Abstract
Coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2 share high homology in genomic sequences. Simple sequence repeats (SSRs) are found in their genomes and variations of SSRs among these phages are observed. Analyses on regions of sequences in T7M and T3 genomes that are likely derived from phage recombination, as well as the counterparts in ϕYeO3-12 and ϕSG-JL2, have been discussed by Lin in “Simple sequence repeat variations expedite phage divergence: mechanisms of indels and gene mutations” [1]. These regions are referred to as recombinant regions. The focus here is on SSRs in the whole genome and regions of sequences outside the recombinant regions, referred to as non-recombinant regions. This article provides SSR counts, relative abundance, relative density, and GC contents in the complete genome and non-recombinant regions of these phages. SSR period sizes and motifs in the non-recombinant regions of phage genomes are plotted. Genomic sequence changes between T7M and T3 due to insertions, deletions, and substitutions are also illustrated. SSRs and nearby sequences of T7M in the non-recombinant regions are compared to the sequences of ϕYeO3-12 and ϕSG-JL2 in the corresponding positions. The sequence variations of SSRs due to vertical evolution are classified into four categories and tabulated: (1) insertion/deletion of SSR units, (2) expansion/contraction of SSRs without alteration of genome length, (3) changes of repeat motifs, and (4) generation/loss of repeats.
Abbreviations: SSR, simple sequence repeat
Keywords: Simple sequence repeats, T7M, Bacteriophage genome, SSR variability classification
Specifications Table
| Subject area | Biology |
| More specific subject area | Genome evolution and sequence mutations |
| Type of data | Figure, tables |
| How data was acquired | Analysis of genomic sequences |
| Data format | Analyzed |
| Experimental factors | Genome sequences were retrieved from NCBI for analysis. |
| Experimental features | Software (ClustalW, IMEx) and manual analysis of the sequences, manual characterization and analysis |
| Data source location | National Chiao Tung University, Hsinchu, Taiwan |
| Data accessibility | Data are within this article. |
Value of the data
-
•
Revealing different types of sequence changes of SSRs by vertical evolution of genomes.
-
•
Detailed SSR distributions may aid in identifying broader patterns of phage evolution.
-
•
Provides a guideline for classification of SSR variations in genome comparisons.
-
•
Variations of SSRs in phages may be applied to phage typing.
-
•
Assists researchers studying T7M, T3, ϕYeO3-12, and ϕSG-JL2 related phages in making sequence comparisons.
1. Data
Fig. 1 plots the distribution of SSR period sizes and motifs in the non-recombinant regions of the genomes of phages T7M, T3, ϕYeO3-12, and ϕSG-JL2. Table 1 illustrates differences in genomic sequences between T7M and T3. Table 2, Table 3 provide SSR counts, relative abundance, relative density, and GC contents in the complete genomes and non-recombinant regions for T7M, T3, ϕYeO3-12, and ϕSG-JL2. The four classes of SSR variations, (1) insertion/deletion of SSR units, (2) expansion/contraction of SSRs without alteration of genome length, (3) changes of repeat motifs, and (4) generation/loss of repeats, in T7M non-recombinant regions relative to counterpart regions of ϕYeO3-12 and ϕSG-JL2 are tabulated in Table 4, Table 5, Table 6, Table 7, Table 8, Table 9.
Fig. 1.
The distribution of SSR period sizes and motifs in the non-recombinant regions of phage genomes. SSRs in the non-recombinant regions of T7M and T3 as well as the counterparts in ϕYeO3-12 and ϕSG-JL2 are compared. (A) Counts of mono- to hexanucleotide SSRs. (B) Mononucleotide motifs. (C) Dinucleotide motifs. (D) Trinucleotide motifs. T7M, black; ϕYeO3-12, red; ϕSG-JL2, green; T3, yellow.
Table 1.
Difference in genomic sequences between T7M and T3.
| T7M nt | T7M→T3 change | Location | Amino acid changea |
|---|---|---|---|
| 26-27 | Insertion of C | Terminal repeat | |
| 9606-9607 | Deletion of CG | Gene 3 | GVRKVG→CTQGR |
| 9627 | Deletion of G | Gene 3 | |
| 9971 | Deletion of G | Gene 3 | WL→GV |
| 9975-9976 | Insertion of G | Gene 3 | |
| 22153 | C→T | Gene 10B | T→I |
| 22171 | C→T | Gene 10B | T→I |
| 23105 | G→A | Gene 12 | A→T |
| 23156 | C→A | Gene 12 | L→I |
| 24245 | A→G | Gene 12 | N→D |
| 24659 | G→A | Gene 12 | G→R |
| 25496-25497 | Insertion of AGGGGGG | Between ϕ13 and gene 13 | |
| 37998-37999 | Insertion of C | Terminal repeat |
Change from T7M to T3 is shown by single letter codes of amino acids.
Table 2.
SSR counts, relative abundance, and relative density in the complete genome and non-recombinant regions.
| Size bp | SSR count | RAakb−1 | RDbbp/kb | Size bp | SSR count | RAakb−1 | RDbbp/kb | |
|---|---|---|---|---|---|---|---|---|
| Complete genome | Non-recombinant regionsc | |||||||
| T7M | 38202 | 192 | 5.0 | 39.7 | 25664 | 119 | 4.6 | 37.4 |
| ϕYeO3-12 | 39600 | 207 | 5.2 | 40.8 | 26813 | 147 | 5.5 | 43.5 |
| ϕSG-JL2 | 38815 | 195 | 5.0 | 39.3 | 26335 | 135 | 5.1 | 40.3 |
| T3 | 38208 | 192 | 5.0 | 39.9 | 25670 | 119 | 4.6 | 37.6 |
Relative abundance: number of SSRs present in per kb of sequence.
Relative density: the total length (bp) contributed by SSRs per kb of sequence.
Excluding the two recombination regions in T7M and T3, and the counterpart regions in ϕYeO3-12 and ϕSG-JL2.
Table 3.
Nucleotide compositions and GC contents of genomic sequences and SSRs in the complete genome versus non-recombinant regionsa of phages.
| T7M | ϕYeO3-12 | ϕSG-JL2 | T3 | |||||
| Complete genome | ||||||||
|
% in complete genomic sequence |
||||||||
| A | 26.4 | 26.2 | 26.0 | 26.4 | ||||
| T | 23.7 | 23.2 | 23.2 | 23.7 | ||||
| G | 26.5 | 27.0 | 27.0 | 26.5 | ||||
| C | 23.4 | 23.6 | 23.8 | 23.4 | ||||
| GC | 49.9 | 50.6 | 50.9 | 49.9 | ||||
|
% in SSRs |
||||||||
| A | 23.5 (-2.9) | 25.2 (-1.0) | 22.6 (-3.4) | 23.4 (-3.0) | ||||
| T | 24.6 (1.0) | 22.1 (-1.1) | 23.8 (0.6) | 24.5 (0.9) | ||||
| G | 26.0 (-0.5) | 27.0 (0.0) | 27.1 (0.1) | 26.2 (-0.3) | ||||
| C | 25.8 (2.4) | 25.7 (2.1) | 26.5 (2.7) | 25.9 (2.5) | ||||
| GC | 51.8 (1.9) | 52.7 (2.2) | 53.6 (2.8) | 52.0 (2.1) | ||||
| Non-recombinant regionsa | ||||||||
|
% in non-recombinant regions of genome |
||||||||
| A | 26.1 | 26.2 | 26.2 | 26.1 | ||||
| T | 23.5 | 23.3 | 23.2 | 23.5 | ||||
| G | 26.6 | 26.6 | 26.8 | 26.6 | ||||
| C | 23.8 | 23.9 | 23.9 | 23.8 | ||||
| GC | 50.4 | 50.5 | 50.6 | 50.4 | ||||
|
% in SSRs |
||||||||
| A | 22.8 (-3.3) | 25.6 (-0.7) | 22.0 (-4.2) | 22.7 (-3.4) | ||||
| T | 24.6 (1.1) | 22.0 (-1.3) | 23.0 (-0.2) | 24.5 (1.0) | ||||
| G | 25.7 (-1.0) | 25.5 (-1.1) | 27.7 (1.0) | 25.9 (-0.7) | ||||
| C | 26.9 (3.1) | 26.9 (3.1) | 27.3 (3.5) | 26.9 (3.2) | ||||
| GC | 52.6 (2.1) | 52.4 (2.0) | 55.0 (4.4) | 52.9 (2.4) | ||||
Only the sequences of sense strands are considered. The number in parenthesis indicates the percent change compared to the complete genomes or the non-recombinant regions of genomes.
Excluding the two recombination regions in T7M and T3, and the counterpart regions in ϕYeO3-12 and ϕSG-JL2.
Table 4.
Indels of SSR repeat units in the non-recombinant regions of T7M and counterparts in ϕYeO3-12 and ϕSG-JL2.
| T7M nt |
Sequence in phage |
|
|---|---|---|
| T7M | ϕYeO3-12 | |
| 26 | CCCCCCC | CCCCCC- |
| 25497 | GGGGGGGGG | -----GGGG |
| 37998 | CCCCCCC | CCCCCC- |
| T7M | ϕSG-JL2 | |
| 26 | CCCCCCC | CCCCCC- |
| 7704 | ACACACAC | ACACAC-- |
| 25497 | GGGGGGGGG | -----GGGG |
| 37998 | CCCCCCC | CCCCCC- |
Table 5.
Repeat expansion/contraction without alteration of sequence length in the T7M non-recombinant regions and counterparts of ϕYeO3-12 and ϕSG-JL2.
| T7M nt |
Sequence in phage |
|
|---|---|---|
| T7M | ϕYeO3-12 | |
| 8183 | TCACACACGG | TCTCACACTG |
| 10777 | GTGTGTG | GCCTGTG |
| 17930 | CACCACCACCA | CACCGCCACCA |
| 26004 | GCGCGCG | GCGCGAG |
| T7M | ϕSG-JL2 | |
| 6218 | CTGATGATGATGG | CTAATGATGATGG |
| 8183-8192 | TCACACACGG | TCGAACACAG |
| 8525-8530 | CGGGGG | AAGGGG |
| 11576-11584 | GTGGTGGTG | GTGGTGGCG |
| 17930-17940 | CACCACCACCA | CACCGCCACCA |
| 26004-26010 | GCGCGCG | GCGCGAG |
Repeat unit is underlined.
Table 6.
Repeat motif changes in the non-recombinant regions of T7M compared to counterpart regions of ϕYeO3-12.
| T7M nt | T7M | ϕYeO3-12 |
|---|---|---|
| 1930 | ACGCAGGCAGCAGG | ACGCAGGACGCAGG |
| 4125 | GTATCTATC | GTATATACC |
| 5919 | CAACGAAATGAAATC | CAACGAAACGAAATC |
| 6218 | CTGATGATGATGG | CTAATAATGATGG |
| 8178 | GTCACTCACA | GCTACTCTCA |
| 11627 | CTTTCGTCCGTCA | CGTTCGTTCGTCA |
| 12316 | GGAGAAGGAGAAGGAGA | GAAGAAGGAGAAGGAGA |
| 12700 | AATCAATCAAGCAC | AGTCAATCACTCAC |
| 17742 | GACATAACATAG | GTCATAGCATAG |
| 19669 | TGCTGCTGCCA | TGCAGCAGCAC |
| 20456 | CTGCTGCTGCTG | CGGCTGCGGCTG |
| 21313 | CTGGCTGGTCTTGT | CTTGCTGGTCTGGT |
| 24066 | ACCCATACCCTTCCTT | ACCCATACCCATCGTT |
| 24935 | AAGGGTAGGGT | AAGGGTAGAGT |
| 26592 | TCCGGGGGA | TCAAAGGTA |
SSRs and surrounding sequences are listed. Repeats in ϕYeO3-12 that have at least 3 copies for a mononucleotide or 2 copies for longer repeat periods, but different motifs from those in T7M, are considered. The repeat units with differing motifs between the two phages are underlined.
Table 7.
SSR generation in the non-recombinant regions of T7M compared to counterpart regions of ϕYeO3-12.
| T7M nt | T7M | ϕYeO3-12 |
|---|---|---|
| 1857 | GACCGACC | GGATGAAC |
| 7220 | GCTGACTGAA | ACTGAGTGAA |
| 9237 | CCAAGACAAGAA | CCAAGATAAGAA |
| 9965 | AGTGGCGTGGCT | GGTGGAGTGGCT |
| 10159 | GGCTGGCTGG | GGCTGGTTAG |
| 11106 | TCTGGTCTGGTGGTa | TCTGGTCTGGCGGT |
| 11576 | GTGGTGGTG | GTGGAGGCG |
| 19278 | AATTGCAATTGC | AACTGCAATTGC |
| 20211 | GCAGGCAG | GCAGGCCG |
| 20350 | TCAGGTCAGG | TCCGGTCAGG |
| 25654 | GCTGTGCTGTC | GCTGTGTTGGC |
| 25892 | GTCAATTTCAATT | GTCAATTTCAACT |
| 26016 | CAGACAGA | CAGACCGA |
| 36359 | CCAACCAAC | TCAACCGAC |
| 37140 | GCGTTAGCGTTAG | GCGTTAGCATTGG |
The newly generated repeat unit in T7M is underlined. The repeat sequence displays at least 3 iterations of a mononuceotide repeat unit or 2 contiguous iterations of a di- to hexanucleotide repeat unit. Repeat sequences in ϕYeO3-12 that are also present in T7M are not considered.
The sequence has a newly generated GGT repeat in addition to a motif change CTGGT, and both are underlined in this table.
Table 8.
Repeat motif changes in the non-recombinant regions of T7M compared to counterpart regions of ϕSG-JL2.
| T7M nt | T7M | ϕSG-JL2 |
|---|---|---|
| 4125 | GTATCTATC | GTGTCTACC |
| 5088 | AGCTGCTGGCTGCTG | AGCTGCTAGCTGCTG |
| 11627 | CTTTCGTCCGTCA | CGTTCGTTCGTCA |
| 12316 | GGAGAAGGAGAAGGAGA | GAAGAAGGAGAAGGAGA |
| 17593 | CGATGACGATGA | CGATGATGACGA |
| 17742 | GACATAACATAG | GTCATAGCATAG |
| 19669 | TGCTGCTGCCA | TGCAGCAGCAC |
| 20456 | CTGCTGCTGCTG | CGGCTGCGGCTG |
| 21313 | CTGGCTGGTCTTGT | CTGGCTGGTCTGGT |
| 24066 | ACCCATACCCTTCCTT | ACCCATACCCATCCTT |
| 24935 | AAGGGTAGGGT | AGGGGTAGAGT |
| 26592 | TCCGGGGGA | TCAAAGGTA |
| 37648 | TACTTACTGCT | TACTTGCTGCT |
SSRs and surrounding sequences are listed. Repeats in ϕSG-JL2 that have at least 3 copies for a mononucleotide or 2 copies for longer repeat periods, but different motifs from those in T7M, are considered. The repeat units with differing motifs between the two phages are underlined.
Table 9.
SSR generation in the non-recombinant regions of T7M compared to counterpart regions of ϕSG-JL2.
| T7M nt | T7M | ϕSG-JL2 |
|---|---|---|
| 1930 | ACGCAGGCAGCAG | ACGCAGGCCAAGG |
| 4996 | GGCTGGCTATAT | GGCTGGTTATAT |
| 5582 | AACCTGAACCTG | AAGCTGAACCTA |
| 5731 | ACTTTCTTTA | longa |
| 5919 | CAACGAAATGAAATC | longa |
| 8178 | GTCACTCACA | GTCACTCGAA |
| 9237 | CCAAGACAAGAA | CCAAGATAAGAA |
| 9965 | AGTGGCGTGGCT | GGTGGAGTGGCT |
| 10159 | GGCTGGCTGG | GGCTGGTTAG |
| 11106 | TCTGGTCTGGTGGTb | TCTGGTCTGGCGGT |
| 12700 | AATCAATCAAG | AGTCAATCACC |
| 16958 | ATCAAGCAAGG | ATTAAGCAAGG |
| 19278 | AATTGCAATTGC | AACTGCAATTGC |
| 20211 | GCAGGCAG | GCAGGCCG |
| 20350 | TCAGGTCAGG | TCCGGTCAGG |
| 25654 | GCTGTGCTGTC | GCTGTGTTGGC |
| 25892 | GTCAATTTCAATTA | GTCAATTCCAATTA |
| 26016 | CAGACAGA | CAGACCGA |
| 26335 | CAAGTCAAGTC | CGAGTCAAGTC |
| 36359 | CCAACCAAC | TCAACCGAC |
| 37140 | GCGTTAGCGTTAG | GCGTTAGCATTGG |
The newly generated repeat unit in T7M is underlined. The repeat sequence consists of at least 3 iterations of a mononuceotide or 2 contiguous iterations of a di- to hexanucleotide. Repeat sequences in ϕSG-JL2 that are also present in T7M are not considered.
The sequence is longer in ϕSG-JL2 and does not align well to that of T7M in this region.
The sequence has a newly generated GGT repeat in addition to a motif change CTGGT, and both are underlined in this table.
2. Experimental design, materials and methods
2.1. Genome sequences and recombinant regions
The genome sequence of T7M is in NCBI under the accession number GenBank: JX421753 [1]. Genome sequences of ϕYeO3-12, ϕSG-JL2, and T3 are acquired from GenBank accession numbers GenBank: AJ251805 [2], GenBank: NC_010807 [3], and GenBank: AJ318471 [4], respectively. Sequences were aligned by ClustalW [5], and differences between phages are compared. The T7M sequence nt 13245-16687 and 26695-35789 align to T3 nt 13243-16685 and 26700-35794, respectively, and likely arise from a recombination between a ϕYeO3-12-like phage and a T7-like phage, as suggested for T3 [4]. These regions and the counterparts in ϕYeO3-12 and ϕSG-JL2 are referred to as recombinant regions, and the rest of the genomes are referred to as non-recombinant regions [1].
2.2. Simple sequence repeats
Simple sequence repeats were searched in phage genomes or non-recombinant regions by IMEx [6]. Unless otherwise specified, the minimum repeat units for mono- to hexanucleotide were 5, 3, 3, 2, 2, 2. Repeats sequences were not standardized.
Acknowledgements
The author thanks JCH for editing the manuscript.
Footnotes
Transparency data associated with this article can be found in the online version at doi:10.1016/j.dib.2016.06.035.
Transparency document. Supplementary material
Supplementary material
References
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