dc.contributor.author |
Van Zyl, Leonardo Joaquim
|
|
dc.contributor.author |
Nemavhulani, Shonisani
|
|
dc.contributor.author |
Cass, James
|
|
dc.contributor.author |
Cowan, Don A.
|
|
dc.contributor.author |
Trindade, Marla
|
|
dc.date.accessioned |
2017-01-23T09:06:21Z |
|
dc.date.available |
2017-01-23T09:06:21Z |
|
dc.date.issued |
2016-12-03 |
|
dc.description |
Additional file 1: Figure S1. Whole genome alignment of phage Shbh1
with six of its closest relatives. Similarly coloured regions indicate homology
or local collinear blocks (LCB) between nucleotide sequences, with the level
of similarity indicated by the height of the bars within each LCB. Genome
alignments were performed using MAUVE. |
en_ZA |
dc.description |
Additional file 2: Table S1. Predicted open reading frames on Shpa
and closest BLASTp hit on the NCBI database. |
en_ZA |
dc.description |
Additional file 3: Table S2. Predicted open reading frames on Mgbh1
and closest BLASTp hit on the NCBI database. |
en_ZA |
dc.description |
Additional file 4: Table S3. Predicted open reading frames on Shbh1
and closest BLASTp hit on the NCBI database. |
en_ZA |
dc.description |
Additional file 5: Figure S2. GC skew analysis of the Shbh1 genome
showing putative replication origin (ori) and termination sites (ter)
calculated using a window size of 1000 bp and a step size of 100 bp. |
en_ZA |
dc.description |
Additional file 6: Figure S4. GC skew analysis of the Shpa genome
showing putative replication origin (ori) and termination sites (ter)
calculated using a window size of 1000 bp and a step size of 100 bp. |
en_ZA |
dc.description |
Additional file 7: Figure S3. GC skew analysis of the Mgbh1 genome
showing putative replication origin (ori) and termination sites (ter)
calculated using a window size of 1000 bp and a step size of 100 bp. |
en_ZA |
dc.description.abstract |
BACKGROUND : Soda lakes are unique environments in terms of their physical characteristics and the biology they
harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and
consequently few bacteriophages that infect bacteria from haloalkaline environments have been described.
METHODS : Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on
two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each
phage in its host was investigated and the genome sequences determined and analysed by comparison with
known phages.
RESULTS : Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family.
Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and
have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two
different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative
analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial
amino acid similarity with previously described Bacillus infecting phages
(Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel.
CONCLUSION : The addition of these phages to current databases should help with metagenome/metavirome
annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and
vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to
these phages. |
en_ZA |
dc.description.department |
Genetics |
en_ZA |
dc.description.librarian |
am2017 |
en_ZA |
dc.description.sponsorship |
The National Research Foundation (NRF) of South
Africa |
en_ZA |
dc.description.uri |
http://www.virologyj.com |
en_ZA |
dc.identifier.citation |
Van Zyl, LJ, Nemavhulani, S, Cass, J, Cowan, DA & Trindade, M 2016, 'Three novel bacteriophages isolated from the East African Rift Valley soda lakes', Virology Journal, vol. 13, art. no. 204, pp. 1-14. |
en_ZA |
dc.identifier.issn |
1743-422X |
|
dc.identifier.other |
10.1186/s12985-016-0656-6 |
|
dc.identifier.uri |
http://hdl.handle.net/2263/58600 |
|
dc.language.iso |
en |
en_ZA |
dc.publisher |
BioMed Central |
en_ZA |
dc.rights |
© The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License. |
en_ZA |
dc.subject |
Bacteriophage |
en_ZA |
dc.subject |
Myoviridae |
en_ZA |
dc.subject |
Siphoviridae |
en_ZA |
dc.subject |
Paracoccus |
en_ZA |
dc.subject |
Soda lakes |
en_ZA |
dc.title |
Three novel bacteriophages isolated from the East African Rift Valley soda lakes |
en_ZA |
dc.type |
Article |
en_ZA |