1
|
Singh V, West G, Fiocchi C, Cominelli F, Good CE, Jacobs MR, Rodriguez-Palacios A. Genomes of Bacteroides ovatus, B. cellulosilyticus, B. uniformis, Phocaeicola vulgatus, and P. dorei isolated from gut cavernous fistulous tract micropathologies in Crohn's disease. Microbiol Resour Announc 2024; 13:e0115223. [PMID: 38411071 PMCID: PMC11008141 DOI: 10.1128/mra.01152-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Surgically removed bowels from Crohn's disease patients exhibit a novel form of micropathologies known as cavernous fistulous tract microlesions (CavFT), resembling fissures. We announce the genomes/plasmids and antimicrobial resistance genes of six CavFT bacterial isolates representing the Bacteroidota genera Bacteroides and Phocaeicola. Plasmids were identified in Bacteroides cellulosilyticus and Phocaeicola vulgatus.
Collapse
Affiliation(s)
- Vaidhvi Singh
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Gail West
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Claudio Fiocchi
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Fabio Cominelli
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Caryn E. Good
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael R. Jacobs
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Alexander Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| |
Collapse
|
2
|
Oh EJ, Hwang IS, Park IW, Oh CS. Comparative Genome Analyses of Clavibacter michiganensis Type Strain LMG7333 T Reveal Distinct Gene Contents in Plasmids From Other Clavibacter Species. Front Microbiol 2022; 12:793345. [PMID: 35178040 PMCID: PMC8844524 DOI: 10.3389/fmicb.2021.793345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Clavibacter michiganensis, a Gram-positive, plant-pathogenic bacterium belonging to Actinobacteria, is a causal agent of bacterial canker in tomatoes. Although LMG7333T is the type strain of C. michiganensis, it has not been used in many studies, probably because of a lack of the complete genome sequence being available. Therefore, in this study, the complete genome sequence of this type strain was obtained, and comparative genome analysis was conducted with the genome sequences of two other C. michiganensis strains and type strains of Clavibacter species, of which their complete genome sequences are available. C. michiganensis LMG7333T carries one chromosome and two plasmids, pCM1 and pCM2, like two other C. michiganensis strains. All three chromosomal DNA sequences were almost identical. However, the DNA sequences of two plasmids of LMG7333T are similar to those of UF1, but different from those of NCPPB382, indicating that both plasmids carry distinct gene content among C. michiganensis strains. Moreover, 216 protein-coding sequences (CDSs) were only present in the LMG7333T genome compared with type strains of other Clavibacter species. Among these 216 CDSs, approximately 83% were in the chromosome, whereas others were in both plasmids (more than 6% in pCM1 and 11% in pCM2). However, the ratio of unique CDSs of the total CDSs in both plasmids were approximately 38% in pCM1 and 30% in pCM2, indicating that the high gene content percentage in both plasmids of C. michiganensis are different from those of other Clavibacter species, and plasmid DNAs might be derived from different origins. A virulence assay with C. michiganensis LMG7333T using three different inoculation methods, root-dipping, leaf-clipping, and stem injection, resulted in typical disease symptoms, including wilting and canker in tomato. Altogether, our results indicate that two plasmids of C. michiganensis carry distinct gene content, and the genome information of the type strain LMG7333T will help to understand the genetic diversity of the two plasmids of Clavibacter species, including C. michiganensis.
Collapse
Affiliation(s)
- Eom-Ji Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - In Sun Hwang
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - In Woong Park
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea.,Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| |
Collapse
|
3
|
Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains. Appl Environ Microbiol 2020; 86:AEM.02873-19. [PMID: 31924620 DOI: 10.1128/aem.02873-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections.IMPORTANCE Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensis sensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.
Collapse
|
4
|
Hwang IS, Oh EJ, Lee HB, Oh CS. Functional Characterization of Two Cellulase Genes in the Gram-Positive Pathogenic Bacterium Clavibacter michiganensis for Wilting in Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:491-501. [PMID: 30345870 DOI: 10.1094/mpmi-08-18-0227-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Diverse plant pathogens secrete cellulases to degrade plant cell walls. Previously, the plasmid-borne cellulase gene celA was shown to be important for the virulence of the gram-positive bacterium Clavibacter michiganensis in tomato. However, details of the contribution of cellulases to the development of wilting in tomato have not been well-determined. To better understand the contribution of cellulases to the virulence of C. michiganensis in tomato, a mutant lacking cellulase activity was generated and complemented with truncated forms of certain cellulase genes, and virulence of those strain was examined. A celA mutant of the C. michiganensis type strain LMG7333 lost its cellulase activity and almost all its ability to cause wilting in tomato. The cellulase catalytic domain and cellulose-binding domain of CelA together were sufficient for both cellulase activity and the development of wilting in tomato. However, the expansin domain did not affect virulence or cellulase activity. The celA ortholog of Clavibacter sepedonicus restored the full virulence of the celA mutant of C. michiganensis. Another cellulase gene, celB, located in the chromosome, carries a single-base deletion in most C. michiganensis strains but does not carry a functional signal peptide in its N terminus. Nevertheless, an experimentally modified CelB protein with a CelA signal peptide was secreted and able to cause wilting in tomato. These results indicate that cellulases are major virulence factors of C. michiganensis that causes wilting in tomato. Furthermore, there are natural variations among cellulase genes directly affecting their function.
Collapse
Affiliation(s)
- In Sun Hwang
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Eom-Ji Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Han Beoyl Lee
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104, Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104, Korea
| |
Collapse
|
5
|
Hwang IS, Oh EJ, Kim D, Oh CS. Multiple plasmid-borne virulence genes of Clavibacter michiganensis ssp. capsici critical for disease development in pepper. THE NEW PHYTOLOGIST 2018; 217:1177-1189. [PMID: 29134663 DOI: 10.1111/nph.14896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/12/2017] [Indexed: 05/24/2023]
Abstract
Clavibacter michiganensis ssp. capsici is a Gram-positive plant-pathogenic bacterium causing bacterial canker disease in pepper. Virulence genes and mechanisms of C. michiganensis ssp. capsici in pepper have not yet been studied. To identify virulence genes of C. michiganensis ssp. capsici, comparative genome analyses with C. michiganensis ssp. capsici and its related C. michiganensis subspecies, and functional analysis of its putative virulence genes during infection were performed. The C. michiganensis ssp. capsici type strain PF008 carries one chromosome (3.056 Mb) and two plasmids (39 kb pCM1Cmc and 145 kb pCM2Cmc ). The genome analyses showed that this bacterium lacks a chromosomal pathogenicity island and celA gene that are important for disease development by C. michiganensis ssp. michiganensis in tomato, but carries most putative virulence genes in both plasmids. Virulence of pCM1Cmc -cured C. michiganensis ssp. capsici was greatly reduced compared with the wild-type strain in pepper. The complementation analysis with pCM1Cmc -located putative virulence genes showed that at least five genes, chpE, chpG, ppaA1, ppaB1 and pelA1, encoding serine proteases or pectate lyase contribute to disease development in pepper. In conclusion, C. michiganensis ssp. capsici has a unique genome structure, and its multiple plasmid-borne genes play critical roles in virulence in pepper, either separately or together.
Collapse
Affiliation(s)
- In Sun Hwang
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| | - Eom-Ji Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| | - Donghyuk Kim
- Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| |
Collapse
|
6
|
Lu Y, Ishimaru CA, Glazebrook J, Samac DA. Comparative Genomic Analyses of Clavibacter michiganensis subsp. insidiosus and Pathogenicity on Medicago truncatula. PHYTOPATHOLOGY 2018; 108:172-185. [PMID: 28952422 DOI: 10.1094/phyto-05-17-0171-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Clavibacter michiganensis is the most economically important gram-positive bacterial plant pathogen, with subspecies that cause serious diseases of maize, wheat, tomato, potato, and alfalfa. Much less is known about pathogenesis involving gram-positive plant pathogens than is known for gram-negative bacteria. Comparative genome analyses of C. michiganensis subspecies affecting tomato, potato, and maize have provided insights on pathogenicity. In this study, we identified strains of C. michiganensis subsp. insidiosus with contrasting pathogenicity on three accessions of the model legume Medicago truncatula. We generated complete genome sequences for two strains and compared these to a previously sequenced strain and genome sequences of four other subspecies. The three C. michiganensis subsp. insidiosus strains varied in gene content due to genome rearrangements, most likely facilitated by insertion elements, and plasmid number, which varied from one to three depending on strain. The core C. michiganensis genome consisted of 1,917 genes, with 379 genes unique to C. michiganensis subsp. insidiosus. An operon for synthesis of the extracellular blue pigment indigoidine, enzymes for pectin degradation, and an operon for inositol metabolism are among the unique features. Secreted serine proteases belonging to both the pat-1 and ppa families were present but highly diverged from those in other subspecies.
Collapse
Affiliation(s)
- You Lu
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
| | - Carol A Ishimaru
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
| | - Jane Glazebrook
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
| | - Deborah A Samac
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
| |
Collapse
|
7
|
Li X, Tambong J, Yuan KX, Chen W, Xu H, Lévesque CA, De Boer SH. Re-classification of Clavibacter michiganensis subspecies on the basis of whole-genome and multi-locus sequence analyses. Int J Syst Evol Microbiol 2017; 68:234-240. [PMID: 29160202 PMCID: PMC5882085 DOI: 10.1099/ijsem.0.002492] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA-DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov.
Collapse
Affiliation(s)
- Xiang Li
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - James Tambong
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Kat Xiaoli Yuan
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - Wen Chen
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Huimin Xu
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - C André Lévesque
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Solke H De Boer
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| |
Collapse
|
8
|
Thapa SP, Pattathil S, Hahn MG, Jacques MA, Gilbertson RL, Coaker G. Genomic Analysis of Clavibacter michiganensis Reveals Insight Into Virulence Strategies and Genetic Diversity of a Gram-Positive Bacterial Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:786-802. [PMID: 28677494 DOI: 10.1094/mpmi-06-17-0146-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial canker disease. In this study, we sequenced and assembled genomes of 11 C. michiganensis subsp. michiganensis strains isolated from infected tomato fields in California as well as five Clavibacter strains that colonize tomato endophytically but are not pathogenic in this host. The analysis of the C. michiganensis subsp. michiganensis genomes supported the monophyletic nature of this pathogen but revealed genetic diversity among strains, consistent with multiple introduction events. Two tomato endophytes that clustered phylogenetically with C. michiganensis strains capable of infecting wheat and pepper and were also able to cause disease in these plants. Plasmid profiles of the California strains were variable and supported the essential role of the pCM1-like plasmid and the CelA cellulase in virulence, whereas the absence of the pCM2-like plasmid in some pathogenic C. michiganensis subsp. michiganensis strains revealed it is not essential. A large number of secreted C. michiganensis subsp. michiganensis proteins were carbohydrate-active enzymes (CAZymes). Glycome profiling revealed that C. michiganensis subsp. michiganensis but not endophytic Clavibacter strains is able to extensively alter tomato cell-wall composition. Two secreted CAZymes found in all C. michiganensis subsp. michiganensis strains, CelA and PelA1, enhanced pathogenicity on tomato. Collectively, these results provide a deeper understanding of C. michiganensis subsp. michiganensis diversity and virulence strategies.
Collapse
Affiliation(s)
- Shree P Thapa
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Sivakumar Pattathil
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | - Michael G Hahn
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | | | - Robert L Gilbertson
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Gitta Coaker
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| |
Collapse
|
9
|
Tambong JT. Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops. PLoS One 2017; 12:e0172295. [PMID: 28319117 PMCID: PMC5358740 DOI: 10.1371/journal.pone.0172295] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/02/2017] [Indexed: 11/18/2022] Open
Abstract
Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria.
Collapse
Affiliation(s)
- James T. Tambong
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail:
| |
Collapse
|