Widespread homologous recombination within and between Streptomyces species

J. R. Doroghazi & D. H. Buckley, ISME Journal, 2010

Supplementary Information

Figure S1. Maximum likelihood trees for all loci from the 53 Streptomyces species described in Guo et al. (Guo et al., 2008). Maximum likelihood trees were created using the tree bisection reconnection algorithm in PAUP and incongruence between trees was then evaluated using the Shimodaira-Hasegawa test (Table S2). In Guo et al., 2008 ‘griseoplanus’ was misidentified and should be ‘flavogriseus 45-CD’ while ‘flavogriseus’is‘flavogriseus Heim’

Figure S2. Example of graphical output from RDP 2.0 (Martin et al., 2005b) and Reticulate (Jakobsen and Easteal, 1996) used to assess evidence for recombination. The data is for the event documented in the first row of Table S3 which involves transfer of atpD between graminofaciens and yanii at positions 1728:2391. The incompatibility matrix presents alignments of concatenated sequences for graminofaciens and yanii along the horizontal and vertical axes with incompatible sites indicated by white blocks in the matrix. Given the sequence divergence between these two species small blocks in the figure may be due to homeoplasy or recombination, but the large block corresponding to the atpD gene shows clear evidence of recombination between these species. This event is also clearly evident in the three way comparison of sequence similarity performed by RDP. These figures can be used to qualitatively observe the events detected in Table S3.

Table S1. Properties of the loci used in Streptomyces MLSA.

Gene / Length /  / Sites / D / P / ρ / θw / ρ/θw
Interspecies / 16S rRNA / 1389 / 0.0162 / 104 / -0.850 / n.s. / 0.0061 / 0.0163 / 0.37
recA / 504 / 0.0766 / 168 / -0.690 / n.s. / 0.0704 / 0.0625 / 1.13
atpD / 496 / 0.0746 / 146 / -0.220 / n.s. / 0.0121 / 0.0511 / 0.24
rpoB / 540 / 0.0832 / 197 / -0.624 / n.s. / 0.0546 / 0.0645 / 0.85
gyrB / 423 / 0.1179 / 145 / -0.601 / n.s. / 0.1280 / 0.0748 / 1.71
trpB / 571 / 0.0853 / 193 / -1.030 / n.s. / 0.2150 / 0.0567 / 3.80
Intraspecies
recA / 504 / 0.0000 / 0 / n.d. / n.d. / n.d. / n.d. / n.d.
atpD / 496 / 0.0009 / 3 / -0.849 / n.s. / n.d. / 0.0014 / n.d.
rpoB / 540 / 0.0022 / 7 / -0.799 / n.s. / 0.1470 / 0.0031 / 47.6
gyrB / 417 / 0.0017 / 3 / -0.035 / n.s. / 0.0025 / 0.0017 / 1.47
trpB / 571 / 0.0039 / 8 / 0.451 / n.s. / 0.0092 / 0.0033 / 2.76

Values for Tajima’s D were not significant (n.s.). Values for ρ and θw were calculated using LDhat (McVean et al.2002) and are expressed per site with ρ expressed as the rate of gene conversion, ρ= 2Ner/2.Values of ρ and θw could not be determined (n.d.) for certain loci due to the low number of polymorphic sites observed.

Table S2. Shimodaira-Hasegawa test implemented on trees from Figure S1. Values are the probability that the level of incongruence observed could be due to chance. Rows present the sequences used to assess tree topology, columns the tree topology being tested. ‘Concat’ stands for the concatenated sequence. Recombination is expected to yield significant incongruence between trees.

Concat. / 16S / recA / atpD / rpoB / gyrB / trpB
Con / -- / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
16S / 0.000 / -- / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
recA / 0.020 / 0.000 / -- / 0.000 / 0.000 / 0.000 / 0.020
atpD / 0.140 / 0.000 / 0.000 / -- / 0.000 / 0.000 / 0.000
rpoB / 0.002 / 0.000 / 0.000 / 0.000 / -- / 0.000 / 0.000
gyrB / 0.001 / 0.000 / 0.000 / 0.000 / 0.000 / -- / 0.000
trpB / 0.030 / 0.000 / 0.009 / 0.000 / 0.000 / 0.0000 / --

Table S3. Recombination events detected withRDP 2.0(Martin et al., 2005b). Columns identify the gene daughter (recipient) and donor, the sequence region, and p-values from 8 different statistical tests for recombination(Boni et al., 2007; Gibbs et al., 2000; Holmes et al., 1999; Martin et al., 2005a; Padidam et al., 1999; Posada and Crandall, 2001; Smith, 1992). Gene boundaries in the concatenated sequence are as follows: 16S rRNA, 1:1389; recA, 1390:1893; atpD, 1894:2389; rpoB, 2390:2929; gyrB, 2930:3352; trpB, 3353:3923. The abbreviation, u(x), indicates an unknown donor, with support for the existence of an unknown donor calculated through the use of sequence from isolate x. Heim is used for flavogrisues Heim.

Daughter / Donor / Region / RDP / Geneconv / Bootscan / Max Chi / Chimaera / SiScan / 3Seq / LARD
yanii / graminofaciens / 1728:2391 / 6.2x10-10 / 1.1x10-6 / 1.4x10-9 / 5.2x10-5 / 1.3x10-6 / 2.1x10-6 / 5.2x10-10 / 3.2x10-30
pulveraceus / graminofaciens / 1728:2391 / 6.2x10-10 / 1.1x10-6 / 1.4x10-9 / 5.2x10-5 / 1.3x10-6 / 2.1x10-6 / 5.2x10-10 / 3.2x10-30
galilaeus / u(Heim) / 151:1449 / 1.2x10-6 / 2.5x10-11 / 4.6x10-10 / 1.0x10-6 / 1.0x10-6 / 2.8x10-7 / 5.8x10-12 / 4.1x10-39
albus / u(Heim) / 151:1449 / 1.2x10-6 / 2.5x10-11 / 4.6x10-10 / 1.0x10-6 / 1.0x10-6 / 2.8x10-7 / 5.8x10-12 / 4.1x10-39
vinaceus / u(Heim) / 151:1449 / 1.2x10-6 / 2.5x10-11 / 4.6x10-10 / 1.0x10-6 / 1.0x10-6 / 2.8x10-7 / 5.8x10-12 / 4.1x10-39
argenteolus / u(Heim) / 151:1449 / 1.2x10-6 / 2.5x10-11 / 4.6x10-10 / 1.0x10-6 / 1.0x10-6 / 2.8x10-7 / 5.8x10-12 / 4.1x10-39
spiroverticillatus / u(Heim) / 151:1449 / 1.2x10-6 / 2.5x10-11 / 4.6x10-10 / 1.0x10-6 / 1.0x10-6 / 2.8x10-7 / 5.8x10-12 / 4.1x10-39
aureus / bobili / 2484:3807 / 2.5x10-5 / NS / NS / 3.6x10-8 / 1.5x10-9 / 1.7x10-3 / 1.9x10-9 / 7.1x10-36
graminofaciens / nojiriensis / 1893:2300 / 4.0x10-7 / 6.7x10-7 / 1.9x10-8 / 6.9x10-4 / 3.7x10-3 / 4.9x10-7 / 2.1x10-2 / 1.0x10-35
peucetius / nojiriensis / 1893:2300 / 4.0x10-7 / 6.7x10-7 / 1.9x10-8 / 6.9x10-4 / 3.7x10-3 / 4.9x10-7 / 2.1x10-2 / 1.0x10-35
atroolivaceus / mediolani / 2920:3339 / 1.6x10-6 / 3.9x10-5 / 8.4x10-5 / 2.8x10-8 / 3.5x10-7 / 1.2x10-5 / 1.1x10-6 / 2.4x10-25
Heim / cyaneofuscatus / 1812:2898 / 1.3x10-6 / 1.3x10-4 / 6.5x10-7 / 6.6x10-3 / 2.0x10-4 / 1.5x10-8 / 2.2x10-5 / 1.6x10-18
griseolus / cyaneofuscatus / 1812:2898 / 1.3x10-6 / 1.3x10-4 / 6.5x10-7 / 6.6x10-3 / 2.0x10-4 / 1.5x10-8 / 2.2x10-5 / 1.6x10-18
fulvorobeus / cyaneofuscatus / 1812:2898 / 1.3x10-6 / 1.3x10-4 / 6.5x10-7 / 6.6x10-3 / 2.0x10-4 / 1.5x10-8 / 2.2x10-5 / 1.6x10-18
laceyi / Heim / 1757:2391 / 1.3x10-7 / 9.5x10-7 / 1.2x10-9 / 6.2x10-6 / 1.1x10-4 / 1.0x10-7 / 5.3x10-3 / 2.6x10-33
spiroverticillatus / laceyi / 2292:3627 / NS / NS / NS / NS / 1.2x10-6 / NS / NS / 3.0x10-30
subrutilus / venezuelae / 2987:3263 / NS / NS / NS / 2.3x10-6 / 2.0x10-3 / NS / NS / 1.3x10-27
albovinaceus / caviscabies / 2598:3753 / NS / NS / NS / 4.2x10-4 / 2.5x10-2 / 1.1x10-7 / 2.5x10-2 / 7.0x10-10
griseinus / caviscabies / 2598:3753 / NS / NS / NS / 4.2x10-4 / 2.5x10-2 / 1.1x10-7 / 2.5x10-2 / 7.0x10-10
mediolani / caviscabies / 2598:3753 / NS / NS / NS / 4.2x10-4 / 2.5x10-2 / 1.1x10-7 / 2.5x10-2 / 7.0x10-10
kanamyceticus / venezuelae / 1892:2491 / NS / NS / 6.2x10-2 / 2.9x10-4 / NS / 8.6x10-6 / NS / 1.6x10-15
atroolivaceus / virginiae / 2398:2820 / 6.1x10-2 / NS / 1.2x10-3 / 1.4x10-2 / NS / NS / NS / 3.9x10-15
cyaneus / bobili / 3066:3487 / NS / NS / NS / 4.8x10-3 / 1.6x10-3 / 3.7x10-8 / NS / 5.6x10-18

Supplementary References

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Gibbs MJ, Armstrong JS, Gibbs AJ. (2000).Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics16: 573-582.

Holmes EC, Worobey M, Rambaut A. (1999).Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol16: 405-409.

Jakobsen IB, Easteal S. (1996).A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comp Appl Bioscience12: 291-295.

Martin DP, Posada D, Crandall KA, Williamson C. (2005).A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. Aids Research and Human Retroviruses21: 98-102.

Padidam M, Sawyer S, Fauquet CM. (1999).Possible emergence of new geminiviruses by frequent recombination. Virology265: 218-225.

Posada D, Crandall KA. (2001).Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci USA98: 13757-13762.

Smith JM. (1992).Analyzing the mosaic structure of genes. J Mol Evol34: 126-129.

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