Nematode Phylogenetics & Barcoding Primers
These are the primers used by the Blaxter lab to PCR amplify and sequence the small subunit ribosomal RNAs of nematodes.
UPDATED February 2004
UPDATED July 2005 with primers from Floyd et al Mol Ecol Notes and Meldal et al "Nematode phylogeny", in preparation
For a diagram of the placement of these primers in SSU sequence, please see the Carnorhabditis elegans figure.or the Hypsibius dujardini figure
OLD
NAME NEW
NAME Position in C.
elegans sequence Comment Sequence Lgth Tm [new] SSU_F_01 5' end from Medlin 1988 AACCTGGTTGATCCTGCCAGT 20 HMSSU_GplusT SSU_F_03 30-53 variant of F_04 GCTTGTCTCAAAGATTAAGCCATGC 24 67.5 HMSSUGplus SSU_F_06 30-51 variant of F_04 GCTTGTCTCAAAGATTAAGCCAT 22 62.3 G18S4 SSU_F_04 30-49 from Jim Garey GCTTGTCTCAAAGATTAAGCC 20 A SSU_F_07 39-57 AAAGATTAAGCCATGCATG 19 5F SSU_F_05 83-102 limited use GAAACTGCGAAYGGCTCATT 20 Nem_18S_F 111-123 from Floyd et al 2005 CGCGAATRGCTCATTACAACAGC 22F SSU_F_22 411-428 TCCAAGGAAGGCAGCAGGC 19 22R SSU_R_22 429-411 GCCTGCTGCCTTCCTTGGA 19 9FX SSU_F_11 530-550 AAGTCTGGTGCCAGCAGCCGC 21 9F SSU_F_09 573-591 limited use CGCGGTAATTCCAGCTCCA 19 9R SSU_R_09 584-565 AGCTGGAATTACCGCGGCTG 20 HMSSU_9Rplus SSU_R_10 584-561 AGCTGGAATTACCGCGGCTGCTGG 24 77.4 24F SSU_F_24 868-887 AGRGGTGAAATYCGTGGACC 20 SSU_F_24_1 868-887 from Meldal et al. AGAGGTGAAATTCTTGGATC HMSSU_24Rpl SSU_R_24 885-868 has 5' C-clamp CCCCRRTCCAAGAATTTCACCTC 25 67.4 26R SSU_R_26 927-907 CATTCTTGGCAAATGCTTTCG 21 Nem_18S_R 998-1015 from Floyd et al GGCGATCAGATACCGCCC 2R SSU_R_02 1147-1128 limited use CCGTCAATTYYTTTRAGTTT 20 2FX SSU_F_02 1108-1129 GGAAGGGCACCACCAGGAGTGG 22 23F SSU_F_23 1280-1298 ATTCCGATAACGAGCGAGA 19 23R SSU_R_23 1298-1280 TCTCGCTCGTTATCGGAAT 19 13R SSU_R_13 1438-1419 GGGCATCACAGACCTGTTA 19 18P SSU_R_81 3' end TGATCCWKCYGCAGGTTCAC 20 [new] SSU_R_82 3' end from Medlin 1988 TGATCCTTCTGCAGGTTCACCTAC 24
Placement of the SSU primers in the Caenorhabditis elegans (Nematode) sequence
Placement of the SSU primers in the Hypsibius dujardini (Tardigrade) sequence
