Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile
Edwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease “Edwardsiellosis”. It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this stud...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Veterinary Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2023.1140655/full |
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| author | Muhammad Nafees Ur Rehman Farman Ullah Dawar Jifeng Zeng Jifeng Zeng Lixia Fan Wei Feng Mengqi Wang Nuo Yang Guiying Guo Jiping Zheng Jiping Zheng |
| author_facet | Muhammad Nafees Ur Rehman Farman Ullah Dawar Jifeng Zeng Jifeng Zeng Lixia Fan Wei Feng Mengqi Wang Nuo Yang Guiying Guo Jiping Zheng Jiping Zheng |
| author_sort | Muhammad Nafees Ur Rehman |
| collection | DOAJ |
| description | Edwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease “Edwardsiellosis”. It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this study, we investigated the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002 isolated from hatchlings of the Siamese crocodile. The genome of SC002 consisted of one circular chromosome of length 3,662,469 bp with a 57.29% G+C content and four novel plasmids. A total of 3,734 protein-coding genes, 12 genomic islands (GIs), 7 prophages, 48 interspersed repeat sequences, 248 tandem repeat sequences, a CRISPR component with a total length of 175 bp, and 171 ncRNAs (tRNA = 106, sRNA = 37, and rRNA = 28) were predicted. In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). Pan-genome and comparative genome analyses of the complete sequenced genomes confirmed their evolutionary relationships. The present study confirmed that E. tarda SC002 is a potential pathogen bearing a bulk amount of antibiotic resistance, virulence, and pathogenic genes and its open pan-genome may enhance its host range in the future. |
| first_indexed | 2024-04-10T05:11:14Z |
| format | Article |
| id | doaj.art-1dee883a8873413e91ceeab0dd4e3957 |
| institution | Directory Open Access Journal |
| issn | 2297-1769 |
| language | English |
| last_indexed | 2024-04-10T05:11:14Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Veterinary Science |
| spelling | doaj.art-1dee883a8873413e91ceeab0dd4e39572023-03-09T07:08:28ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692023-03-011010.3389/fvets.2023.11406551140655Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodileMuhammad Nafees Ur Rehman0Farman Ullah Dawar1Jifeng Zeng2Jifeng Zeng3Lixia Fan4Wei Feng5Mengqi Wang6Nuo Yang7Guiying Guo8Jiping Zheng9Jiping Zheng10Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaDepartment of Zoology, Kohat University of Science and Technology, Kohat, PakistanLaboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaOne Health Institute, Hainan University, Haikou, ChinaLaboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaLaboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaLaboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaLaboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaLaboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaLaboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, ChinaOne Health Institute, Hainan University, Haikou, ChinaEdwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease “Edwardsiellosis”. It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this study, we investigated the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002 isolated from hatchlings of the Siamese crocodile. The genome of SC002 consisted of one circular chromosome of length 3,662,469 bp with a 57.29% G+C content and four novel plasmids. A total of 3,734 protein-coding genes, 12 genomic islands (GIs), 7 prophages, 48 interspersed repeat sequences, 248 tandem repeat sequences, a CRISPR component with a total length of 175 bp, and 171 ncRNAs (tRNA = 106, sRNA = 37, and rRNA = 28) were predicted. In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). Pan-genome and comparative genome analyses of the complete sequenced genomes confirmed their evolutionary relationships. The present study confirmed that E. tarda SC002 is a potential pathogen bearing a bulk amount of antibiotic resistance, virulence, and pathogenic genes and its open pan-genome may enhance its host range in the future.https://www.frontiersin.org/articles/10.3389/fvets.2023.1140655/fullEdwardsiella tarda SC002genome annotationpan-genomegenome sequencingcomparative genomics |
| spellingShingle | Muhammad Nafees Ur Rehman Farman Ullah Dawar Jifeng Zeng Jifeng Zeng Lixia Fan Wei Feng Mengqi Wang Nuo Yang Guiying Guo Jiping Zheng Jiping Zheng Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile Frontiers in Veterinary Science Edwardsiella tarda SC002 genome annotation pan-genome genome sequencing comparative genomics |
| title | Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile |
| title_full | Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile |
| title_fullStr | Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile |
| title_full_unstemmed | Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile |
| title_short | Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile |
| title_sort | complete genome sequence analysis of edwardsiella tarda sc002 from hatchlings of siamese crocodile |
| topic | Edwardsiella tarda SC002 genome annotation pan-genome genome sequencing comparative genomics |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2023.1140655/full |
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