Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile

Muhammad Nafees Ur Rehman; Farman Ullah Dawar; Jifeng Zeng; Lixia Fan; Wei Feng; Mengqi Wang; Nuo Yang; Guiying Guo; Jiping Zheng

doi:10.3389/fvets.2023.1140655

Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile

Front Vet Sci. 2023 Mar 9:10:1140655. doi: 10.3389/fvets.2023.1140655. eCollection 2023.

Authors

Muhammad Nafees Ur Rehman¹, Farman Ullah Dawar², Jifeng Zeng^{1

3}, Lixia Fan¹, Wei Feng¹, Mengqi Wang¹, Nuo Yang¹, Guiying Guo¹, Jiping Zheng^{1

3}

Affiliations

¹ Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China.
² Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan.
³ One Health Institute, Hainan University, Haikou, China.

Abstract

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.

Keywords: Edwardsiella tarda SC002; comparative genomics; genome annotation; genome sequencing; pan-genome.

Grants and funding

This study received funding from the National Natural Science Foundation of China (Grants 32060788 to JZe and 32060131 to JZh) and the Hainan Provincial Natural Science Foundation of China (Grants 321MS007 to GG, 821MS029 to NY, 821RC1052 to LF, and 2019RC084 to JZh).