Appendix 2. Primers and conditions for 64 molecular markers

Marker

/ Linkage group / Primer 1 / Primer 2 / Anneal T°C / [Mg]
mM / PCR product
(bps) /

Enzyme

/ Band sizes1
TcTex12 / I / ATTGACGTCTCGGAAGAGGA / ACCTCCTGTTGCACCATTTC / 55 / 3.5 / 400 / HaeIII / 400/500
AGK / I / ATTGTTGGGGCCTGGAAATA / TGAACGTATGGTCCAGCGTA / 57 / 2.0 / 400 / NaeI / 100+125/200
1D545 / I / AGCTACAGCCTGACCACCAC / CACATCCGCCCAGACTCTAT / 55 / 1.5 / 150/100 bp / 150/100
ASPK / I / GACTCAACCCATCACCTGCT / GCAACGGTTCTCACAACTGA / 55 / 1.5 / 350bp / MnlI / 150+200/350
GMPS / II / ACCGTCAATGTGTGGATGAG / GATGCCGATGAGAAAGTGCT / 55 / 1.5 / 550 / AluI / 200+170+150/
200+170+130
LC1 / II / ACAATGGCCAAGGCAACTAC / TTCCTGGGAATCCACCTATG / 55 / 2.7 / >1,000 / MspI / 500/200+300
ALAD2 / II / AGACATGGAAAGTGGCAGGT / GAGGCCCTAACGCCTAAATC / 55 / 3.5 / 600 / MnlI / 150+250/300
DMAT / III / GGACATTCGTGTGGAGTGAA / GGGCACGTCTGACAGTAACA / 50 / 1.5 / 250/200 / 250/200
TUA1 / III / GGCCATGAGTTGCTTCTTTC / AGGAAACGCAGTCAAGGGTA / 55 / 1.5 / 500 / MspI / 140+150+175/
140+150+200
LC6 / III / GACATGTGCAGTGGAAGACG / TTGTGCTGGAGCCAAGTATCT / 55 / 1.5 / 400 / MspI / 300+100/400
RPS5 / III / GCAAGACTCCAAGCGCTACTA / CCTGCTCCATGTGGTACTGA / 55 / 1.5 / 500 / MspI / 150/200
TSB / III / AAGTCTACTGTTCGCATTGCTG / GTCCTCACGCTTTAGGTAAATCTC / 50 / 1.5 / 800 / AlwNI / 800/600
THI / III / TCACGCGTTCCATCATTTTA / GGCTCATATTGGGGTTGTTG / 54 / 2.5 / 400 / MnlI / 270+150/320
PAI / III / CCCTGCTTCACAATGGACTC / GGGTTGCTGTACCAGCTTTG / 54 / 2.5 / 300 / MnlI / 180/250
TUA2 / IV / CACAAACACAAGTACCGTTGGT / AAGGTCAGGGGGAAGATCC / 50 / 1.5 / 400 / HaeIII / 150+175/
150+200
PF20 / IV / CATGAGCATCCAACGATAGGTA / CCCCATTTTGATGAAGAAGTTG / 50 / 1.5 / 600 / HaeIII / 300/400
PRT / IV / CTCGCCTTCAGACGCTACTT / CCAGACATGACGATGATTCG / 54 / 2.5 / 900 / MnlI / 900/400+250
135+125
PF26 / V / AGCTATGAGATTAGGCAACTGG / GTTTACAAGAACGCCTGGTTTC / 50 / 1.5 / 375 / HaeIII / 200/225
ALDO / V / GTTGGAGTTCCATCGTCGTT / GTGGCTCCTCTCTGAACTGC / 55 / 3.5 / 600/330 / 330/600
HSP70b / VI / AGTGTGGTAGGCGTGAAAGC / AACGCACATTTCACTGGTCA / 55 / 1.5 / 300 / HaeIII / 300/250
PF14 / VI / ATGTGTGCGTGTCCGAAGTA / CCACGTGGACAGTTGAAAGA / 55 / 1.5 / 220/200 / 220/200
PP1 / VI / GCGACGATTATGTTTGCTGA / GTGTCACCCCGATTCAGTTT / 55 / 1.5 / 200 / MspI / 150/200
CDC48 / VI / AGTCCGCAGCACTGGTCTAC / AAGCTTGCACTGCATTGTTG / 55 / 1.5 / 210 / MspI / 210/180
ACOR / VI / CCCATTGCATTTCTGCAGTT / TGGGAGGAGGAGGCTAGG / 55 / 1.5 / 400 / ScrFI / 300/250
BI52 / VI / GCTTTAGCTGGCCAAAATGA / CAATCCGGGCTATTGTCTTG / 55 / 1.5 / 200 / MspI / 100/200
FA2 / VII / TCGTTGTGTGTGAGGTGGAT / CACGCAATGCATGAATAAGG / 55 / 1.5 / 220/210 / 220/210
PRF / VII / CGAGGTGCTTCAAGAGTTCC / GCACCCGGATCTTGTACTTC / 60 / 3.5 / 500 / MspI / 150/220
ZSP12 / VII / GAGGTCGCGGGGGAA / GCGAGTGCGGAATCAAA / 55 / 3.5 / 800 / DdeI / 500+300/
500+300+250
HSP70A2 / VIII / AGCTGCTGCAGGACTTCTTC / GCTGGTTGTCGGAGTAGGTC / 55 / 2.7 / 400 / HaeIII / 180/200
OEE32 / VIII / AAGCAGGTTTTCCGTCACAG / GCCTCGTAGATCAGGTCGAA / 55 / 3.5 / 550 / HaeIII / 100+200/
200+300
STK / VIII / GTCCCGGTAGTCCGGTAAGT / GCGTGGTGCAGTCAATGTAG / 55 / 1.5 / 550/200 / 200/550
OEE12 / IX / GGAGCTGCTGAAGGAGAACG / AGCGAGTCGGGGAAATAGGG / 55 / 3.5 / 750 / HaeIII / 200+325/
200+300+325
NIT1 / IX / GCAGCAGGGCATAGCAGTAG / CGCGCACCAAAACGGGCTAA / 60 / 3.5 / 300 / ScrF1 / 150/300
VPS26 / IX / GAAATCATGGACGGAGCTCC / GAAGAAGGGCAAGCACGCCT / 55 / 3.0 / 250 / RsaI / 250/200
BI99 / IX / CTTTGAACCTGGCAGTCCAT / AACACCAAGCTGGCAGTTCT / 55 / 3.5 / 600 / HhaI / 300+200/200
PRI / IX / ACCTGTCCTGGTTTGAGCAG / GGCCTCTACTTGCACTCCAT / 55 / 1.5 / 250 / MspI / 250+200/250
TRX1 / IX / TTCCGTCCTCACCAAAGTTC / CCAGCAGAATTGACAGCAAA / 55 / 3.5 / 200 / ScrFI / 200/150
DC1 / IX / TGGCGGACATCATACAACAG / CCTGGATGCTTGCGTAATTT / 53 / 3.0 / 600/700bp / 600/700bp
KAT / X / GTAACGGTGTCATGCCAGTAAG / CACGACTACCGTAGCAGACTCA / 50 / 1.5 / 200 / MspI / 200/150
GP40 / XI / CCCCGATTTCGAACTTGATA / ATAAGTGCGAGGGGGACACT / 50 / 1.5 / 400 / MspI / 150+220/400
CRY1 / XI / CTGGCTGGAAGTTTGCTGAT / AGTATTCCGCTGACCACGAC / 60 / 3.5 / 200/190 / 200/190
Cna19 / XI / GAAGAAGGGCAAGCACGCCT / AAAATGGGATGCGCAGTTAG / 55 / 1.5 / 200 / HaeIII / 100/125+75
BQ80 / XI / ACGGAGGAAAGTTTTGGTTCC / GGCCTCTACTTGCACTCCAT / 55 / 1.5 / 280 / HaeIII / 260+250/
275+250
RPL4 / XI / GGGTACTGGTAACGCTCGTC / AGGCTCTCCACCACAATCAT / 55 / 1.5 / 250 / HaeIII / 150/200
LC2 / XII/XIII / GGATTATCTCCCGCTGTCTG / AAATCGAGGACCTGCCTCTT / 55 / 1.5 / 350 / HphI / 150+>200/
150+<200
LC3 / XII/XIII / TGCACAACACAACAAGCAGA / ACAGGCGAGGACACAGCTAC / 55 / 1.5 / 400 / HaeIII / 190+100/300
ODA92 / XII/XIII / ACTGATGAGGGGCTTTCG / TCGCGTTCGCTTTACACC / 55 / 3.5 / 400 / MspI / 110+310/130+310
TSA / XII/XIII / GAACGATGAACGCACTGAAG / TTCTGCATGATGGGGTTGTA / 55 / 1.5 / 800 / HaeIII / 310+200+150/
290+200+150
LAO / XII/XIII / TCTTACAGCGACCGGATTTC / GACACCACATCAGGGCTACA / 60 / 3.5 / 200 / HaeIII / 150/200
RPL9 / XII/XIII / TAACTGACACGCTGGAATGC / GTGATAGCAAGGAGCCGAAG / 54 / 1.0 / 400bp /

HaeIII

/ 200/200+175
Septin / XII/XIII / TTGATAACACTACAGCGGCACT / CCGGACTTGAGTTTTATGAGG / 53 / 1.5 / 200/300bp / 200/300bp
IGPS / XIV / ACTACGATGTCTGGCGAGGT / CGGGTCCATCTTCTTTGCTA / 55 / 1.5 / 850 / RsaI / 350+250+210/
250+210+200+150
IDA5 / XIV / AGTCCGAGTACGACGAGTCC / TGCAAGCTATCCACGTATGC / 55 / 1.5 / 290/310 / 290/310
CCS12 / XIV / GGAAGGTGGTGATGCAAGTT / CACTATGCAGGAATGGTGA / 55 / 1.5 / 350 / NlaIII / 100+150/100+200
ASB / XV / GGGCTAGGCCCTTTACCTC / AGCTCCCGCACTGTTTGTAG / 50 / 1.5 / 600 / RsaI / 300+350/
100+200+350
BE05 / XV / CCGGTCAAGTAGGTGCTGTT / TACGTAGCGGGTTTGAGCTT / 50 / 1.5 / 250 / HaeIII / 250/200
FA4 / XVI/XVII / GGAACGGTGACTGTCGGTAG / ACGCAAAGCCGGTAACATAG / 55 / 3.5 / 300 / MspI / 170/150
ARS2 / XVIII / CAAAGGTCGAGGAGAAGTCG / AAGAGCACCGACCTGGATTA / 55 / 3.5 / 400 / HaeIII / 300+190/300+225
S926 / XIX / TGGTGGAGATCAACATCGAG / CGCACATAGAATTTGCAAGC / 55 / 1.5 / 400/380 / 400/380
LC5 / XIX / ACGCAGATGCATGGTGTAAA / AAAGTCAATTGCACCCGGTA / 55 / 1.5 / 200 / MspI / 200/150
EB1 / XIX / ACAGCTCCTCCTCGGTGTACT / GGCTACGAGAAGGAAAAGGACT / 55 / 1.5 / 500 / MspI / 500/
200+150+120
ODA3 / XIX / aggggaagaagaaggagcag / gcaacagacacaacccaaga / 53 / 1.0 / 350 / MnlI / 150+200/350
BQ82 / ND / TCCCACATCTTCCTTCCTTG / CCCTAGTGAGGTCTGCTTCG / 55 / 1.5 / 230/200 / 230/200
BI72 / ND / CAGGAACATCGTGATGCTGTA / CTGGCCTTGTCCTTGTTCTC / 57 / 1.5 / 600 / RsaI / 600/500

1 Band sizes are the scored fragments for 137c-derived strain and CC1952 strain.

2 Indicates that the sequence of the primers was obtained from Dr. Laurens Mets (University of Chicago).

Accession numbers for acronym entries not in ChlamyDB or Table 2. ACOR: BI873565; AGK: BM519173; ALAD: U19876; ALDO: X69969; ARS: X52304; ASPK: AF014927;CCS1: U71000; CDC48: BU647835; Cna19: BE337032; DC1: BU646668;EB1: BG843058; FA4: BI718037; FNR1: U10545; GP40: AF525923; HSP70A: M76725 HSP70B: X96502; KAT: AF205377; LAO: U78797; PP1: AF156101; PRF: BQ821551; PRI: BU653640; TRX: X78822; S926: X62135; STK: AF33023; TcTex1: AF039437; VPS26: BM003137; ZSP: S44199.

Accession numbers for unknown ESTs: BE05: BE056715; BI99: BI993933, BI52: BI528510, BQ80: BQ808040; and BQ82: BQ824925.

1