A novel termini analysis theory using HTS data alone for the identification of Enterococcus phage EF4-like genome termini

BMC Genomics

Yigang Tong¹  Yubao Chen²  Wei Wang¹  Zhiyi Zhang¹  Zhiqiang Mi¹  Hang Fan¹  Yong Huang¹  Guangqian Pei¹  Xiaoping An¹  Shasha Li¹  Yahui Wang³  Xianglilan Zhang¹ 

[1]State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P.R. China

[2]Beijing Computing Center, Beijing 100094, P.R. China

[3]School of Life Science & Technology, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, P.R. China

关键词: Genome termini;    Phage;    Antibiotic-resistant Enterococcus;    Termini analysis theory;   

Others  :  1208965
DOI  :  10.1186/s12864-015-1612-3

 received in 2014-07-04, accepted in 2015-05-04,  发布年份 2015

【 摘 要 】

Background

Enterococcus faecalis and Enterococcus faecium are typical enterococcal bacterial pathogens. Antibiotic resistance means that the identification of novel E. faecalis and E. faecium phages against antibiotic-resistant Enterococcus have an important impact on public health. In this study, the E. faecalis phage IME-EF4, E. faecium phage IME-EFm1, and both their hosts were antibiotic resistant. To characterize the genome termini of these two phages, a termini analysis theory was developed to provide a wealth of terminal sequence information directly, using only high-throughput sequencing (HTS) read frequency statistics.

Results

The complete genome sequences of phages IME-EF4 and IME-EFm1 were determined, and our termini analysis theory was used to determine the genome termini of these two phages. Results showed 9 bp 3′ protruding cohesive ends in both IME-EF4 and IME-EFm1 genomes by analyzing frequencies of HTS reads. For the positive strands of their genomes, the 9 nt 3′ protruding cohesive ends are 5′-TCATCACCG-3′ (IME-EF4) and 5′-GGGTCAGCG-3′ (IME-EFm1). Further experiments confirmed these results. These experiments included mega-primer polymerase chain reaction sequencing, terminal run-off sequencing, and adaptor ligation followed by run-off sequencing.

Conclusion

Using this termini analysis theory, the termini of two newly isolated antibiotic-resistant Enterococcus phages, IME-EF4 and IME-EFm1, were identified as the byproduct of HTS. Molecular biology experiments confirmed the identification. Because it does not require time-consuming wet lab termini analysis experiments, the termini analysis theory is a fast and easy means of identifying phage DNA genome termini using HTS read frequency statistics alone. It may aid understanding of phage DNA packaging.

【 授权许可】

   
2015 Zhang et al.; licensee BioMed Central.

【 图 表 】

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