sex markers has been made possible. In this study, we used genome-wide information combined with molecular biology techniques from marker sequences to further establish a rapid method for DNA insertion variant detection in the intron of O. punctatus erc2 gene, which can be used to rapidly, accurately, and efficiently identify whether DNA insertion occurs in the intron of O. punctatus erc2 gene to be detected, and to identify the sex of O. punctatus to be detected. It could also be distinguished by agarose gel electrophoresis, which would shorten the time for accurate identification and improves the detection efficiency. Homozygous comparison of male and female individuals showed that the length of the DNA fragment of the erc2 gene was 239 bp on chromosome X1 and 1173 bp on chromosome Y. It can therefore be inferred that a 934 bp insertion fragment exists on the Y chromosome. The PCR amplification results showed that two DNA fragments of 1173 bp and 239 bp could be amplified in male O. punctatus, and the 1173 bp fragment was a marker fragment specific to the variant intron erc2 gene, while only a single DNA fragment of 239 bp was amplified in female O. punctatus. It has important significance and application value in the study of neurotransmitter transmission and environmental adaptability of female and male fish based on erc2 gene, as well as the identification of male and female sex, the preparation of high male fry, and family breeding.
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Affiliation(s)
- Pingrui Xu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS). Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yongshuang Xiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS). Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Zhizhong Xiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS). Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Weihai Hao Huigan Marine Biotechnology Co, Weihai, China
| | - Jun Li
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS). Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
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Moffat AD, Höing L, Santos-Aberturas J, Markwalder T, Malone JG, Teufel R, Truman AW. Understanding the biosynthesis, metabolic regulation, and anti-phytopathogen activity of 3,7-dihydroxytropolone in Pseudomonas spp. mBio 2024; 15:e0102224. [PMID: 39207110 PMCID: PMC11481866 DOI: 10.1128/mbio.01022-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
The genus Pseudomonas is a prolific source of specialized metabolites with significant biological activities, including siderophores, antibiotics, and plant hormones. These molecules play pivotal roles in environmental interactions, influencing pathogenicity, inhibiting microorganisms, responding to nutrient limitation and abiotic challenges, and regulating plant growth. These properties mean that pseudomonads are suitable candidates as biological control agents against plant pathogens. Multiple transposon-based screens have identified a Pseudomonas biosynthetic gene cluster (BGC) associated with potent antibacterial and antifungal activities, which produces 7-hydroxytropolone (7-HT). In this study, we show that this BGC also makes 3,7-dihydroxytropolone (3,7-dHT), which has strong antimicrobial activity toward Streptomyces scabies, a potato pathogen. Through metabolomics and reporter assays, we unveil the involvement of cluster-situated genes in generating phenylacetyl-coenzyme A, a key precursor for tropolone biosynthesis via the phenylacetic acid catabolon. The clustering of these phenylacetic acid genes within tropolone BGCs is unusual in other Gram-negative bacteria. Our findings support the interception of phenylacetic acid catabolism via an enoyl-CoA dehydratase encoded in the BGC, as well as highlighting an essential role for a conserved thioesterase in biosynthesis. Biochemical assays were used to show that this thioesterase functions after a dehydrogenation-epoxidation step catalyzed by a flavoprotein. We use this information to identify diverse uncharacterized BGCs that encode proteins with homology to flavoproteins and thioesterases involved in tropolone biosynthesis. This study provides insights into tropolone biosynthesis in Pseudomonas, laying the foundation for further investigations into the ecological role of tropolone production.IMPORTANCEPseudomonas bacteria produce various potent chemicals that influence interactions in nature, such as metal-binding molecules, antibiotics, or plant hormones. This ability to synthesize bioactive molecules means that Pseudomonas bacteria may be useful as biological control agents to protect plants from agricultural pathogens, as well as a source of antibiotic candidates. We have identified a plant-associated Pseudomonas strain that can produce 3,7-dihydroxytropolone, which has broad biological activity and can inhibit the growth of Streptomyces scabies, a bacterium that causes potato scab. Following the identification of this molecule, we used a combination of genetic, chemical, and biochemical experiments to identify key steps in the production of tropolones in Pseudomonas species. Understanding this biosynthetic process led to the discovery of an array of diverse pathways that we predict will produce new tropolone-like molecules. This work should also help us shed light on the natural function of antibiotics in nature.
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Affiliation(s)
- Alaster D. Moffat
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Lars Höing
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | | | - Tim Markwalder
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Jacob G. Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Robin Teufel
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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Bohada-Lizarazo DP, Bravo-Sanabria KD, Cárdenas-Malpica P, Rodríguez R. Comparative Genomic Analysis of Mycobacterium tuberculosis Isolates Circulating in North Santander, Colombia. Trop Med Infect Dis 2024; 9:197. [PMID: 39330886 PMCID: PMC11436241 DOI: 10.3390/tropicalmed9090197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/17/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024] Open
Abstract
Tuberculosis (TB) is an important infectious disease in relation to global public health and is caused species of the Mycobacterium tuberculosis complex (MTBC). In this study, we used whole-genome sequencing (WGS) and comparative genomics to investigate the genetic diversity of M. tuberculosis (Mtb) isolates circulating in North Santander (NS), Colombia. WGS was used for the phylogenetic and lineage characterization of 18 isolates of Mtb typed with orphan genotypes from 11 municipalities of NS between 2015 and 2018. The isolates studied were included in six sublineages from L4; the most frequent were 4.1.2.1, 4.3.3, and 4.3.4.2, corresponding to a proportion of 22.2%. The genome analysis conducted allowed the identification of a set of genetic variants mainly associated with determinants of virulence and evasion of the immune system (PPE34 and PE_PGRS2); adaptation and survival (PGL/p-HBAD); stress response (sigJ and sigM); geographic variability (PPE34); and carbohydrate and lipid metabolism (aldA, rocA, and cyp144). This is the first description of the molecular epidemiology of Mtb isolates circulating in NS achieved through WGS. It was possible to perform comparative genomics analyses between Mtb isolates against the universal reference H37Rv and Colombian UT205 genome, which can help us to understand the local genetic diversity and is relevant for epidemiological studies, providing insight into TB transmission dynamics in NS.
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Affiliation(s)
- Diana Patricia Bohada-Lizarazo
- Centro Experimental de Diagnóstico e Investigación Molecular-CEDIMOL, Universidad de Pamplona, Pamplona 503050, Colombia; (K.D.B.-S.); (R.R.)
- Grupo de Investigación en Recursos Naturales, Universidad de Pamplona, Pamplona 503050, Colombia;
- Departamento de Bacteriología y Laboratorio Clínico, Facultad de Salud, Universidad de Pamplona, Pamplona 503050, Colombia
| | - Karen Dayana Bravo-Sanabria
- Centro Experimental de Diagnóstico e Investigación Molecular-CEDIMOL, Universidad de Pamplona, Pamplona 503050, Colombia; (K.D.B.-S.); (R.R.)
- Departamento de Bacteriología y Laboratorio Clínico, Facultad de Salud, Universidad de Pamplona, Pamplona 503050, Colombia
| | - Paola Cárdenas-Malpica
- Grupo de Investigación en Recursos Naturales, Universidad de Pamplona, Pamplona 503050, Colombia;
- Departamento de Bacteriología y Laboratorio Clínico, Facultad de Salud, Universidad de Pamplona, Pamplona 503050, Colombia
| | - Raúl Rodríguez
- Centro Experimental de Diagnóstico e Investigación Molecular-CEDIMOL, Universidad de Pamplona, Pamplona 503050, Colombia; (K.D.B.-S.); (R.R.)
- Grupo de Investigación en Recursos Naturales, Universidad de Pamplona, Pamplona 503050, Colombia;
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Márquez EJ, Gómez-Chavarría DA, Alzate JF. Exploring the mitochondrial genomes and phylogenetic relationships of trans-Andean Bryconidae species (Actinopterygii: Ostariophysi: Characiformes). PLoS One 2024; 19:e0300830. [PMID: 39190628 PMCID: PMC11349099 DOI: 10.1371/journal.pone.0300830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Comparative mitogenomics and its evolutionary relationships within Bryconidae remains largely unexplored. To bridge this gap, this study assembled 15 mitogenomes from 11 Bryconidae species, including five newly sequenced. Salminus mitogenomes, exceeding 17,700 bp, exhibited the largest size, contrasting with a median size of 16,848 bp in the remaining species (Brycon and Chilobrycon). These mitogenomes encode 37 typical mitochondrial genes, including 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and exhibit the conserved gene arrangement found in most fish species. Phylogenetic relationships, based on the maximum-likelihood method, revealed that the trans-Andean species (found in northwestern South America) clustered into two main sister clades. One clade comprised the trans-Andean species from the Pacific slope, Brycon chagrensis and Chilobrycon deuterodon. The other clade grouped the trans-Andean species from the Magdalena-Cauca Basin Brycon moorei and Salminus affinis, with their respective cis-Andean congeners (found in eastern South America), with Brycon rubricauda as its sister clade. Since the current members of Brycon are split in three separated lineages, the systematic classification of Bryconidae requires further examination. This study provides novel insights into mitogenome characteristics and evolutionary pathways within Bryconidae, standing as crucial information for prospective phylogenetic and taxonomic studies, molecular ecology, and provides a valuable resource for environmental DNA applications.
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Affiliation(s)
- Edna Judith Márquez
- Laboratorio de Biología Molecular y Celular, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Medellín, Medellín, Antioquia, Colombia
| | - Daniel Alfredo Gómez-Chavarría
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Juan Fernando Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
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Yutin N, Tolstoy I, Mutz P, Wolf YI, Krupovic M, Koonin EV. DNA polymerase swapping in Caudoviricetes bacteriophages. Virol J 2024; 21:200. [PMID: 39187833 PMCID: PMC11348598 DOI: 10.1186/s12985-024-02482-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/21/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Viruses with double-stranded (ds) DNA genomes in the realm Duplodnaviria share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order Crassvirales encode DNAPs of different families. METHODS Groups of phages in which DNAP swapping likely occurred were identified as subtrees of a defined depth in a comprehensive evolutionary tree of tailed bacteriophages that included phages with DNAPs of different families. The DNAP swaps were validated by constrained tree analysis that was performed on phylogenetic tree of large terminase subunits, and the phage genomes encoding swapped DNAPs were aligned using Mauve. The structures of the discovered unusual DNAPs were predicted using AlphaFold2. RESULTS We identified four additional groups of tailed phages in the class Caudoviricetes in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage genome replication. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication. CONCLUSIONS Replacement of the DNAP gene by one encoding a DNAP of a different family occurred on many independent occasions during the evolution of different families of tailed phages, in some cases, resulting in very closely related phages encoding unrelated DNAPs. DNAP swapping was likely driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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Juri G, Ripa RR, Premoli AC. Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia. J Hered 2024; 115:588-599. [PMID: 38869982 DOI: 10.1093/jhered/esae032] [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: 11/14/2023] [Revised: 05/14/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024] Open
Abstract
Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia, used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.
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Affiliation(s)
- Gabriela Juri
- Instituto de Investigaciones en Recursos Naturales, Agroecología y Desarrollo Rural, Universidad Nacional de Río Negro - CONICET, Río Negro, Argentina
| | - Ramiro R Ripa
- Grupo de Genética Ecolgica, Evolutiva y de la Conservación, Instituto de Investigaciones en Biodiversidad y Medioambiente, Universidad Nacional del Comahue - CONICET, Río Negro, Argentina
| | - Andrea C Premoli
- Grupo de Genética Ecolgica, Evolutiva y de la Conservación, Instituto de Investigaciones en Biodiversidad y Medioambiente, Universidad Nacional del Comahue - CONICET, Río Negro, Argentina
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Zhang YX, Zhang C, Zhang RL, Zhao HG. Yushaniadezhui (Poaceae, Bambusoideae), a new bamboo species from Yunnan, China. PHYTOKEYS 2024; 246:1-14. [PMID: 39183963 PMCID: PMC11344174 DOI: 10.3897/phytokeys.246.130177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 07/25/2024] [Indexed: 08/27/2024]
Abstract
A new bamboo species, Yushaniadezhui, from Kunming, Yunnan, China is described and illustrated in this paper. The new species used to be misidentified as Y.polytricha. Based on careful comparison of morphological features and molecular phylogeny evidence, we confirmed its identity as a new member of the genus Yushania. Yushaniadezhui resembles Y.maculata, Y.polytricha and Y.weixiensis in several aspects, such as culm height and branch complement structure. However, the glabrous culm leaf sheaths and internodes, the absence of auricles and oral setae on most foliage leaves, except the one-year-old foliage leaves, the pubescence on the adaxial surface of the one-year-old foliage leaves and its limestone habitat preference can readily distinguish this new species from its related taxa. Moreover, we emphasise that individuals from various populations and molecular markers with different inheritance patterns for phylogeny reconstruction should be included in new species discovery, especially in plant groups with complex evolutionary histories.
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Affiliation(s)
- Yu-Xiao Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Chao Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Ru-Li Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Hu-Gang Zhao
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, ChinaSouthwest Forestry UniversityKunmingChina
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Jaglan AB, Verma R, Vashisth M, Virmani N, Bera BC, Vaid RK, Anand T. A novel lytic phage infecting MDR Salmonella enterica and its application as effective food biocontrol. Front Microbiol 2024; 15:1387830. [PMID: 39211316 PMCID: PMC11358711 DOI: 10.3389/fmicb.2024.1387830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 07/01/2024] [Indexed: 09/04/2024] Open
Abstract
Salmonella enterica is a foodborne pathogen associated with both typhoid and non-typhoid illness in humans and animals. This problem is further exacerbated by the emergence of antibiotic-resistant strains of Salmonella enterica. Therefore, to meet public health and safety, there is a need for an alternative strategy to tackle antibiotic-resistant bacteria. Bacteriophages or (bacterial viruses), due to their specificity, self-dosing, and antibiofilm activity, serve as a better approach to fighting against drug-resistant bacteria. In the current study, a broad-host range lytic phage phiSalP219 was isolated against multidrug-resistant Salmonella enterica serotypes Paratyphi from a pond water sample. Salmonella phage phiSalP219 was able to lyse 28/30 tested strains of Salmonella enterica. Salmonella phage phiSalP219 exhibits activity in acidic environments (pH3) and high temperatures (70°C). Electron microscopy and genome analysis revealed that phage phiSalP219 is a member of class Caudoviricetes. The genome of Salmonella phage phiSalP219 is 146Kb in size with 44.5% GC content. A total of 250 Coding Sequence (CDS) and 25 tRNAs were predicted in its genome. Predicted open reading frames (ORFs) were divided into five groups based on their annotation results: (1) nucleotide metabolism, (2) DNA replication and transcription, (3) structural proteins, (4) lysis protein, and (5) other proteins. The absence of lysogeny-related genes in their genome indicates that Salmonella phage phiSalP219 is lytic in nature. Phage phiSalP219 was also found to be microbiologically safe (due to the absence of toxin or virulence-related genes) in the control of Salmonella enterica serovar Typhimurium infections in the ready-to-eat meat and also able to eradicate biofilm formed by the same bacterium on the borosilicate glass surface.
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Affiliation(s)
- Anu Bala Jaglan
- ICAR – National Research Centre on Equines, Hisar, India
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Ravikant Verma
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | | | - Nitin Virmani
- ICAR – National Research Centre on Equines, Hisar, India
| | - B. C. Bera
- ICAR – National Research Centre on Equines, Hisar, India
| | - R. K. Vaid
- ICAR – National Research Centre on Equines, Hisar, India
| | - Taruna Anand
- ICAR – National Research Centre on Equines, Hisar, India
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