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Martínez-Gallardo MJ, Villicaña C, Yocupicio-Monroy M, Alcaraz-Estrada SL, Salazar-Salinas J, Mendoza-Vázquez OF, Damazo-Hernández G, León-Félix J. Comparative genomic analysis of Pseudomonas aeruginosa strains susceptible and resistant to carbapenems and aztreonam isolated from patients with healthcare-associated infections in a Mexican hospital. Mol Genet Genomics 2024; 299:29. [PMID: 38472486 DOI: 10.1007/s00438-024-02122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
Pseudomonas aeruginosa (PA) is an important opportunistic pathogen that causes different infections on immunocompromised patients. Within PA accessory genome, differences in virulence, antibiotic resistance and biofilm formation have been described between strains, leading to the emergence of multidrug-resistant strains. The genome sequences of 17 strains isolated from patients with healthcare-associated infections in a Mexican hospital were genomically and phylogenetically analyzed and antibiotic resistance genes, virulence genes, and biofilm formation genes were detected. Fifteen of the 17 strains were resistant to at least two of the carbapenems meropenem, imipenem, and the monobactam aztreonam. The antibiotic resistance (mexA, mexB, and oprM) and the biofilm formation (pslA and pslD) genes were detected in all strains. Differences were found between strains in accessory genome size. The strains had different sequence types, and seven strains had sequence types associated with global high risk epidemic PA clones. All strains were represented in two groups among PA global strains. In the 17 strains, horizontally acquired resistance genes to aminoglycosides and beta-lactams were found, mainly, and between 230 and 240 genes that encode virulence factors. The strains under study were variable in terms of their accessory genome, antibiotic resistance, and virulence genes. With these characteristics, we provide information about the genomic diversity of clinically relevant PA strains.
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Affiliation(s)
- María José Martínez-Gallardo
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Culiacán, Sinaloa, Mexico
| | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Culiacán, Sinaloa, Mexico
| | - Martha Yocupicio-Monroy
- Postgraduate in Genomic Sciences, Universidad Autónoma de la Ciudad de México (UACM), Mexico City, Mexico
| | | | | | | | | | - Josefina León-Félix
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Culiacán, Sinaloa, Mexico.
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2
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Verma N, Sharma T, Bhardwaj A, Vemuluri VR. Comparative genomics and characterization of a multidrug-resistant Acinetobacter baumannii VRL-M19 isolated from a crowded setting in India. Infect Genet Evol 2024; 118:105549. [PMID: 38181886 DOI: 10.1016/j.meegid.2023.105549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/17/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024]
Abstract
A crowded vegetable market serves as a mass gathering, posing a potential risk for infection transmission. In this study, we isolated a multidrug-resistant Acinetobacter baumannii strain, VRL-M19, from the air of such a market and conducted comparative genomics and phenotypic characterization. Antimicrobial susceptibility testing, genome sequencing using Illumina HiSeq X10, and pan-genome analysis with 788 clinical isolates identified core, accessory, and unique drug-resistant determinants. Mutational analysis of drug-resistance genes, virulence factor annotation, in vitro pathogenicity assessment, subsystem analysis, Multilocus sequence typing, and whole genome phylogenetic analysis were performed. VRL-M19 exhibited multidrug resistance with 69 determinants, and analysis across 788 clinical isolates and 350 Indian isolates revealed more accessory genes (52 out of 69) in the Indian isolates. Multiple mutations were observed in drug target modification genes, and the strain was identified as a moderate biofilm-former with 55 virulence factors. Whole genome phylogenetics indicated a close relationship between VRL-M19 and clinical A. baumannii strains. In conclusion, our comprehensive study suggests that VRL-M19 is a multidrug-resistant, potential pathogen with biofilm-forming capabilities, closely associated with clinical A. baumannii strains.
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Affiliation(s)
- Neha Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tina Sharma
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anshu Bhardwaj
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Venkata Ramana Vemuluri
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Ji G, Long Y, Cai G, Wang A, Yan G, Li H, Gao G, Xu K, Huang Q, Chen B, Li L, Li F, Nishio T, Shen J, Wu X. The chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica plants. J Exp Bot 2024:erae079. [PMID: 38421062 DOI: 10.1093/jxb/erae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Indexed: 03/02/2024]
Abstract
The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of domestication remains largely unclear without high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome, (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29,744 core genes, 23,306 dispensable genes, and 1,896 private genes. We resequenced 53 accessions, which represent six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that wild B. oleracea population had the highest level of diversity and represented the more closely related population of horticultural B. oleracea. Additionally, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease resistance genes during domestication selection. Our results provide deep insights into B. oleracea domestication and will facilitate Brassica crop genetic improvement.
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Affiliation(s)
- Gaoxiang Ji
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ying Long
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Guangqin Cai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Guixin Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hao Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Guizhen Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Kun Xu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qian Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Biyun Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Lixia Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Feng Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aza-Aoba, Aramaki, Aoba-ku, Sendai, 980-0845, Japan
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiaoming Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
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Pena-Fernández N, Ocejo M, van der Graaf-van Bloois L, Lavín JL, Kortabarria N, Collantes-Fernández E, Hurtado A, Aduriz G. Comparative pangenomic analysis of Campylobacter fetus isolated from Spanish bulls and other mammalian species. Sci Rep 2024; 14:4347. [PMID: 38388650 PMCID: PMC10884003 DOI: 10.1038/s41598-024-54750-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/15/2024] [Indexed: 02/24/2024] Open
Abstract
Campylobacter fetus comprises two closely related mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv). The latter causes bovine genital campylobacteriosis, a sexually-transmitted disease endemic in Spain that results in significant economic losses in the cattle industry. Here, 33 C. fetus Spanish isolates were whole-genome sequenced and compared with 62 publicly available C. fetus genomes from other countries. Genome-based taxonomic identification revealed high concordance with in silico PCR, confirming Spanish isolates as Cff (n = 4), Cfv (n = 9) and Cfv biovar intermedius (Cfvi, n = 20). MLST analysis assigned the Spanish isolates to 6 STs, including three novel: ST-76 and ST-77 for Cfv and ST-78 for Cff. Core genome SNP phylogenetic analysis of the 95 genomes identified multiple clusters, revealing associations at subspecies and biovar level between genomes with the same ST and separating the Cfvi genomes from Spain and other countries. A genome-wide association study identified pqqL as a Cfv-specific gene and a potential candidate for more accurate identification methods. Functionality analysis revealed variations in the accessory genome of C. fetus subspecies and biovars that deserve further studies. These results provide valuable information about the regional variants of C. fetus present in Spain and the genetic diversity and predicted functionality of the different subspecies.
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Affiliation(s)
- Nerea Pena-Fernández
- SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Carretera de Oviedo, s/n, 33300, Villaviciosa, Spain
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Medelin Ocejo
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Linda van der Graaf-van Bloois
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jose Luís Lavín
- Department of Applied Mathematics, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Nekane Kortabarria
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain
| | - Esther Collantes-Fernández
- Animal Health Department, Faculty of Veterinary Sciences, SALUVET, Complutense University of Madrid, Ciudad Universitaria s/n, 28040, Madrid, Spain
| | - Ana Hurtado
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain.
| | - Gorka Aduriz
- Animal Health Department, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park 812L, 48160, Derio, Spain.
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Mumtaz MN, Irfan M, Siraj S, Khan A, Khan H, Imran M, Khan IA, Khan A. Whole-genome sequencing of extensively drug-resistant Salmonella enterica serovar Typhi clinical isolates from the Peshawar region of Pakistan. J Infect Public Health 2024; 17:271-282. [PMID: 38134602 DOI: 10.1016/j.jiph.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Typhoid fever, caused by Salmonella enterica serovar Typhi, is a significant public health concern due to the escalating of antimicrobial resistance (AMR), with limited treatment options for extensively drug-resistant (XDR) S. Typhi strains pose a serious threat to disease management and control. This study aimed to investigate the genomic characteristics, epidemiology and AMR genes of XDR S. Typhi strains from typhoid fever patients in Pakistan. METHODOLOGY We assessed 200 patients with enteric fever symptoms, confirming 65 S. Typhi cases through culturing and biochemical tests. Subsequent antimicrobial susceptibility testing revealed 40 cases of extensively drug-resistant (XDR) and 25 cases of multi-drug resistance (MDR). Thirteen XDR strains were selected for whole-genome sequencing, to analyze their sequence type, phylogenetics, resistance genes, pathogenicity islands, and plasmid sequences using variety of data analysis resources. Pangenome analysis was conducted for 140 XDR strains, including thirteen in-house and 127 strains reported from other regions of Pakistan, to assess their genetic diversity and functional annotation. RESULTS MLST analysis classified all isolates as sequence type 1 (ST-1) with 4.3.1.1. P1 genotype characterization. Prophage and Salmonella Pathogenicity Island (SPI) analysis identified intact prophages and eight SPIs involved in Salmonella's invasion and replication within host cells. Genome data analysis revealed numerous AMR genes including dfrA7, sul1, qnrS1, TEM-1, Cat1, and CTX-M-15, and SNPs associated with antibiotics resistance. IncY, IncQ1, pMAC, and pAbTS2 plasmids, conferring antimicrobial resistance, were detected in a few XDR S. Typhi strains. Phylogenetic analysis inferred a close epidemiological linkage among XDR strains from different regions of Pakistan. Pangenome was noted closed among these strains and functional annotation highlighted genes related to metabolism and pathogenesis. CONCLUSION This study revealed a uniform genotypic background among XDR S. Typhi strains in Pakistan, signifying a persistence transmission of a single, highly antibiotic-resistant clone. The closed pan-genome observed underscores limited genetic diversity and highlights the importance of genomic surveillance for combating drug-resistant typhoid infections.
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Affiliation(s)
- Mah Noor Mumtaz
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Sami Siraj
- Institute of Pharmaceutical Sciences, Khyber Medical University (KMU), Peshawar, Pakistan
| | - Aslam Khan
- Department of Pathology, Medical Teaching Institution MTI, Hayatabad Medical Complex (HMC), Peshawar, Pakistan
| | - Hizbullah Khan
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Imran
- Research center for Advanced Materials Science (RCAMS), Chemistry Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan.
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Anbazhagan S, Himani KM, Karthikeyan R, Prakasan L, Dinesh M, Nair SS, Lalsiamthara J, Abhishek, Ramachandra SG, Chaturvedi VK, Chaudhuri P, Thomas P. Comparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains. Int Microbiol 2024; 27:101-111. [PMID: 37202587 DOI: 10.1007/s10123-023-00374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Brucella abortus and Brucella melitensis are the primary etiological agents of brucellosis in large and small ruminants, respectively. There are limited comparative genomic studies involving Brucella strains that explore the relatedness among both species. In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. Both species shared a common gene pool representing 2884 genes out of a total 3244 genes. SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. The analysis for virulence genes revealed that virB3, virB7, ricA, virB5, ipx5, wbkC, wbkB, and acpXL genes were highly conserved in most of the Brucella strains. Interestingly, virB10 gene was found to have high variability among the B. abortus strains. The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. In conclusion, the analysis revealed a highly shared core genome among two Brucella species. SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. Strains with absence or high polymorphism of virulence genes can be exploited for the development of novel vaccine candidates effective against both B. abortus and B. melitensis.
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Affiliation(s)
- S Anbazhagan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, India
| | - K M Himani
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - R Karthikeyan
- Division of Epidemiology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Lakshmi Prakasan
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - M Dinesh
- Division of Pathology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Sonu S Nair
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Jonathan Lalsiamthara
- Department of Molecular Microbiology & Immunology, SOM, OHSU, Portland, OR, US, 97239, USA
| | - Abhishek
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - S G Ramachandra
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, India
| | - V K Chaturvedi
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India
| | - Pallab Chaudhuri
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India.
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, 243122, India.
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Zaccaron AZ, Stergiopoulos I. Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes. BMC Biol 2024; 22:25. [PMID: 38281938 PMCID: PMC10823647 DOI: 10.1186/s12915-024-01818-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes the tomato pathogen Cladosporium fulvum, which is the first fungal plant pathogen from which avirulence (Avr) genes were ever cloned and in which loss of Avr genes is often reported as a means of overcoming recognition by cognate tomato Cf resistance genes. A recent near-complete reference genome assembly of C. fulvum isolate Race 5 revealed a compartmentalized genome architecture and the presence of an accessory chromosome, thereby creating a basis for studying genome plasticity in fungal plant pathogens and its impact on avirulence genes. RESULTS Here, we obtained near-complete genome assemblies of four additional C. fulvum isolates. The genome assemblies had similar sizes (66.96 to 67.78 Mb), number of predicted genes (14,895 to 14,981), and estimated completeness (98.8 to 98.9%). Comparative analysis that included the genome of isolate Race 5 revealed high levels of synteny and colinearity, which extended to the density and distribution of repetitive elements and of repeat-induced point (RIP) mutations across homologous chromosomes. Nonetheless, structural variations, likely mediated by transposable elements and effecting the deletion of the avirulence genes Avr4E, Avr5, and Avr9, were also identified. The isolates further shared a core set of 13 chromosomes, but two accessory chromosomes were identified as well. Accessory chromosomes were significantly smaller in size, and one carried pseudogenized copies of two effector genes. Whole-genome alignments further revealed genomic islands of near-zero nucleotide diversity interspersed with islands of high nucleotide diversity that co-localized with repeat-rich regions. These regions were likely generated by RIP, which generally asymmetrically affected the genome of C. fulvum. CONCLUSIONS Our results reveal new evolutionary aspects of the C. fulvum genome and provide new insights on the importance of genomic structural variations in overcoming host resistance in fungal plant pathogens.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA.
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Villani F, Guarracino A, Ward RR, Green T, Emms M, Pravenec M, Prins P, Garrison E, Williams RW, Chen H, Colonna V. Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery. bioRxiv 2024:2024.01.10.575041. [PMID: 38260597 PMCID: PMC10802574 DOI: 10.1101/2024.01.10.575041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics linked-read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome length was on average 2.4 times greater than the corresponding length of the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between Pirl1l1, Cromogranine expression, TNF-α levels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.
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Affiliation(s)
- Flavia Villani
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Rachel R Ward
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Tomomi Green
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Madeleine Emms
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Pjotr Prins
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Erik Garrison
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert W. Williams
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center
| | - Vincenza Colonna
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
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9
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Choi DG, Baek JH, Han DM, Khan SA, Jeon CO. Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions. BMC Genomics 2024; 25:28. [PMID: 38172677 PMCID: PMC10765913 DOI: 10.1186/s12864-023-09945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. RESULTS E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. CONCLUSIONS Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.
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Affiliation(s)
- Dae Gyu Choi
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Shehzad Abid Khan
- Atta‑ur‑Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000, Islamabad, Pakistan
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea.
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10
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Dias RS, Kremer FS, da Costa de Avila LF. In silico prospection of Lactobacillus acidophilus strains with potential probiotic activity. Braz J Microbiol 2023; 54:2733-2743. [PMID: 37801223 PMCID: PMC10689588 DOI: 10.1007/s42770-023-01139-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/26/2023] [Indexed: 10/07/2023] Open
Abstract
Lactic acid bacteria (LAB) are fermentative microorganisms and perform different roles in biotechnological processes, mainly in the food and pharmaceutical industries. Among the LAB, Lactobacillus acidophilus is a species that deserves to be highlighted for being used both in prophylaxis and in the treatment of pathologies. Most of the metabolites produced by this species are linked to the inhibition of pathogens. In this study, we utilized a pangenomic and metabolic annotation analysis using Roary and BlastKOALA, ML-based probiotic activity prediction with iProbiotic and whole-genome similarity using ANI to identify strains of L. acidophilus with potential probiotic activity. According to the results in BlastKOALA and iProbiotics, L. acidophilus NCTC 13721 had the greatest potential among the 64 strains tested, both in terms of its ability to be a Lactobacillus spp. probiotic, when in the amount of genes involved in the metabolism of organic acids and quorum sensing. In addition, DSM 20079 proved to be promising for prospecting new probiotic Lactobacillus from BlastKOALA analyses, as they presented similar results in the number of genes involved in the production of lactic acid, acetic acid, hydrogen peroxide, except for quorum sensing where the NCTC 13721 strain had 14 more genes. L. acidophilus NCTC 13721 and L. acidophilus La-5 strains showed greater ability to be Lactobacillus spp. probiotic capacity, showing 84.8% and 51.9% capacity in the iProbiotics tool, respectively. When analyzed in ANI, none of the evaluated strains showed genomic similarity with NCTC 13721. In contrast, the DSM 20079 strain showed genomic similarity with all evaluated strains except NCTC 13721. Furthermore, eight strains with characteristics with approximately 100% genomic similarity to La-5 were listed: S20_1, LA-5, FSI4, APC2845, LA-G80-111, DS1_1A, LA1, and BCRC 14065. Therefore, according to the findings in iProbiotics and BlastKoala, among the 64 strains evaluated, NCTC 13721 is the most promising strain to be used for future in vitro studies.
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Affiliation(s)
- Rafaella Sinnott Dias
- Post-Graduate Program in Health Sciences, Universidade Federal do Rio Grande - FURG, Faculty of Medicine, Academic Area of the University Hospital, Rio Grande, RS, Brazil.
| | - Frederico Schmitt Kremer
- Bioinformatics Laboratory, Technological Development Center, Federal University of Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | - Luciana Farias da Costa de Avila
- Post-Graduate Program in Health Sciences, Universidade Federal do Rio Grande - FURG, Faculty of Medicine, Academic Area of the University Hospital, Rio Grande, RS, Brazil
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11
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Bonnici V, Mengoni C, Mangoni M, Franco G, Giugno R. PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies. J Biomed Inform 2023; 148:104552. [PMID: 37995844 DOI: 10.1016/j.jbi.2023.104552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/06/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023]
Abstract
Pangenomics was originally defined as the problem of comparing the composition of genes into gene families within a set of bacterial isolates belonging to the same species. The problem requires the calculation of sequence homology among such genes. When combined with metagenomics, namely for human microbiome composition analysis, gene-oriented pangenome detection becomes a promising method to decipher ecosystem functions and population-level evolution. Established computational tools are able to investigate the genetic content of isolates for which a complete genomic sequence is available. However, there is a plethora of incomplete genomes that are available on public resources, which only a few tools may analyze. Incomplete means that the process for reconstructing their genomic sequence is not complete, and only fragments of their sequence are currently available. However, the information contained in these fragments may play an essential role in the analyses. Here, we present PanDelos-frags, a computational tool which exploits and extends previous results in analyzing complete genomes. It provides a new methodology for inferring missing genetic information and thus for managing incomplete genomes. PanDelos-frags outperforms state-of-the-art approaches in reconstructing gene families in synthetic benchmarks and in a real use case of metagenomics. PanDelos-frags is publicly available at https://github.com/InfOmics/PanDelos-frags.
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Affiliation(s)
- Vincenzo Bonnici
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 53/a (Campus), Parma, 43124, PR, Italy.
| | - Claudia Mengoni
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, VR, Italy
| | - Manuel Mangoni
- Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy; Department of Experimental Medicine, Sapienza University of Rome, Rome (RM), Italy
| | - Giuditta Franco
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, VR, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Strada le Grazie, 15, Verona, 37134, VR, Italy
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12
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Nguyen HN, Sharp GM, Stahl-Rommel S, Velez Justiniano YA, Castro CL, Nelman-Gonzalez M, O’Rourke A, Lee MD, Williamson J, McCool C, Crucian B, Clark KW, Jain M, Castro-Wallace SL. Microbial isolation and characterization from two flex lines from the urine processor assembly onboard the international space station. Biofilm 2023; 5:100108. [PMID: 36938359 PMCID: PMC10020673 DOI: 10.1016/j.bioflm.2023.100108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/13/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
Urine, humidity condensate, and other sources of non-potable water are processed onboard the International Space Station (ISS) by the Water Recovery System (WRS) yielding potable water. While some means of microbial control are in place, including a phosphoric acid/hexavalent chromium urine pretreatment solution, many areas within the WRS are not available for routine microbial monitoring. Due to refurbishment needs, two flex lines from the Urine Processor Assembly (UPA) within the WRS were removed and returned to Earth. The water from within these lines, as well as flush water, was microbially evaluated. Culture and culture-independent analysis revealed the presence of Burkholderia, Paraburkholderia, and Leifsonia. Fungal culture also identified Fusarium and Lecythophora. Hybrid de novo genome analysis of the five distinct Burkholderia isolates identified them as B. contaminans, while the two Paraburkholderia isolates were identified as P. fungorum. Chromate-resistance gene clusters were identified through pangenomic analysis that differentiated these genomes from previously studied isolates recovered from the point-of-use potable water dispenser and/or current NCBI references, indicating that unique populations exist within distinct niches in the WRS. Beyond genomic analysis, fixed samples directly from the lines were imaged by environmental scanning electron microscopy, which detailed networks of fungal-bacterial biofilms. This is the first evidence of biofilm formation within flex lines from the UPA onboard the ISS. For all bacteria isolated, biofilm potential was further characterized, with the B. contaminans isolates demonstrating the most considerable biofilm formation. Moreover, the genomes of the B. contaminans revealed secondary metabolite gene clusters associated with quorum sensing, biofilm formation, antifungal compounds, and hemolysins. The potential production of these gene cluster metabolites was phenotypically evaluated through biofilm, bacterial-fungal interaction, and hemolytic assays. Collectively, these data identify the UPA flex lines as a unique ecological niche and novel area of biofilm growth within the WRS. Further investigation of these organisms and their resistance profiles will enable engineering controls directed toward biofilm prevention in future space station water systems.
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Affiliation(s)
| | | | | | | | | | | | - Aubrie O’Rourke
- Exploration Research and Technology, NASA Kennedy Space Center, Merritt Island, FL, USA
| | | | - Jill Williamson
- Space Systems Department, NASA Marshall Space Flight Center, Huntsville, AL, USA
| | | | - Brian Crucian
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX, USA
| | | | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Sarah L. Castro-Wallace
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, TX, USA
- Corresponding author.
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13
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González-Gómez JP, Lozano-Aguirre LF, Medrano-Félix JA, Chaidez C, Gerba CP, Betancourt WQ, Castro-Del Campo N. Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis. Parasitol Res 2023; 122:2641-2650. [PMID: 37676306 DOI: 10.1007/s00436-023-07963-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Cyclospora cayetanensis is an enteric coccidian parasite responsible for gastrointestinal disease transmitted through contaminated food and water. It has been documented in several countries, mostly with low-socioeconomic levels, although major outbreaks have hit developed countries. Detection methods based on oocyst morphology, staining, and molecular testing have been developed. However, the current MLST panel offers an opportunity for enhancement, as amplification of all molecular markers remains unfeasible in the majority of samples. This study aims to address this challenge by evaluating two approaches for analyzing the genetic diversity of C. cayetanensis and identifying reliable markers for subtyping: core homologous genes and mitochondrial genome analysis. A pangenome was constructed using 36 complete genomes of C. cayetanensis, and a haplotype network and phylogenetic analysis were conducted using 33 mitochondrial genomes. Through the analysis of the pangenome, 47 potential markers were identified, emphasizing the need for more sequence data to achieve comprehensive characterization. Additionally, the analysis of mitochondrial genomes revealed 19 single-nucleotide variations that can serve as characteristic markers for subtyping this parasite. These findings not only contribute to the selection of molecular markers for C. cayetanensis subtyping, but they also drive the knowledge toward the potential development of a comprehensive genotyping method for this parasite.
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Affiliation(s)
- Jean P González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México
| | - Luis F Lozano-Aguirre
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A, 62210, Cuernavaca, Morelos, México
| | - José A Medrano-Félix
- Investigadoras e Investigadores por México-Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional Para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a El dorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, Mexico
| | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México
| | - Charles P Gerba
- Department of Environmental Science, Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W, Calle Agua Nueva, Tucson, AZ, 85745, USA
| | - Walter Q Betancourt
- Department of Environmental Science, Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W, Calle Agua Nueva, Tucson, AZ, 85745, USA
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México.
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14
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Manzano-Morales S, Liu Y, González-Bodí S, Huerta-Cepas J, Iranzo J. Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. Genome Biol 2023; 24:250. [PMID: 37904249 PMCID: PMC10614367 DOI: 10.1186/s13059-023-03089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. RESULTS Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. CONCLUSIONS Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.
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Affiliation(s)
- Saioa Manzano-Morales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Barcelona Supercomputing Centre (BSC-CNS) - Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yang Liu
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Sara González-Bodí
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
| | - Jaime Iranzo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.
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15
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Hong H, Yang SM, Kim E, Kim HJ, Park SH. Comprehensive metagenomic analysis of stress-resistant and -sensitive Listeria monocytogenes. Appl Microbiol Biotechnol 2023; 107:6047-6056. [PMID: 37542576 DOI: 10.1007/s00253-023-12693-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/07/2023]
Abstract
Listeria monocytogenes is a pathogenic bacterium which can live in adverse environments (low pH, high salinity, and low temperature). Even though there are various whole genome sequencing (WGS) data on L. monocytogenes, investigations on genetic differences between stress-resistant and -sensitive L. monocytogenes grown under stress environments have been not fully examined. This study aims to investigate and compare genetic characteristics between stress-resistant and -sensitive L. monocytogenes using whole genome sequencing (WGS). A total of 47 L. monocytogenes strains (43 stress-resistant and 4 stress-sensitive) were selected based on the stress-resistance tests under pH 3, 5% salt concentration, and 1 °C. The sequencing library for WGS was prepared and sequenced using an Illumina MiSeq. Genetic characteristics of two different L. monocytogenes groups were examined to analyze the pangenome, functionality, virulence, antibiotic resistance, core, and unique genes. The functionality of unique genes in the stress-resistant L. monocytogenes was distinct compared to the stress-sensitive L. monocytogenes, such as carbohydrate and nucleotide transport and metabolism. The lisR virulence gene was detected more in the stress-resistant L. monocytogenes than in the stress-sensitive group. Five stress-resistant L. monocytogenes strains possessed tet(M) antibiotic resistance gene. This is the first study suggesting that deep genomic characteristics of L. monocytogenes may have different resistance level under stress conditions. This new insight will aid in understanding the genetic relationship between stress-resistant and -sensitive L. monocytogenes strains isolated from diverse resources. KEY POINTS: • Whole genomes of L. monocytogenes isolated from three different sources were analyzed. • Differences in two L. monocytogenes groups were identified in functionality, virulence, and antibiotic resistance genes. • This study first examines the association between resistances and whole genomes of stress-resistant and -sensitive L. monocytogenes.
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Affiliation(s)
- Hyunhee Hong
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
| | - Seung Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Technology, Kyung-Hee University, Gyeonggi-Do, Yongin, 17104, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Technology, Kyung-Hee University, Gyeonggi-Do, Yongin, 17104, Republic of Korea
| | - Hyun Jung Kim
- Korea Food Research Institute, Wanju-Gun, Jeollabuk-Do, Republic of Korea
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA.
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16
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Rajput A, Chauhan SM, Mohite OS, Hyun JC, Ardalani O, Jahn LJ, Sommer MO, Palsson BO. Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family. Food Microbiol 2023; 115:104334. [PMID: 37567624 DOI: 10.1016/j.fm.2023.104334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 08/13/2023]
Abstract
Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Omkar S Mohite
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA
| | - Omid Ardalani
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Leonie J Jahn
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
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17
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Bhattacharya A, Das S, Bhattacharjee MJ, Mukherjee AK, Khan MR. Comparative pangenomic analysis of predominant human vaginal lactobacilli strains towards population-specific adaptation: understanding the role in sustaining a balanced and healthy vaginal microenvironment. BMC Genomics 2023; 24:565. [PMID: 37740204 PMCID: PMC10517566 DOI: 10.1186/s12864-023-09665-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/09/2023] [Indexed: 09/24/2023] Open
Abstract
The vaginal microenvironment of healthy women has a predominance of Lactobacillus crispatus, L. iners, L. gasseri, and L. jensenii. The genomic repertoire of the strains of each of the species associated with the key attributes thereby regulating a healthy vaginal environment needs a substantial understanding.We studied all available human strains of the four lactobacilli across different countries, isolated from vaginal and urinal sources through phylogenetic and pangenomic approaches. The findings showed that L. iners has the highest retention of core genes, and L. crispatus has more gene gain in the evolutionary stratum. Interestingly, L. gasseri and L. jensenii demonstrated major population-specific gene-cluster gain/loss associated with bacteriocin synthesis, iron chelating, adherence, zinc and ATP binding proteins, and hydrolase activity. Gene ontology enrichment analysis revealed that L. crispatus strains showed greater enrichment of functions related to plasma membrane integrity, biosurfactant, hydrogen peroxide synthesis, and iron sequestration as an ancestral derived core function, while bacteriocin and organic acid biosynthesis are strain-specific accessory enriched functions. L. jensenii showed greater enrichment of functions related to adherence, aggregation, and exopolysaccharide synthesis. Notably, the key functionalities are heterogeneously enriched in some specific strains of L. iners and L. gasseri.This study shed light on the genomic features and their variability that provides advantageous attributes to predominant vaginal Lactobacillus species maintaining vaginal homeostasis. These findings evoke the need to consider region-specific candidate strains of Lactobacillus to formulate prophylactic measures against vaginal dysbiosis for women's health.
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Affiliation(s)
- Anupam Bhattacharya
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, 781035, Assam, India
| | - Sushmita Das
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, 781035, Assam, India
- Department of Biotechnology, Gauhati University, Guwahati, 781014, Assam, India
| | - Maloyjo Joyraj Bhattacharjee
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, 781035, Assam, India.
| | - Ashis K Mukherjee
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, 781035, Assam, India
| | - Mojibur Rohman Khan
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, 781035, Assam, India.
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Hyun JC, Palsson BO. Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome. Genome Biol 2023; 24:183. [PMID: 37553643 PMCID: PMC10411014 DOI: 10.1186/s13059-023-03028-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life. RESULTS We construct pangenomes for 183 bacterial species from 54,085 genomes and identify their core genomes using a novel statistical model to estimate genome-specific error rates and underlying gene frequencies. The core genomes are then integrated into a phylogenetic tree to reconstruct the core genome of the last bacterial common ancestor (LBCA), yielding three main results: First, the gene content of modern and ancestral core genomes are diverse at the level of individual genes but are similarly distributed by functional category and share several poorly characterized genes. Second, the LBCA core genome is distinct from any individual modern core genome but has many fundamental biological systems intact, especially those involving translation machinery and biosynthetic pathways to all major nucleotides and amino acids. Third, despite this metabolic versatility, the LBCA core genome likely requires additional non-core genes for viability, based on comparisons with the minimal organism, JCVI-Syn3A. CONCLUSIONS These results suggest that many cellular systems commonly conserved in modern bacteria were not just present in ancient bacteria but were nearly immutable with respect to short-term intraspecies variation. Extending this analysis to other domains of life will likely provide similar insights into more distant ancestral species.
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Affiliation(s)
- Jason C Hyun
- Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA, USA
| | - Bernhard O Palsson
- Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA, USA.
- Department of Bioengineering, University of California, La Jolla, San Diego, CA, USA.
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Liu L, Yu W, Cai K, Ma S, Wang Y, Ma Y, Zhao H. Identification of vaccine candidates against rhodococcus equi by combining pangenome analysis with a reverse vaccinology approach. Heliyon 2023; 9:e18623. [PMID: 37576287 PMCID: PMC10413060 DOI: 10.1016/j.heliyon.2023.e18623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant R. equi and the fact that there is no currently licensed effective vaccine against R. equi warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of R. equi. We then used the RV approach to examine the subcellular localization, host and gut flora homology, antigenicity, transmembrane helices, physicochemical properties, and immunogenicity of the core proteins to select potential vaccine candidates. The vaccine candidates were then subjected to epitope mapping to predict the exposed antigenic epitopes that possess the ability to bind with major histocompatibility complex I/II (MHC I/II) molecules. These vaccine candidates and epitopes will form a library of elements for the development of a polyvalent or universal vaccine against R. equi. Sixteen R. equi complete proteomes were found to contain 6,238 protein families, and the core proteins consisted of 3,969 protein families (∼63.63% of the pangenome), reflecting a low degree of intraspecies genomic variability. From the pool of core proteins, 483 nonhost homologous membrane and extracellular proteins were screened, and 12 vaccine candidates were finally identified according to their antigenicity, physicochemical properties and other factors. These included four cell wall/membrane/envelope biogenesis proteins; four amino acid transport and metabolism proteins; one cell cycle control, cell division and chromosome partitioning protein; one carbohydrate transport and metabolism protein; one secondary metabolite biosynthesis, transport and catabolism protein; and one defense mechanism protein. All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. Thus, we utilized an analytical strategy that combines pangenome analysis and RV to generate a peptide antigen library that simplifies the development of multivalent or universal vaccines against R. equi and can be applied to the development of other vaccines.
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Affiliation(s)
- Lu Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Wanli Yu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Kuojun Cai
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Siyuan Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yanfeng Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yuhui Ma
- Zhaosu Xiyu Horse Industry Co., Ltd. Zhaosu County 835699, Yili Prefecture, Xinjiang, China
| | - Hongqiong Zhao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
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20
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Huff M, Hulse-Kemp AM, Scheffler BE, Youngblood RC, Simpson SA, Babiker E, Staton M. Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. BMC Genomics 2023; 24:409. [PMID: 37474911 PMCID: PMC10357881 DOI: 10.1186/s12864-023-09514-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Muscadine grape (Vitis rotundifolia) is resistant to many of the pathogens that negatively impact the production of common grape (V. vinifera), including the bacterial pathogen Xylella fastidiosa subsp. fastidiosa (Xfsf), which causes Pierce's Disease (PD). Previous studies in common grape have indicated Xfsf delays host immune response with a complex O-chain antigen produced by the wzy gene. Muscadine cultivars range from tolerant to completely resistant to Xfsf, but the mechanism is unknown. RESULTS We assembled and annotated a new, long-read genome assembly for 'Carlos', a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We used these resources to construct an initial pan-genome for three cultivars of muscadine and one cultivar of common grape. This pan-genome contains a total of 34,970 synteny-constrained entries containing genes of similar structure. Comparison of resistance gene content between the 'Carlos' and common grape genomes indicates an expansion of resistance (R) genes in 'Carlos.' We further identified genes involved in Xfsf response by transcriptome sequencing 'Carlos' plants inoculated with Xfsf. We observed 234 differentially expressed genes with functions related to lipid catabolism, oxidation-reduction signaling, and abscisic acid (ABA) signaling as well as seven R genes. Leveraging public data from previous experiments of common grape inoculated with Xfsf, we determined that most differentially expressed genes in the muscadine response were not found in common grape, and three of the R genes identified as differentially expressed in muscadine do not have an ortholog in the common grape genome. CONCLUSIONS Our results support the utility of a pan-genome approach to identify candidate genes for traits of interest, particularly disease resistance to Xfsf, within and between muscadine and common grape.
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Affiliation(s)
- Matthew Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, 27606, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27606, USA
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA
| | - Ebrahiem Babiker
- USDA-ARS Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, 39470, USA.
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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Singh RP, Kumari K, Sharma PK, Ma Y. Characterization and in-depth genome analysis of a halotolerant probiotic bacterium Paenibacillus sp. S-12, a multifarious bacterium isolated from Rauvolfia serpentina. BMC Microbiol 2023; 23:192. [PMID: 37464310 PMCID: PMC10353221 DOI: 10.1186/s12866-023-02939-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes. RESULTS Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability. CONCLUSION The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD-20742, USA
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing, China
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22
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Thorwall S, Trivedi V, Ottum E, Wheeldon I. Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis. Metab Eng 2023; 78:223-234. [PMID: 37369325 DOI: 10.1016/j.ymben.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis. Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling the identification of targets for metabolic engineering of bioproduction hosts.
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Affiliation(s)
- Sarah Thorwall
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
| | - Varun Trivedi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
| | - Eva Ottum
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA; Center for Industrial Biotechnology, University of California, Riverside, CA 92521, USA; Integrative Institute for Genome Biology, University of California, Riverside, CA 92521, USA.
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23
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Prakash JAJ, Jacob JJ, Rachel T, Vasudevan K, Amladi A, Iyadurai R, Manesh A, Veeraraghavan B. Genomic analysis of Brucella melitensis reveals new insights into phylogeny and evolutionary divergence. Indian J Med Microbiol 2023; 44:100360. [PMID: 37356834 DOI: 10.1016/j.ijmmb.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/17/2023] [Accepted: 02/08/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE Brucellosis is a bacterial zoonotic disease caused by genus Brucella. The disease is often transmitted to humans by direct or indirect contact with infected livestock or from laboratory exposure. In this study two clinical isolates of Brucella melitensis were subjected to whole genome sequencing (WGS) using Ion Torrent PGM and Oxford Nanopore MinIon platform. METHODS The two hybrid complete genomes were subjected to core gene SNP analysis to identify the relative evolutionary position. To distinguish between the various lineages of B. melitensis, Pangenome analysis was carried out. RESULTS Phylogenetic analysis revealed that both the study isolates (ST8) clustered along the other Asian isolates that formed genotype II. Genome wide analyses of 326 B melitensis isolates suggests 2171 gene clusters were shared across all the genomes while 3552 gene clusters were considered as accessory genes. CONCLUSION Here we attempted to provide the gain and loss of six unique genes that defined the phylogenetic lineages and complex evolutionary process. As the severity and prevalence of human brucellosis is increasing a better understanding of Brucella genomics and transmission dynamics is needed.
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Affiliation(s)
- John Antony Jude Prakash
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Tanya Rachel
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Anushree Amladi
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Ramya Iyadurai
- Department of General Medicine Unit V, Christian Medical College and Hospital, Vellore 632004, Tamil Nadu, India.
| | - Abi Manesh
- Department of Infectious Diseases, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
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Ahmed OY, Rossi M, Gagie T, Boucher C, Langmead B. SPUMONI 2: improved classification using a pangenome index of minimizer digests. Genome Biol 2023; 24:122. [PMID: 37202771 PMCID: PMC10197461 DOI: 10.1186/s13059-023-02958-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 05/03/2023] [Indexed: 05/20/2023] Open
Abstract
Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a novel sampled document array. By incorporating minimizers, SPUMONI 2's index is 65 times smaller than minimap2's for a mock community pangenome. SPUMONI 2 achieves a speed improvement of 3-fold compared to SPUMONI and 15-fold compared to minimap2. We show SPUMONI 2 achieves an advantageous mix of accuracy and efficiency in practical scenarios such as adaptive sampling, contamination detection and multi-class metagenomics classification.
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Affiliation(s)
- Omar Y. Ahmed
- Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
| | - Massimiliano Rossi
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL USA
| | - Travis Gagie
- Faculty of Computer Science, Dalhousie University, Halifax, NS Canada
| | - Christina Boucher
- Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
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25
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Gong Y, Li Y, Liu X, Ma Y, Jiang L. A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? J Anim Sci Biotechnol 2023; 14:73. [PMID: 37143156 PMCID: PMC10161434 DOI: 10.1186/s40104-023-00860-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/01/2023] [Indexed: 05/06/2023] Open
Abstract
As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future, pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this review, we mainly discuss how pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.
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Affiliation(s)
- Ying Gong
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yefang Li
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xuexue Liu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, 37 allées Jules Guesde, Toulouse, 31000, France
| | - Yuehui Ma
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Lin Jiang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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Henaut-Jacobs S, Passarelli-Araujo H, Venancio TM. Comparative genomics and phylogenomics of Campylobacter unveil potential novel species and provide insights into niche segregation. Mol Phylogenet Evol 2023; 184:107786. [PMID: 37105244 DOI: 10.1016/j.ympev.2023.107786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/17/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023]
Abstract
Campylobacter is a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies on Campylobacter generally focus on specific pathogenic species such as C. coli and C. jejuni. Currently, there are thousands of publicly available Campylobacter genomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all available Campylobacter genomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III of C. coli is in fact a novel species (referred here as Campylobacter spp12). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinct Campylobacter species. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics of Campylobacter species with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that the Campylobacter genus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.
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Affiliation(s)
- Sarah Henaut-Jacobs
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.
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27
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Commichaux S, Rand H, Javkar K, Molloy EK, Pettengill JB, Pightling A, Hoffmann M, Pop M, Jayeola V, Foley S, Luo Y. Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation. BMC Genomics 2023; 24:165. [PMID: 37016310 PMCID: PMC10074901 DOI: 10.1186/s12864-023-09245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to horizontal transfer. RESULTS SNP analysis confirmed that the clinical isolates formed a single, nearly-clonal clade with evidence for ancestry in California going back a decade. The clinical clade had a large core genome (4,399 genes) and a large and sparsely distributed accessory genome (2,577 genes, at least 64% on plasmids). At least 20 plasmid types occurred in the clinical clade, more than were found in the literature for Salmonella Newport. A small number of plasmids, 14 from 13 clinical isolates and 17 from 8 farm isolates, were found to be highly similar (> 95% identical)-indicating they might be related by horizontal transfer. Phylogenetic analysis was unable to determine the geographic origin, isolation source, or time of transfer of the plasmids, likely due to their promiscuous and transient nature. However, our resampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within the NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation. CONCLUSION Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak. Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution.
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Affiliation(s)
- Seth Commichaux
- Center for Food Safety and Nutrition, Food and Drug Administration, Laurel, MD, USA.
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
- Biological Science Graduate Program, University of Maryland, College Park, MD, USA.
| | - Hugh Rand
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Kiran Javkar
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, USA
| | - Erin K Molloy
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - James B Pettengill
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Arthur Pightling
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Maria Hoffmann
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Victor Jayeola
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Steven Foley
- Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR, USA
| | - Yan Luo
- Center for Food Safety and Nutrition, Food and Drug Administration, College Park, MD, USA
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Karthik K, Anbazhagan S, Chitra MA, Sridhar R. Comparative phylogenomics of Trueperella pyogenes reveals host-based distinction of strains. Antonie Van Leeuwenhoek 2023; 116:343-351. [PMID: 36598708 DOI: 10.1007/s10482-022-01806-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Trueperella pyogenes, an opportunistic pathogen causes various ailments in different animals. Different strains from different animals have distinct characters phenotypically and genotypically. Hence understanding the strains in a particular geographical location helps in framing the preventive measures. Comparative genomics of all the available T. pyogenes genome in the NCBI was conducted to understand the relatedness among strains. Whole genome phylogeny showed host associated clustering of strains recovered from swine lungs. Core genome phylogeny also showed host associated clustering mimicking whole genome phylogeny results. MLST analysis showed that there was higher diversity among cattle strains. Multidimensional scaling revealed five swine clusters, two cattle and buffalo clusters. Pangenome analysis also showed that T. pyogenes had an open genome with 57.09% accessory genome. Host specific genes were identified by pangenome analysis, and (R)-citramalate synthase was specific for swine strains of Asian origin. Host specifc genes identified by pangenome analysis can be exploited for developing a molecular assay to specifically identify the strains. The study shows that MLST having higher discriminatory power can be used as an epidemiological tool for strain discrimination of T. pyogenes.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India.
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, Tamil Nadu, 642126, India.
| | - Subbaiyan Anbazhagan
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, 500078, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
| | - Ramaswamy Sridhar
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
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Botelho J, Tüffers L, Fuss J, Buchholz F, Utpatel C, Klockgether J, Niemann S, Tümmler B, Schulenburg H. Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa. EBioMedicine 2023; 90:104532. [PMID: 36958270 PMCID: PMC10053402 DOI: 10.1016/j.ebiom.2023.104532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named A, B, and C). Here, we assessed phylogroup-specific evolutionary dynamics across available and also new P. aeruginosa genomes. METHODS In this genomic analysis, we first generated new genome assemblies for 18 strains of the major P. aeruginosa clone type (mPact) panel, comprising a phylogenetically diverse collection of clinical and environmental isolates for this species. Thereafter, we combined these new genomes with 1991 publicly available P. aeruginosa genomes for a phylogenomic and comparative analysis. We specifically explored to what extent antimicrobial resistance (AMR) genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and "masked" (RGP-free) genomes, and to what extent this variation differs among the phylogroups. FINDINGS We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, inter- and intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events. Finally, we provide here the mPact panel of diverse P. aeruginosa strains that may serve as a valuable reference for functional analyses. INTERPRETATION Altogether, our results highlight distinct pangenome characteristics of the P. aeruginosa phylogroups, which are possibly influenced by variation in the abundance of CRISPR-Cas systems and are shaped by the differential distribution of other defence systems and AMR genes. FUNDING German Science Foundation, Max-Planck Society, Leibniz ScienceCampus Evolutionary Medicine of the Lung, BMBF program Medical Infection Genomics, Kiel Life Science Postdoc Award.
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Affiliation(s)
- João Botelho
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
| | - Leif Tüffers
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany; Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Florian Buchholz
- Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Hinrich Schulenburg
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany; Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.
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Santos RGD, Hurtado R, Rodrigues DLN, Lima A, Dos Anjos WF, Rifici C, Attili AR, Tiwari S, Jaiswal AK, Spier SJ, Mazzullo G, Morais-Rodrigues F, Gomide ACP, de Jesus LCL, Aburjaile FF, Brenig B, Cuteri V, Castro TLDP, Seyffert N, Santos A, Góes-Neto A, de Jesus Sousa T, Azevedo V. Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation. Res Microbiol 2023; 174:103998. [PMID: 36375718 DOI: 10.1016/j.resmic.2022.103998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.
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Affiliation(s)
- Roselane Gonçalves Dos Santos
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Raquel Hurtado
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Diego Lucas Neres Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alessandra Lima
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Claudia Rifici
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Anna Rita Attili
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Sandeep Tiwari
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Arun Kumar Jaiswal
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sharon J Spier
- Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA, USA.
| | - Giuseppe Mazzullo
- Department of Veterinary Science, University of Messina (Italy), Polo Universitario dell'Annunziata, 98168 Messina (ME), Italy.
| | - Francielly Morais-Rodrigues
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Anne Cybelle Pinto Gomide
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luís Cláudio Lima de Jesus
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
| | - Vincenzo Cuteri
- School of Biosciences and Veterinary Medicine, University of Camerino (Italy), Via Circonvallazione 93/95, 62024 Matelica (MC), Italy.
| | - Thiago Luiz de Paula Castro
- Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil; Postgraduate Program in Immunology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil; Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil.
| | - Núbia Seyffert
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Postgraduate Program in Microbiology, Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil.
| | - Anderson Santos
- Department of Computer Science, Federal University of Uberlandia, Uberlandia, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais Brazil.
| | - Thiago de Jesus Sousa
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Vasco Azevedo
- Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Jia Y, Xu M, Hu H, Chapman B, Watt C, Buerte B, Han N, Zhu M, Bian H, Li C, Zeng Z. Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication. BMC Biol 2023; 21:25. [PMID: 36747211 PMCID: PMC9903521 DOI: 10.1186/s12915-022-01503-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. RESULTS Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. CONCLUSIONS Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.
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Affiliation(s)
- Yong Jia
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Mingrui Xu
- grid.410595.c0000 0001 2230 9154College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Haifei Hu
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Brett Chapman
- grid.1025.60000 0004 0436 6763Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia
| | - Calum Watt
- grid.1025.60000 0004 0436 6763Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150 Australia ,grid.516230.30000 0005 0233 6218Intergrain Pty Ltd, Bibra Lake, WA 6163 Australia
| | - B. Buerte
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ning Han
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Muyuan Zhu
- grid.13402.340000 0004 1759 700XInstitute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia. .,Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA, 6151, Australia.
| | - Zhanghui Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China. .,Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou, 311121, China.
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Petersen C, Sørensen T, Nielsen MR, Sondergaard TE, Sørensen JL, Fitzpatrick DA, Frisvad JC, Nielsen KL. Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events. IMA Fungus 2023; 14:3. [PMID: 36726175 PMCID: PMC9893605 DOI: 10.1186/s43008-023-00108-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
The Penicillia are known to produce a wide range natural products-some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.
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Affiliation(s)
- Celine Petersen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
| | - Trine Sørensen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
| | - Mikkel R. Nielsen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Niels-Bohrs Vej 8, 6700 Esbjerg, Denmark
| | - Teis E. Sondergaard
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
| | - Jens L. Sørensen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Niels-Bohrs Vej 8, 6700 Esbjerg, Denmark
| | - David A. Fitzpatrick
- grid.95004.380000 0000 9331 9029Department of Biology, Maynooth University, Maynooth, W23 F2K8 Ireland
| | - Jens C. Frisvad
- grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads B221, 2800 Kgs, Lyngby, Denmark
| | - Kåre L. Nielsen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
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Sun Y, Xiao W, Wang QN, Wang J, Kong XD, Ma WH, Liu SX, Ren P, Xu LN, Zhang YJ. Multiple variation patterns of terpene synthases in 26 maize genomes. BMC Genomics 2023; 24:46. [PMID: 36707768 PMCID: PMC9881264 DOI: 10.1186/s12864-023-09137-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
Terpenoids are important compounds associated with the pest and herbivore resistance mechanisms of plants; consequently, it is essential to identify and explore terpene synthase (TPS) genes in maize. In the present study, we identified 31 TPS genes based on a pan-genome of 26 high-quality maize genomes containing 20 core genes (present in all 26 lines), seven dispensable genes (present in 2 to 23 lines), three near-core genes (present in 24 to 25 lines), and one private gene (present in only 1 line). Evaluation of ka/ks values of TPS in 26 varieties revealed that TPS25 was subjected to positive selection in some varieties. Six ZmTPS had ka/ks values less than 1, indicating that they were subjected to purifying selection. In 26 genomes, significant differences were observed in ZmTPS25 expression between genes affected by structural variation (SV) and those not affected by SV. In some varieties, SV altered the conserved structural domains resulting in a considerable number of atypical genes. The analysis of RNA-seq data of maize Ostrinia furnacalis feeding revealed 10 differentially expressed ZmTPS, 9 of which were core genes. However, many atypical genes for these responsive genes were identified in several genomes. These findings provide a novel resource for functional studies of ZmTPS.
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Affiliation(s)
- Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Wenqing Xiao
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Qing-Nan Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jing Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiang-Dong Kong
- Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wen-Hui Ma
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Si-Xian Liu
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Ping Ren
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Li-Na Xu
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Wang J, Yang W, Zhang S, Hu H, Yuan Y, Dong J, Chen L, Ma Y, Yang T, Zhou L, Chen J, Liu B, Li C, Edwards D, Zhao J. A pangenome analysis pipeline provides insights into functional gene identification in rice. Genome Biol 2023; 24:19. [PMID: 36703158 PMCID: PMC9878884 DOI: 10.1186/s13059-023-02861-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking. RESULTS To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants' position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus (qPH8-1) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS). CONCLUSIONS Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.
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Affiliation(s)
- Jian Wang
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Wu Yang
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Shaohong Zhang
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Haifei Hu
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China ,grid.1025.60000 0004 0436 6763Western Crop Genetics Alliance, Murdoch University, Murdoch, Western Australia 6150 Australia
| | - Yuxuan Yuan
- grid.10784.3a0000 0004 1937 0482School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Jingfang Dong
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Luo Chen
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yamei Ma
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Tifeng Yang
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Lian Zhou
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jiansong Chen
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Bin Liu
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Chengdao Li
- grid.1025.60000 0004 0436 6763Western Crop Genetics Alliance, Murdoch University, Murdoch, Western Australia 6150 Australia
| | - David Edwards
- grid.1012.20000 0004 1936 7910School of Biological Sciences and Centre for Applied Bioinformatics, University of Western Australia, Perth, WA Australia
| | - Junliang Zhao
- grid.135769.f0000 0001 0561 6611Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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Johansson P, Säde E, Hultman J, Auvinen P, Björkroth J. Pangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum. BMC Genomics 2022; 23:818. [PMID: 36494615 PMCID: PMC9733070 DOI: 10.1186/s12864-022-09032-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains with different lifestyles in foods. METHODS We selected as diverse a set of strains as possible in terms of sources, previous genotyping results and geographical distribution, and included also 10 publicly available genomes in our analyses. We studied genomic taxonomy using pairwise average nucleotide identity (ANI) and calculation of digital DNA-DNA hybridisation (dDDH) scores. Phylogeny analyses were done using the core gene set of 1141 single-copy genes and a set of housekeeping genes commonly used for lactic acid bacteria. In addition, the pangenome and core genome sizes as well as some properties, such as acquired antimicrobial resistance (AMR), important due to the growth in foods, were analysed. RESULTS Genome relatedness indices and phylogenetic analyses supported the recently suggested classification that restores the taxonomic position of L. gelidum subsp. gasicomitatum back to the species level as L. gasicomitatum. Genome properties, such as size and coding potential, revealed limited intraspecies variation and showed no attribution to the source of isolation. The distribution of the unique genes between species and subspecies was not associated with the previously documented lifestyle in foods. None of the strains carried any acquired AMR genes or genes associated with any known form of virulence. CONCLUSION Genome-wide examination of strains confirms that the proposition to restore the taxonomic position of L. gasicomitatum is justified. It further confirms that the distribution and lifestyle of L. gelidum and L. gasicomitatum in foods have not been driven by the evolution of functional and phylogenetic diversification detectable at the genome level.
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Affiliation(s)
- Per Johansson
- grid.7737.40000 0004 0410 2071Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Elina Säde
- grid.7737.40000 0004 0410 2071Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Jenni Hultman
- grid.7737.40000 0004 0410 2071Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Johanna Björkroth
- grid.7737.40000 0004 0410 2071Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
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Marone MP, Singh HC, Pozniak CJ, Mascher M. A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes. Plant Methods 2022; 18:128. [PMID: 36461065 PMCID: PMC9719158 DOI: 10.1186/s13007-022-00964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects. RESULTS We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive. CONCLUSION Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/ . The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly .
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Affiliation(s)
- Marina Püpke Marone
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany
- Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, Brazil
| | - Harmeet Chawla Singh
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Curtis J Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Martin Mascher
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Usadel B. Solanaceae pangenomes are coming of graphical age to bring heritability back. aBIOTECH 2022; 3:233-236. [PMID: 36533266 PMCID: PMC9755766 DOI: 10.1007/s42994-022-00087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato, respectively. The latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenome versus a single reference dramatically improves heritability in tomato.
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Affiliation(s)
- Björn Usadel
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University, Düsseldorf, Germany
- IBG-4 Bioinformatics, BioSC, Forschungszentrum Jülich, Jülich, Germany
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Torres-Miranda A, Melis-Arcos F, Garrido D. Characterization and Identification of Probiotic Features in Lacticaseibacillus Paracasei Using a Comparative Genomic Analysis Approach. Probiotics Antimicrob Proteins 2022; 14:1211-1224. [PMID: 36201155 DOI: 10.1007/s12602-022-09999-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2022] [Indexed: 12/25/2022]
Abstract
Lacticaseibacillus paracasei species are widely used for their health-promoting properties in food and agricultural applications. These bacteria have been isolated from various habitats such as the oral cavity, cereals, vegetables, meats, and dairy products conferring them the ability to consume different carbohydrates. Two subspecies are recognized, Lacticaseibacillus paracasei subsp. paracasei and Lacticaseibacillus paracasei subsp. tolerans according to their acid production from carbohydrates. Some strains are currently used as probiotics. In this study, we performed a comparative genomic analysis of 181 genomes of the Lacticaseibacillus paracasei species to reveal genomic differences at the subspecies level and to reveal adaptive and probiotic features, and special emphasis is given to inulin consumption. No clear distinction at the subspecies level for L. paracasei was shown using a phylogenetic tree with orthologous genes from the core-genome set. In general, a good correlation was observed between genomic distance and isolation origin, suggesting that L. paracasei strains are adapted to their natural habitat, giving rise to genetic differences at the genomic level. A low frequency of undesirable characteristics such as plasmids, prophages, antibiotic resistance genes, absence of virulence factors, and frequent bacteriocin production supports these species being good candidates for use as probiotics. Lastly, we found that the inulin gene cluster in L. paracasei strains seems to differ slightly in the presence or absence of some genes but maintains a core defined by at least three fructose-PTS proteins, one hypothetical protein, and extracellular β-fructosidase. Finally, we conclude that further work has to be done for L. paracasei subspecies classification. Improving outgroup selection criteria is a key factor for their correct subspecies assignation.
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Affiliation(s)
- Alexis Torres-Miranda
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile
| | - Felipe Melis-Arcos
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile.
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Ribeiro IDA, Bach E, Passaglia LMP. Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family. Mol Phylogenet Evol 2022; 177:107624. [PMID: 36084857 DOI: 10.1016/j.ympev.2022.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.
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Affiliation(s)
- Igor Daniel Alves Ribeiro
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Evelise Bach
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, RS, Brazil.
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Gourlie R, McDonald M, Hafez M, Ortega-Polo R, Low KE, Abbott DW, Strelkov SE, Daayf F, Aboukhaddour R. The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB. BMC Biol 2022; 20:239. [PMID: 36280878 PMCID: PMC9594970 DOI: 10.1186/s12915-022-01433-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements. RESULTS A comparative genome analysis revealed an open pangenome, with an abundance of accessory genes (~ 57%) reflecting Ptr's adaptability. A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated in this work in addition to previously assembled genomes. We also discovered the involvement of large mobile elements associated with Ptr's effectors: ToxA, the gene encoding for the necrosis effector, was found as a single copy within a 143-kb 'Starship' transposon (dubbed 'Horizon') with a clearly defined target site and target site duplications. 'Horizon' was located on different chromosomes in different isolates, indicating mobility, and the previously described ToxhAT transposon (responsible for horizontal transfer of ToxA) was nested within this newly identified Starship. Additionally, ToxB, the gene encoding the chlorosis effector, was clustered as three copies on a 294-kb element, which is likely a different putative 'Starship' (dubbed 'Icarus') in a ToxB-producing isolate. ToxB and its putative transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and 'Icarus' were both present in a different non-coding isolate. This suggests that ToxB may have been mobile at some point during the evolution of the Ptr genome which is contradictory to the current assumption of ToxB vertical inheritance. Finally, the genome architecture of Ptr was defined as 'one-compartment' based on calculated gene distances and evolutionary rates. CONCLUSIONS These findings together reflect on the highly plastic nature of the Ptr genome which has likely helped to drive its worldwide adaptation and has illuminated the involvement of giant transposons in facilitating the evolution of virulence in Ptr.
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Affiliation(s)
- Ryan Gourlie
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Megan McDonald
- grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, UK
| | - Mohamed Hafez
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Rodrigo Ortega-Polo
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Kristin E. Low
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - D. Wade Abbott
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Stephen E. Strelkov
- grid.17089.370000 0001 2190 316XFaculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB Canada
| | - Fouad Daayf
- grid.21613.370000 0004 1936 9609Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB Canada
| | - Reem Aboukhaddour
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
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Harling-Lee JD, Gorzynski J, Yebra G, Angus T, Fitzgerald JR, Freeman TC. A graph-based approach for the visualisation and analysis of bacterial pangenomes. BMC Bioinformatics 2022; 23:416. [PMID: 36209064 PMCID: PMC9548110 DOI: 10.1186/s12859-022-04898-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation. RESULTS Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur, in the new open-source network analysis platform, Graphia. Both the analysis and the visualisation are scalable to datasets of thousands of genome sequences. CONCLUSIONS We anticipate that the approaches presented here will be of great utility to the microbial research community, allowing faster, more intuitive, and flexible interaction with pangenome datasets, thereby enhancing interpretation of these complex data.
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Affiliation(s)
- Joshua D. Harling-Lee
- grid.4305.20000 0004 1936 7988The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG UK
| | - Jamie Gorzynski
- grid.4305.20000 0004 1936 7988The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG UK
| | - Gonzalo Yebra
- grid.4305.20000 0004 1936 7988The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG UK
| | - Tim Angus
- Roslin Innovation Centre, Easter Bush Campus, Edinburgh, EH25 9RG UK
- Janssen Immunology, 1400 McKean Road, Spring House, PA 19477 USA
| | - J. Ross Fitzgerald
- grid.4305.20000 0004 1936 7988The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG UK
| | - Tom C. Freeman
- grid.4305.20000 0004 1936 7988The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG UK
- Roslin Innovation Centre, Easter Bush Campus, Edinburgh, EH25 9RG UK
- Janssen Immunology, 1400 McKean Road, Spring House, PA 19477 USA
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Deb S. Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus. World J Microbiol Biotechnol 2022; 38:231. [PMID: 36205822 DOI: 10.1007/s11274-022-03430-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/30/2022] [Indexed: 10/10/2022]
Abstract
Previous studies were mainly focused on genomic evolution and diversity of type species of Bifidobacterium genus due to their health-promoting effect on host. However, those studies were mainly based on species-level taxonomic resolution, adaptation, and characterization of carbohydrate metabolic features of the bifidobacterial species. Here, a comprehensive analysis of the type strain genome unveils the association of pan-genome evolution with the divergence of metabolic function of the Bifidobacterium genus. This study has also demonstrated that horizontal gene transfer, as well as genome expansion and reduction events, leads to the divergence of metabolic functions in Bifidobacterium genus. Furthermore, the genome-based search of probiotic traits among all the available bifidobacterial type strains gives hints on type species, that could confer health benefits to nutrient-deficient individuals. Altogether, the present study provides insight into the developments of genomic evolution, functional divergence, and potential probiotic type species of the Bifidobacterium genus.
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Affiliation(s)
- Sushanta Deb
- Department of Molecular Biology and Bioinformatics, Tripura University, Suryamaninagar, 799022, Tripura, India. .,All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.
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Karthik K, Anbazhagan S, Chitra MA, Sridhar R. First report of the whole genome of Moraxella bovoculi genotype 1 from India and comparative genomics of Moraxella bovoculi to identify genotype-specific markers. Arch Microbiol 2022; 204:663. [PMID: 36201053 DOI: 10.1007/s00203-022-03276-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/02/2022]
Abstract
Moraxella bovoculi has been isolated frequently from cattle with Infectious bovine keratoconjunctivitis (IBK). Two diverse genotypes of M. bovoculi, 1 and 2 were identified based on whole genome sequence analysis. It is essential to discriminate between the two genotypes to frame prevention and control measures. The whole genome of M. bovoculi TN7 was sequenced and compared to other M. bovoculi strains available in the NCBI database. M. bovoculi TN7 was found to be genotype 1, had an RTX toxin operon and pilA gene that are the known virulence factors in related Moraxella sp., but lacked antimicrobial resistance genes. M. bovoculi was found to have an open pangenome with 4051 (75.31%) accessory genes, and the addition of each new genome adds 18 genes to the pangenome. Comparison of pilin protein amino acid sequences revealed three new sequence types. Furthermore, the presence of linx, nagL, swrC and mdtA genes was found to be genotype 1 specific, whereas hyaD, garR, gbsA, yhdG, gabT, iclR, higB2, hmuU, hmuT and hemS were found only in genotype 2. Polymerase Chain Reaction (PCR) primers were designed and evaluated on strain TN7 plus seven additional strains accessible to us that had not been whole genome sequenced. This initial evaluation of the designed primers for the linX and hyaD genes produced the expected banding patterns on PCR gels for genotypes 1 and 2, respectively, among the 8 strains. The genotype-specific genes identified in this study can be used as markers for accurate diagnosis of genotype 1 isolates and this can aid in the development of autogenous or other molecular vaccines for treatment of infectious bovine keratoconjunctivitis (IBK) in resource-limited research settings.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India. .,Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, Tamil Nadu, India.
| | - Subbaiyan Anbazhagan
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, 500078, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
| | - Ramaswamy Sridhar
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
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Picazo DR, Werner A, Dagan T, Kupczok A. Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance. Genome Biol Evol 2022; 14:6613374. [PMID: 35731940 PMCID: PMC9260185 DOI: 10.1093/gbe/evac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained..
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Affiliation(s)
- Devani Romero Picazo
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Almut Werner
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
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Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol 2022; 20:146. [PMID: 35710371 PMCID: PMC9205054 DOI: 10.1186/s12915-022-01347-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. RESULTS Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. CONCLUSIONS This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.
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Affiliation(s)
- Erwin Tantoso
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Miles Kirsch
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: Northeastern University, Boston, USA
| | - Vladimir Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Zhiya Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: The University of Cambridge, Cambridge, UK
| | - Frank Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore, Republic of Singapore.
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Mohd Saad NS, Neik TX, Thomas WJW, Amas JC, Cantila AY, Craig RJ, Edwards D, Batley J. Advancing designer crops for climate resilience through an integrated genomics approach. Curr Opin Plant Biol 2022; 67:102220. [PMID: 35489163 DOI: 10.1016/j.pbi.2022.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm diversity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.
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Affiliation(s)
- Nur Shuhadah Mohd Saad
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway, 47500, Selangor, Malaysia
| | - William J W Thomas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Junrey C Amas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Aldrin Y Cantila
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ryan J Craig
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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Kim E, Yang SM, Kim IS, Kim HY. Identification of novel molecular targets for Weissella species-specific real-time PCR based on pangenome analysis. Appl Microbiol Biotechnol 2022; 106:4157-4168. [PMID: 35672470 DOI: 10.1007/s00253-022-12003-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/24/2023]
Abstract
Some Weissella species are used in probiotic products because of their beneficial effects in humans, whereas some species are considered as opportunistic pathogens that cause infections in humans. Therefore, an accurate and rapid identification of Weissella species is essential to control pathogenic Weissella species or isolate new functional strains with probiotic effects from their habitat. The objective of our study was to extract novel molecular targets using pangenome analysis for the identification of major Weissella species present in food. With 50 genomes representing 11 Weissella species, novel molecular targets were mined based on their 100% presence in the respective strains of the target species and absence in the strains of non-target bacteria. Primers based on molecular targets showed positive results for the corresponding species, whereas 79 non-target strains showed negative results. Standard curves revealed good linearity in the range of 103-108 colony-forming units per reaction. Our method was successfully applied to 74 Weissella strains isolated from food samples to demonstrate that the molecular targets provided a viable alternative to the 16S rRNA sequence. Furthermore, it was possible to identify and quantify Weissella communities in fermented foods. These results demonstrate that our method can be used for effective and accurate screening for the presence of Weissella species in foods. KEY POINTS: • This is first study to mine novel targets for differentiating 11 Weissella species. • The novel targets showed higher resolution than the 16S rRNA gene sequence. • The PCR method effectively detected Weissella species with opposing properties.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ik-Seon Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
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Bach E, Rangel CP, Ribeiro IDA, Passaglia LMP. Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. Mol Genet Genomics 2022. [PMID: 35612623 DOI: 10.1007/s00438-022-01907-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
Abstract
Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.
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Beier S, Thomson NR. Panakeia - a universal tool for bacterial pangenome analysis. BMC Genomics 2022; 23:265. [PMID: 35382730 PMCID: PMC8985272 DOI: 10.1186/s12864-022-08303-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Background Development of new pan-genome analysis tools is important, as the pangenome of a microbial species has become an important method to define the diversity of a selected taxon, most commonly a species, in the last years. This enables comparison of strains from different ecological niches and can be used to define the functional potential in a bacterial population. It gives us a much better view of microbial genomics than can be gained from singular genomes which after all are just single representatives of a much more varied population. Results We present Panakeia, a tool which strives to be easy to use and providing a detailed view of the pangenome structure which can efficiently be utilised for discovery, or further in-depth analysis, of features of interest. It analyses synteny and multiple structural patterns of the pangenome, giving insights into the biological diversity and evolution of the studied taxon. Panakeia hence provides both broad and detailed information on the structure of a pangenome, for diverse and highly clonal populations of bacteria. Conclusions Previously published pangenome tools often reduce the information to a presence/absence matrix of unconnected genes or generate massive hard to interpret output graphs. However, Panakeia includes synteny and structural information and presents it in a way that can readily be used for further analysis. Panakeia can be downloaded at https://github.com/BioSina/Panakeiatogether with a detailed User Guide.
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Affiliation(s)
- Sina Beier
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Sulston Building, Hinxton, CB10 1RQ, UK.
| | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Sulston Building, Hinxton, CB10 1RQ, UK
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50
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Roux E, Nicolas A, Valence F, Siekaniec G, Chuat V, Nicolas J, Le Loir Y, Guédon E. The genomic basis of the Streptococcus thermophilus health-promoting properties. BMC Genomics 2022; 23:210. [PMID: 35291951 PMCID: PMC8925076 DOI: 10.1186/s12864-022-08459-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
Background Streptococcus thermophilus is a Gram-positive bacterium widely used as starter in the dairy industry as well as in many traditional fermented products. In addition to its technological importance, it has also gained interest in recent years as beneficial bacterium due to human health-promoting functionalities. The objective of this study was to inventory the main health-promoting properties of S. thermophilus and to study their intra-species diversity at the genomic and genetic level within a collection of representative strains. Results In this study various health-related functions were analyzed at the genome level from 79 genome sequences of strains isolated over a long time period from diverse products and different geographic locations. While some functions are widely conserved among isolates (e.g., degradation of lactose, folate production) suggesting their central physiological and ecological role for the species, others including the tagatose-6-phosphate pathway involved in the catabolism of galactose, and the production of bioactive peptides and gamma-aminobutyric acid are strain-specific. Most of these strain-specific health-promoting properties seems to have been acquired via horizontal gene transfer events. The genetic basis for the phenotypic diversity between strains for some health related traits have also been investigated. For instance, substitutions in the galK promoter region correlate with the ability of some strains to catabolize galactose via the Leloir pathway. Finally, the low occurrence in S. thermophilus genomes of genes coding for biogenic amine production and antibiotic resistance is also a contributing factor to its safety status. Conclusions The natural intra-species diversity of S. thermophilus, therefore, represents an interesting source for innovation in the field of fermented products enriched for healthy components that can be exploited to improve human health. A better knowledge of the health-promoting properties and their genomic and genetic diversity within the species may facilitate the selection and application of strains for specific biotechnological and human health-promoting purpose. Moreover, by pointing out that a substantial part of its functional potential still defies us, our work opens the way to uncover additional health-related functions through the intra-species diversity exploration of S. thermophilus by comparative genomics approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08459-y.
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Affiliation(s)
- Emeline Roux
- INRAE, Institut Agro, STLO, Rennes, France.,Université de Lorraine, CALBINOTOX, Nancy, France.,Université de Rennes, INRIA, Campus de Beaulieu, Rennes, France
| | | | | | - Grégoire Siekaniec
- INRAE, Institut Agro, STLO, Rennes, France.,Université de Rennes, INRIA, Campus de Beaulieu, Rennes, France
| | | | - Jacques Nicolas
- Université de Rennes, INRIA, Campus de Beaulieu, Rennes, France
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