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Table 1 PCR primers used in this study

From: Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications

Name

Region of DNA/FISH probe

Primer sequence (5′to3′)

Ref.

28S A

3′ end of the 28S rDNA involving the regions A and B, F primer

AAA CTC TGG TGG AGG TCC GT

[61]

28S B

Internally nested in the regions A and B of the 28S rDNA, R primer

CTT ACC AAA AGT GGC CCA CTA

[61]

28S C1

5′ end of the 28S rDNA adjacent to the ITS2, F primer

ACC CGC TGA ATT TAA GCA T

[62]

28S D2

Internally nested in the region C3 involving D2, C2, D1, C1, R primer

TCC GTG TTT CAA GAC GGG

[63]

ITS1

3′ end of the 18S rDNA adjacent to the ITS1, F primer

TCC GTA GGT GAA CCT GCG G

[64]

ITS2

3′ end of the 5.8S rDNA adjacent to the ITS2, R primer

GCT GCG TTC TTC ATC GAT GC

[64]

ITS3

5′ end of the 5.8S rDNA adjacent to the ITS1, F primer

GCA TCG ATG AAG AAC GCA GC

[64]

ITS4

5′ end of the 28S rDNA adjacent to the ITS2, R primer

TCC TCC GCT TAT TGA TAT GC

[64]

NS1

5′ end of the 18S rDNA F primer

GTA GTC ATA TGC TTG TCT

[64]

NS2

18 S rDNA R primer

GGC TGC TGG CAC CAG ACT TGC

[64]

NS3

18 S rDNA F primer

GCA AGT CTG GTG CCA GCA GCC

[64]

NS4

18 S rDNA R primer

CTT CCG TCA ATT CCT TTA AG

[64]

NS5

18 S rDNA F primer

AAC TTA AAG GAA TTG ACG GAA G

[64]

NS6

18 S rDNA R primer

GCA TCA CAG ACC TGT TAT TGC CTC

[64]

NS7

18 S rDNA F primer

GAG GCA ATA ACA GGT CTG TGA TGC

[64]

NS8

3′ end of the 18S rDNA R primer

TCC GCA GGT TCA CCT ACG GA

[64]

RTX1F1

Rex1 F primer

TTC TCC AGT GCC TTC AAC ACC

[28]

RTX1R3

Rex1 R primer

TCC CTC AGC AGA AAG AGT CTG CTC

[28]

RTX3F1

Rex3 F primer

TAC GGA GAA AAC CCA TTT CG

[65]

RTX3F2

Rex3 F primer

AAC ACC TTG GCT GCG CCT AG

[65]

RTX3F3

Rex3 F primer

CGG TGA YAA AGG GCA GCC CTG

[28]

RTX3R1

Rex3 R primer

AAA GTT CCT CGG TGG CAA GG

[65]

RTX3R2

Rex3 R primer

CCR GGG GTG GAT GAR RTC CGC CC

[65]

RTX3R3

Rex3 R primer

TGG CAG ACN GGG GTG GTG GT

[28]

RTX6F

Rex6 F primer

TAA AGC ATA CAT GGA GCG CCA C

[28]

RTX6R

Rex6 R primer

GGT CCT CTA CCA GAG GCC TGG G

[28]