Skip to main content

Table 1 PCR primers and annealing temperatures used to amplify 10 new markers

From: A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

Gene*

Primers

Sequences

Annealing temp

PCR steps

zic1

zic1_F9

5' GGACGCAGGACCGCARTAYC 3'

57

1st

 

zic1_R967

5' CTGTGTGTGTCCTTTTGTGRATYTT 3'

 

PCR

 

zic1_F16

5' GGACCGCAGTATCCCACYMT 3'

57

2nd

 

zic1_R963

5' GTGTGTCCTTTTGTGAATTTTYAGRT 3'

 

PCR

myh6

myh6_F459

5' CATMTTYTCCATCTCAGATAATGC 3'

53

1st

 

myh6_R1325

5' ATTCTCACCACCATCCAGTTGAA 3'

 

PCR

 

myh6_F507

5' GGAGAATCARTCKGTGCTCATCA 3'

62

2nd

 

myh6_R1322

5' CTCACCACCATCCAGTTGAACAT 3'

 

PCR

RYR3

RYR3_F15

5' GGAACTATYGGTAAGCARATGG 3'

55

1st

 

RYR3_R968

5' TGGAAGAAKCCAAAKATGATGC 3'

 

PCR

 

RYR3_F22

5' TCGGTAAGCARATGGTGGACA 3'

62

2nd

 

RYR3_R931

5' AGAATCCRGTGAAGAGCATCCA 3'

 

PCR

Ptr

Ptr_F458

5' AGAATGGATWACCAACACYTACG 3'

55

1st

 

Ptr_R1248

5' TAAGGCACAGGATTGAGATGCT 3'

 

PCR

 

Ptr_F463

5' GGATAACCAACACYTACGTCAA 3'

62

2nd

 

Ptr_R1242

5' ACAGGATTGAGATGCTGTCCA 3'

 

PCR

tbr1

tbr1_F1

5' TGTCTACACAGGCTGCGACAT 3'

57

1st

 

tbr1_R820

5' GATGTCCTTRGWGCAGTTTTT 3'

 

PCR

 

tbr1_F86

5' GCCATGMCTGGYTCTTTCCT 3'

62

2nd

 

tbr1_R811

5' GGAGCAGTTTTTCTCRCATTC 3'

 

PCR

ENC1

ENC1_F85

5' GACATGCTGGAGTTTCAGGA 3'

53

1st

 

ENC1_R982

5' ACTTGTTRGCMACTGGGTCAAA 3'

 

PCR

 

ENC1_F88

5' ATGCTGGAGTTTCAGGACAT 3'

62

2nd

 

ENC1_R975

5' AGCMACTGGGTCAAACTGCTC 3'

 

PCR

Gylt

Glyt_F559

5' GGACTGTCMAAGATGACCACMT 3'

55

1st

 

Glyt_R1562

5' CCCAAGAGGTTCTTGTTRAAGAT 3'

 

PCR

 

Glyt_F577

5' ACATGGTACCAGTATGGCTTTGT 3'

62

2nd

 

Glyt_R1464

5' GTAAGGCATATASGTGTTCTCTCC 3'

 

PCR

SH3PX3

SH3PX3_F461

5' GTATGGTSGGCAGGAACYTGAA 3'

55

1st

 

SH3PX3_R1303

5' CAAACAKCTCYCCGATGTTCTC 3'

 

PCR

 

SH3PX3_F532

5' GACGTTCCCATGATGGCWAAAAT 3'

62

2nd

 

SH3PX3_R1299

5' CATCTCYCCGATGTTCTCGTA 3'

 

PCR

plagl2

plagl2_F9

5' CCACACACTCYCCACAGAA 3'

55

1st

 

plagl2_R930

5' TTCTCAAGCAGGTATGAGGTAGA 3'

 

PCR

 

plagl2_F51

5' AAAAGATGTTTCACCGMAAAGA 3'

62

2nd

 

plagl2_R920

5' GGTATGAGGTAGATCCSAGCTG 3'

 

PCR

sreb2

sreb2_F10

5' ATGGCGAACTAYAGCCATGC 3'

55

1st

 

sreb2_R1094

5' CTGGATTTTCTGCAGTASAGGAG 3'

 

PCR

 

sreb2_F27

5' TGCAGGGGACCACAMCAT 3'

62

2nd

 

sreb2_R1082

5' CAGTASAGGAGCGTGGTGCT 3'

 

PCR

  1. *Gene markers are named following annotations in ENSEMBLE. zic1, zic family member 1; myh6, myosin, heavy polypeptide 6; RYR3 (si:ch211-189g6.1), novel protein similar to vertebrate ryanodine receptor 3; Ptr (si:ch211-105n9.1), hypothetical protein LOC564097; tbr1, T-box brain 1; ENC1(559445 Entrezgene), similar to ectodermal-neural cortex 1; Glyt (zgc:112079), glycosyltransferase; SH3PX3, similar to SH3 and PX domain containing 3 gene; plagl2, pleiomorphic adenoma gene-like 2; sreb2, Super conserved receptor expressed in brain 2.