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Table 6 The results obtained from the RDP4 analyses exhibiting the recombination beginning and end breakpoints across the LGT-affected genetic loci, and the trajectories of the LGT events of these loci, involving the Staphylococcus phage JD419 and the S. aureus strains

From: Genetic recombination-mediated evolutionary interactions between phages of potential industrial importance and prophages of their hosts within or across the domains of Escherichia, Listeria, Salmonella, Campylobacter, and Staphylococcus

Recombinant strain

(GenBank acc. #)

Major donor

(GenBank acc. #)

Minor donor

(GenBank acc. #)

CDS, for a protein, within a phage genomic region examined

(Coordinates in a phage genome [size in bps])

Recombination beginning and end breakpoints

(99% Cl) *

P-value generated by

the RDP4 algorithm

 

S. aureus strain FDAARGOS_1

(CP026968.1)

S. aureus strain 14,640

(CP053636)

Staphylococcus phage JD419

(MT899504.1)

Lysin, N-acetylmuramoyl-L-alanine amidase

(ID: QOI66741.1) CDS: Complement (759.2213).

(30494.40525 [10,032])

122 (70–833) – Undetermined (1066–2170)

RDP:

GENECONV

BootScan:

MaxChi:

Chimaera:

SiScan:

3Seq:

2.163 × 10− 04

2.204 × 10− 04

2.206 × 10− 04

4.240 × 10− 10

2.510 × 10− 09

2.194 × 10− 07

3.982 × 10− 12

 

Staphylococcus phage JD419

(MT899504.1)

S. aureus strain MRSA107

(CP018629.1)

S. aureus strain N17CSA11

(CP107527.1)

CDS of hypothetical proteins (IDs: QOI66719.1; QOI66720.1; QOI66721.1; QOI66722.1; ): 2663.2962; 3008.3172; 3165.3554; 3554.5020. Putative major teichoic acid biosynthesis (ID: QOI66743.1) CDS: 5020.6930. Hypothetical protein (ID: QOI66723.1) CDS: 6946.7236. Tail fiber (ID: QOI66744.1) CDS: 7236.8819. Tail fiber (ID: QOI66745.1) CDS: 8828.9652. Tail length tape-measure protein (ID: QOI66746.1) CDS: 9652.>10,032.

(30494.40525 [10,032])

3364 (2808–3620) – 10,026 (10016-13)

RDP:

GENECONV

BootScan:

MaxChi:

Chimaera:

SiScan:

3Seq:

6.268 × 10− 35

3.291 × 10− 12

1.842 × 10− 26

1.842 × 10− 26

5.126 × 10− 23

8.802 × 10− 74

-

 

S. aureus strain N17CSA11

(CP107527_1)

S. aureus strain ER01174.3

(CP030712.1)

Staphylococcus phage JD419

(MT899504.1)

Lysin, N-acetylmuramoyl-L-alanine amidase (ID: QOI66741.1) CDS: 759.2213.

(30494.40525 [10,032])

Undetermined (62–875) – Undetermined (1354–2156)

RDP:

GENECONV

BootScan:

MaxChi:

Chimaera:

SiScan:

3Seq:

5.164 × 10− 04

3.711 × 10− 03

1.656 × 10− 03

4.352 × 10− 03

2.199 × 10− 03

1.439 × 10− 14

1.906 × 10− 02

 
  1. CDS - Coding Sequence
  2. Phages names appear according to their designations presented in the NCBI GenBank database
  3. Recombination beginning and end breakpoints (99% Cl) * - The recombination beginning and end breakpoints in the DNA alignment
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BMC Microbiology

ISSN: 1471-2180

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