Supplementary Table 1. Primers for amplification and sequencing SNPs and INDELs.

Genome Position in DSMZ 10140 1 / Gene Name2 / Forward Primer Sequence (5’®3’) / Reverse Primer Sequence (5’®3’) / Product Size (bp) /
SNPs in Non-coding Regions
19098 / igr1 / GTTGCCACGGATACCACTG / GCGTTCGATGTCGCATTC / 368
87537 / igr2 / CCTTGGTCTGCCTTGGTCT / GTCATTACGGGACTCGCTTT / 379
278277 / igr3 / TAGTTGATAGCGTGCGATGC / CCCAGCCATCATCATCTCTT / 432
281374 / igr4 / GACCTTAGTTTGTTGGATTTTGTG / ACATCCTCGCCCTCTTCC / 437
525386 / igr5 / GGGCGATATGATTCCTCAGC / TCCACATGCGAGTAGCCAGT / 879
687000 / igr6 / ACAGGCTCATCCGTGCTATC / AGCAGCACTGCAATCGTATG / 456
959934 / igr7 / ATGTCCGCATGTGTTTCTGG / GCCATAGGATGCAACGTGAA / 451
1456329 / igr8 / GTGCCTGGTGCTCATGTTC / GCATCGACAACCTCGACAC / 477
1636606 / igr9 / CATACTGGCTGCCGACAAAC / ACGGCAATCCAAACAGCAG / 751
1799285 / igr10 / TGGATGTCGTGGCCTAATGA / ATGCCCCAACGATTTGAGAC / 535
1916502 / igr11 / AGAACAAGGTGGGTGATGC / GGGGGAAGACTTCTGGATCT / 499
Synonymous SNPs in Protein-coding Regions
158448 / Balat_0140 / ATATTTGGGACCGGCGAAC / TTCTCGCCATACACCACGTT / 474
175868 / Balat_0153 / GGATCTTTCGATCATCTCGTG / CCACAGGAGCCCATAAACTG / 391
685552 / Balat_0580 / TAGTCCGTACACGACCAGCA / AGATGAACCTGCCATTCACC / 448
1059543 / Balat_0922 / GACCCATTTCACGTTGACCT / AGCATTCCGTGATGATGCT / 410
1299752 / Balat_1125 / GCTGGTTGAACTTGGAGAGC / GGTGCGTGGCTACATCAAC / 428
1496337 / Balat_1296 / GACGCTCTCCCCTACAAGC / AACAGGACCTCGACAAGGAA / 469
1716099 / Balat_1460 / ATGAGCATCGGCAGGAAG / TTGCACTCTACGTGGTGCTC / 454
1880972 / Balat_1590 / CGCAGCACAATTTGGATATG / GGAAGAAGTCCAAGCCTCCT / 452
Non-Synonymous SNPs in Protein-coding Regions
41264 / Balat_0038 / AGGCAGAGTTGGAGTTGCAG / CTAGCGTATTGGCGATGGTC / 390
53321 / Balat_0051 / CCTACCGTCATCGAGTCCAG / CCTTCATCATGCCCTCCTTA / 284
159526 / Balat_0141 / ACTACGAAAGCGCGGGAAC / CTTGTCGAAGGGCACCACA / 480
177292 / Balat_0155 / AAGATTCCCGCGAAAGACAA / TGTCGAGTTGCTGGGTGTTC / 591
459192 / rpsI / AGGCAAAGTGAACCGAAGGA / TCCCATCGAACGTGTGGAC / 703
581139 / Balat_0487 / TGCCGGTAGATGGAGTTGTG / GGCGTGTCGAATATGATGGA / 785
588993 / Balat_0496 / GGTATGGCTTGGCGGTAAGA / CTGGGTTGGCAGTGTGTCTC / 581
594228 / Balat_0500 / ATTCCGGAAGCGTTGAAGAA / GACCGTTGCACTGAGCTGTT / 430
629424 / Balat_0529 / CACGATGAACTGTGCGAGGT / GGTTCCTTGATTTCCGTCCA / 670
769449 / Balat_0653 / GAAGGGATGTGATCCGAAGA / CTATCCCACTCCAGGCTACG / 428
776140 / Balat_0660 / ACAACACCAACACCGGTTCA / TGAGAGCAGATCCTCGACCA / 758
791497 / Balat_0671 / TCGGCATCAAATACGACCAG / GAACGCACCGGGAATGTTAT / 772
839429 / Balat_0710 / CGTGTGGTCGATATCGCTGT / AGGCGGATTTCACAGTGGTC / 641
993008 / Balat_0864 / GGTTCGTCACTTTCGTGCAG / CCACACCACGCGTGTATTTC / 537
1040047 / Balat_0903 / AGGAGTGCCATGTCCGTTTT / AGCCGTAGGCCTTCAACTCA / 710
1108705 / Balat_0971 / GGGACAACGGATACCTCTCG / TGCAGCTTGATGAGGTCCAC / 680
1247696 / Balat_1088 / CCGTCGAAGGTGTAGGTGAT / AGGTGCTTGAATTGCTCAGG / 445
1255074 / Balat_1094 / CGAGGAACCTTCCAACGAAC / CTATGCCGCCAGAGAGAACA / 715
1260073 / glcU / ACGTAGCGGTGGAGGTCCTA / CCGGTCTTGTGCAGAAGGTT / 636
1260380 / glcU / ACGTAGCGGTGGAGGTCCTA / CCGGTCTTGTGCAGAAGGTT / 636
1287609 / Balat_1116a / GGTTCTGCGGTGACGTATGA / AACGTCTTGTGATCGCGTGT / 790
1287610 / Balat_1116b / GGTTCTGCGGTGACGTATGA / AACGTCTTGTGATCGCGTGT / 790
1510874 / cas1 / ACCCGTGCGTAGGAGTATGG / CATTGGGCCCATAGGAAGAA / 584
1635695 / Balat_1395 / TGATCGGCCTACTGCTCGTA / GCTTTGCCCATTAGGGTGAG / 775
1652028 / Balat_1407 / ATCGCGTATGCCTTTCTCGT / CCGTGCGTTTCAACAACAGT / 590
1702641 / oxc / ACAGCAAGCGGAATGTCTTC / GGAGGATGTTTGCAATGGTT / 478
1792217 / Balat_1524 / AGGCGAACGAAAAAGCATGT / AGCAGCACGACTGGGTAGGT / 355
1910309 / Balat_1610 / GTTCGTCGCAGGCTTCATC / ATGCCCTACCCATCCTTGTG / 654
1934708 / Balat_1626 / GTTTGGCAGGGTGGTTAGGA / AGACATGGCCGCTACTGCTT / 782
INDELs
88142033 / INDEL1, tRNA-Ala-GGC / TGATACGCAGAACACGGATT / GCCATGATGTTCCTTTCGTC / 462/5834
902893 / INDEL2, long chain fatty acid-coA ligase / AACCGTCTGCTGCTGTTTCT / CCCCTGAATGAAGGTGATGT / 455/4014
15123733 / INDEL3, CRISPR locus / TTGGATGCAAGCCCTCAATGAAGC / TGAGGGAAGCCGAACTCAATCACA / 659/8734

1 GenBank Accession Number for DSMZ 10140 is CP001606.

2 Gene Name refers to gene name from GenBank.

3 Numbering corresponds to the Bl-04 genome sequence; GenBank Accession Number CP001515.

4 Difference in product sizes depends on presence or absence of the INDEL. The first value is the product size in DSMZ 10140. The second value is the product size in Bl-04.

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