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. Author manuscript; available in PMC: 2016 Feb 22.
Published in final edited form as: Mol Ecol Resour. 2012 May 7;12(5):909–917. doi: 10.1111/j.1755-0998.2012.03150.x

Table 2.

Summary of PCR-RFLP and SNP markers for S. multiplicata and S. bombifrons. Of these markers, a subset reliably distinguishes both species and their hybrids (see Table 3).

Gene name
(abbreviation)
Forward
primer
(5′ -> 3′)
Reverse
primer
(5′ -> 3′)
Restriction
enzyme
S. multiplicata eequence
(5′ -> 3′)
GenBank
accession
number2
S. bombifrons sequence
(5′ -> 3′)
GenBank
accession
number2
hypothetical
Loc496414
GCATTAC
ACGAAAA
GCAAACC
CGGAAGG
CCAACTC
ATGTAT
BtsCI CATG__CTTGGATGAAC
N
CATGCACTTGAAGGAAC
A
hypothetical
Loc496744
GTTCCAA
GCGTGAC
TTGGTT
ATTGCCA
TCTCCAT
CAGACC
TaqI TTCCTTCGAGACACGTG
AGTT
JQ707931 TTCCTTCAAGACACGTG
AGTTT
JQ707932
creatine kinase,
muscle
(ckm)
TAACCTC
CGTGACG
GTCTTC
AAGTGGC
TTCACCC
TTGATG
N/A1 GTTGAGTTT___GTCAG
TGCTAG___________
__GATG___________
_________________
_________________
_________GTGTACTA
ATACGC
JQ707917 GTTGAGTTTTCAGACTG
TGCTAAGACGCATTGTT
AGGATGGAATCCTTAGA
TAGTTCTTTCTTTGGAA
CGGCATGGTGGGAAATA
AGAGGACAGGTGTAGTA
ATACGC
JQ707918
DEAD box
polypeptide 6
(ddx6)
CTGCGTG
CTCAGAT
AGTTGC
TGGACTC
CAAAATG
CAATGA
Hpy188I TGTTCAAAAGACAAGCC
AAGCAGTTTTTTTT
JQ707921 TGTTCAGAAGACAAGCC
AAGCAGTTTTTTTT
JQ707922
desmin, gene 1
(des.1)
CAAAGCC
ATCTTGA
CGTTGA
AGGGACC
TGGAGGA
GAGGTA
CviQI GGCAGCTTCCCCGCCAT
ACCTCTCCTCCAG
GGCAGCTTCCCCGCCGT
ACCTCTCCTCCAG
dual specificity
phosphatase 22
(dusp22)
GCTGGGA
GTTCTGG
AAGACA
GTGCCAA
TCACCAA
CTTTGA
BfuCI CTGACACTCTACAAATA
TCACCGGTCAAAG
CTGACACTCTACAAAGA
TCACCGGTCAAAG
glia maturation
factor gamma
(gmfg)
GATCAGG
AACACCA
GCGACT
CTGACCC
ACAGAGC
GTACAA
BstUI ATGGCTGCGTGGATTAA
CCCCACAAA
ATGGCTGCGCGGATTAA
CCCCACAAA
hydroxyacyl-CoA
dehydrogenase/3-
ketoacyl-CoA
thiolase/enoyl-
CoA hydratase
(trifunctional
protein), alpha
subunit (hadha)
TGGTAGC
CAAAGGG
TTTTTG
GACGCAT
CTGGATG
TCTTCA
BtsCI TACTGA__________G
CCTAGGGTTCT
JQ707929 TACTGGACTGTCGGATG
CCTAGGGTTCT
JQ707930
SRY_box 2
(sox2)
CAGCTCC
CAGACGT
ACATGA
TGGTACT
TCTGCCC
CAGGTA
AvaI ACCTCATCTTCCCACTC
GCGGGCTCCATGT
ACCTCTTCTTCCCACTC
TCGGGCTCCATGT
cytochrome c,
testis_specific
protein
(cyct)
TATTCCC
GGAACCA
AAATGA
AGGGACC
GACACAA
GTGAAC
HpyCH4IV AAAGCCACATCGGTAAT
GATACA
AAAGCCACGTCGGCAAT
GATACA
core promoter
element binding
protein
(copeb)
GATCGAT
GGCTGTC
CCAATA
GTGCTAC
ACCTGGC
GTCTTC
Hpy188I ACGAGCCGTTTTGAAGA
TAAAGCACCACTAGTGC
CGGGG
JQ707915 ACGAGCCGTTCAGAAGA
TAAAGCACCACTAGTGC
CGGGG
JQ707916
BCL2_associated
transcription factor
1
(bclaf)
TTTCCTG
CACGATG
ACAGAG
AGGCCAT
CTCCTTG
GAACTT
Hpy166II GGGGGCGTTTTACCTTT
AAAAAATCTGGAAGCAG
CCCAAAATGGACACACG
ATA
GGGGGCGGTTTACCTTT
AAAAAATCTGGAAGCAG
CCCAAAATGGACACATG
ATA
ets domain
transcription factor
(elf1)
CCGAATC
AACTAGC
CCTGAA
TTCACAT
GGAACCC
TTCTCC
BtgI AGGGCCGCCGCGGTGAG
CGCGNAAGCCCCG
JQ707923 AGGGCCGCTGCGGTGGG
CGCGGAAGCCCCG
JQ707924
GDP_mannose
pyrophosphorylase
A
(gmppa)
TTAGGAT
TGGGGTC
ACTTGG
TATTGGA
GCTGGGG
TGAGAG
BspDI TTGCTCTGTTGGCTGCA
TCGATGGGACTGCT
TTGCTCTGGTGGCTGCA
GCGATGGGACTGCT
glia maturation
factor gamma
(gmfg)
GATCAGG
AACACCA
GCGACT
CTGACCC
ACAGAGC
GTACAA
HpaII TTCACTGAA…CGTGGA…
ATTCACCCTTTTAGTGC
CGGAAGGGTTAAATACC
CTG
JQ707925 TTAACTGAA…CGCGGA…
ATTCACCCTTGTAGTGC
CAGAAGGGTTAAATACA
CTG
JQ707926
ATG2 autophagy
related 2 homolog
B
(atg2b)
ACCATCC
CATGCAT
ACAGGT
TCCATGC
AAACTGT
CTGAGC
HinfI GTGTGAGCCAAGCTGAA
GTCACCTGTCATG
GTGTGAGCCAAGCTGGA
GTCACCTGTCATG
GDP_mannose
pyrophosphorylase
A (gmppa)
TTAGGAT
TGGGGTC
ACTTGG
TATTGGA
GCTGGGG
TGAGAG
Taq I TGGCTGCATCGATGGGA
CTGCT
TGGCTGCAGCGATGGGA
CTGCT
Glyceraldehyde-3-
phosphate
dehydrogenase
(gapdh)
GTTGGTG
TGAACCA
CGAGAA
CTGTGAA
AGCGTGG
ACAGTG
Hpy188I TTGGTCTCT__GAGACT
TGGCTGAGATTAAAGCT
TTTTGGTT
JQ707927 TTGGTCTCTTTGAGACT
TGGCTGGGATTAAAGCT
TTTTTGTT
JQ707928
hmgb2;high-
mobility group box
2
(hmgb2)
CTCGAGT
GCAGCTC
ATTTTG
AATGCCA
GGCTACC
CTTAGAA
MseI AGTTTAAGAGCTTATGT
GGGATTTCTCTGCATAT
TTAATGG
AGTGTAAGAGCTTATGT
GGGATTTCTCTGCATAT
TTAGTGG
hypothetical
Loc496690
GGCTTGG
TGTACGC
TCTCTC
GAAGGCT
CTGCAGG
ACTCTG
DdeI ATCTTCCACACCATCGC
CTACCTGAGTCCACTTC
CGC
ATCTTCCACACCATCGC
CTACCTGACTCCGCTTC
CGC
acidic ribosomal
phosphoprotein P0
(arbp/ rplp0)
TGGAAGC
ACTGACA
AGATGC
CAGGTGA
CCACGGA
TAGCTT
HpyCH4IV AGTTTTGGGGATTTGTG
AGAGTTGTCGTTGTT
JQ707909 AGTTTTGGGGATTTGTG
AGAGTTGACGTTGCN
aldolase A,
fructose_bisphosp
hate
(aldoa)
TCCACGA
GACCCTC
TACCAC
CAGACCC
TGAGTGG
TGGTTT
HaeIII GGGCGGCGCTGCTGCTN
…CGANAAAGGTGTCN
TCCNNCTGGCTGN
GGGCGGCCCTGCTGCTT
…CGACAAAGGTGTCG
TCCCCCTGGCCGG
ATG2 autophagy
related 2 homolog
B
(atg2b)
ACCATCC
CATGCAT
ACAGGT
TCCATGC
AAACTGT
CTGAGC
TaqI TCATGTATCGAAAGCCC
TTATGTACTTTTATA
TCATGTATTGAAAGTCC
TCATGTACTTTTATA
JQ707910
cold inducible
RNA binding
protein
(cirbp)
GCCTCAG
CTTTGAA
ACCAAC
CACCGGA
ACCTCCT
CTGTAG
SspI AACCATTTATAATATTC
TAAAATGTGATGTGCAG
CATCTGCATTATTT
JQ707911 AACCATTTACATTGTTC
TAACATGTGATATGCAG
CCTCTGCATTATTT
JQ707912
COP9 constitutive
photomorphogenic
homolog subunit 3
(cops3)
AATAACA
TGGGCCT
GGTGAA
CCATCCC
GTCCTTC
TGATTA
HinfI GTAAGACCCAGCAATAG
AGTGAGGCTTAGACTCC
TCCAGGGGACGGTCAA
TTCGGGGGGTCTCGTGC
TTCCCCGTGGCTT
JQ707913 GTAAGACGCANCAATAG
AGTGAGGCTTATCCTCC
TCCGAGGTGCCGGTCAA
TTCAGGGGGTCTCGTGC
TCCCCC_TGGGTT
JQ707914
D_dopachrome
tautomerase
(ddt)
CCGCGAT
AGGATAA
CGCTAA
CCAGGCC
TCAATAG
GAATGA
HindIII TGGAAACTTTCCAGAGC
CGAGAATAG
JQ707919 TGGAAGCTTTCTGGAGC
CGAGAATAG
JQ707920
GDP_mannose
pyrophosphorylase
A
(gmppa)
TTAGGAT
TGGGGTC
ACTTGG
TATTGGA
GCTGGGG
TGAGAG
Hpy166II GATCCTAGCGAACAAGA
CGAGTCGGTGTGTAA
GATCCTAGTGAACAAGA
CGAGTCGGTGTGTAA
huntingtin
(htt)
AACTGGG
TTCTGGG
AAAGGT
TTTGCTG
TCCCCAC
ACAGTA
AvaII/
Sau96I
CTC______________
______CTCTTTCTAT
CTCTCCCATATAAAGCA
AAGGTCCTCTTTCTAT
mitochondrially
encoded
cytochrome B
(cytb)
CAATAGC
ATTCTCT
TCAGT
GGGGGTT
ACTAGGG
GGTTTG
Acc1 GCTTCTCAGTGGATAAT
GCCACATTAACCCGTTT
GCTTCTCAGTAGACAAT
GCCACACTAACCCGCTT
1

PCR product length varies (≥50 bp), so size differences can be visualized without restriction enzyme

2

If applicable; see supplemental file for additional sequence information

Restriction Enzyme Target Site = italicized

Single Nucleotide Polymorphism= Bold

Insertions and Deletions = Underline and underscore___