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Nematode population genetics/diversity primer sets
A compilation of primers curated by Barbara Wimmer.
To add primers to this resource please send the sequences and a note as to their use to Barbara.
ITS primer sets Microsatellite primer sets Primers used by the Blaxter Lab for SSU PCR and sequencing
primer
names oligonucleotide
sequence Fragment Approx.
size reference NC 5 GTA GGT GAA CCT GCG GAA GGA TCA
TT ITS1-5.8S-ITS2 rDNA 870bp; 1250bp for Ostertagia
ostertagi Newton et al. (1998) Acta Tropica 69:
1-15 NC 2 TTA GTT TCT TTT CCT CCG CT NC 1 ACG TCT GGT TCA GGG TTG TT ITS-2 400bp Gasser et al. (1993) NAR
21:25252626 NC 2 TTA GTT TCT TTT CCT CCG CT NC 4 TGA AAT TTC GAA CGA AT ITS-2+ NC 2 TTA GTT TCT TTT CCT CCG CT NC 13 ATC GAT GAA GAA CGC AGC part of 5.8S 120bp Newton et al. (1998) Acta Tropica 69:
1-15 NC 1R AAC AAC CCT GAA CCA GAC GT 18S TTG ATT ACG TCC CTG CCC TTT end 18S begin of 26S 1kb Vrain et al. (1992) Fundamental and
Appl. Nemat. 15: 563-573 26S TTT CAC TCG CCG TTA CTA AGG BD1 GTC GTA ACA AGG TTT CCG TA ITS-1 Bowles McManus (1993) Mol. Biochem.
Parasitol. 57:231-9 4S TCT AGA TGC GTT CGA A(G/A)TG TCG
ATG nem1 GCA AGT CTG GTG CCA GCA GC 18S ca. 630bp Foucher Wislon, Mol. Ecol.Note
(2002) nem2 CCG TGT TGA GTC AAA TTA AG TC-1 CGA CAA ACC ACC TTG ATA TTT mt DNA LNC-ND4 403bp Blouin et al. (1995) Genetics141:
1007-1014 TC-4 CAA AGT GAT TCC AAG TCA TTG
GC TC-2 GAA TAG TAA AAT GCC ACT AAA TC-4 CAA AGT GAT TCC AAG TCA TTG
GC TC-1 CGA CAA ACC ACC TTG ATA TTT TC-3 CAA ACA GCG GTG TGC CCC C
Primer set
name sequence Genbank
no. Hcms1 TTG GGT TAC GAT AGC GCA TA U 84474 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 AAT GAA ACT ACC GTG GAG GC Hcms2 CCC GGC CTC ATC ATT TAC U 84475 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 TAG CTG CAA TGG GAC GGA Hcms3 TAT AGG TGC GTA GCC GCC U 84476 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 GGA GTT CGC CCA CGC CA Hcms5 CTC TAA GCC TAT TCA ATC T U 84474 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 GGG GAC CGG AGT TAT GAA TTT Hcms6 CTA CTC CTA TCT TCC GCA CA U 84479 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 TTT GAA CGC TCT AGG TTC CAC Hcms7 TTG TTC ACC GTT GTC GTC CA U884480 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 GTC AGT ACT GGT GCT TGC TT Hcms8 AAA CGT GAG TTA AGG TAT TC U884481 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 CAT CAT CTT TCT GGC TCA A Hcms9 ATT ATG ATA AAC ATA GTG ATA
GG U884482 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 TTC CCG TCC TGC CCC CTT Hcms12 TTA TAC TGG GCT TGA GTT G U884484 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 ATC CTG CCC CGT ATA CTC Hcms13 CGG TCG GTT AGT CTC GTC U884485 Hoekstra et al. (1997), Mol. Biochem.
Parasit. 89:97-107 AAT TTG AGC TTT CTA GGT CCA
CGG MTG 1a ATT GAA AAT TGA CTG CGG CAA
CC T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished ATG TTT CCG TCC AAC CCC TAC
AC MTG 1b TTT AGC CTG TAT CCC ATT GAC
CC T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished ATA TGT TTA TTC CAA TGA GTT
CC MTG 1c ATG CTT TCA TTG ACG TGA TAA
GG T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished TCA GCC GTT ATC AAT TTG GGT
CC MTG 6 TGT TAT TGC CAT CGT GGT CGC
TC T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished CGC CTC TTA TCA GCC CTC ATC
GG MTG 8 ACG TAT TGG TCA GGG ACT GCC
AC T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished TGG AGC AGG TGA GCC CGT ACA
AC MTG 11 CAA CCC AGT CAG TCA GCC CTA
CC T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished GTG TTG GAC CTG GGT TTG TAC
GGC MTG 14 ATT CAG AAC GGT ATT CTG AGC
CGC T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished CAC TTG TTG AAA GCA ACG CCT
CAC MTG 18 GTT GAA AG CAG AGG TCC GAA
TG T. Grillo J. Gilleard, Vet. School,
Uni.Glasgow, unpublished GTT TTG ACG CCT CTT ATC AGC
TC
