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18S rRNA primer sets

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Daniel Vaulot edited this page Oct 24, 2019 · 12 revisions

A compilation of 18S rRNA primer sets for metabarcoding compiled from the literature, mapped onto the reference SSU sequence for Saccharomyces cerevisiae (FU970071, 1799 nucleotides, first nucleotide marked as 1) .

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Columns are as follows

column definition
region gene region targetted. Universal corresponds to primer sets that amplify both prokaryotes and eukaryotes
specificity is the primer specific of a group
primer_set_id id of the primer set in pr2-primers database
primer_set_name name of the primer set (usually from author)
fwd_name forward primer name
fwd_seq forward primer sequence
fwd_start start of forward primer relative to FU970071
fwd_end end of forward primer relative to FU970071
rev_name reverse primer name
rev_seq reverse primer sequence
rev_start start of reverse primer relative to FU970071
rev_end end of reverse primer relative to FU970071
length length of amplified sequence relative to FU970071
reference original reference where primer set was first defined
doi link to original paper

Please report errors or primer sets not listed here in the Issues page of the PR2 primer database.

Contributors

gene_region specificity primer_set_id primer_set_name fwd_name fwd_seq fwd_start fwd_end rev_name rev_seq rev_start rev_end length reference doi
V1-V2 non-metazoa 81 Clerissi_2018 18SV1V2F ACCTGGTTGATCCTGCCA 1 18 18SV1V2R GTARKCCWMTAYMYTACC 324 341 341 Clerissi et al. (2018) https://doi.org/10.3389/fmicb.2018.02043
V1-V2 80 Bik_2012 F04 GCTTGTCTCAAAGATTAAGCC 29 49 R22 GCCTGCTGCCTTCCTTGGA 412 430 402 Bik et al. (2012) https://doi.org/10.1111/j.1365-294X.2011.05297.x
V3-V4 cercozoa 62 Lentendu_2014a Cer2F ATTTCTGCCCTATCAGCT 300 317 Cer1R ATACTAGCACCCCCAACT Lentendu, G. et al. (2014) Molecular Ecology, 23, 3341–3355
V4 40 Zhan Uni18SF AGGGCAAKYCTGGTGCCAGC 549 568 Uni18SR GRCGGTATCTRATCGYCTT 991 1009 461 Zhan et al. 2013 https://doi.org/10.1111/2041-210X.12037
V4 12 Geisen 3NDf GGCAAGTCTGGTGCCAG 551 567 1132r CCGTCAATTHCTTYAART 1132 1149 599 Geisen et al Meth Ecol Evol in press
V4 13 Brate1 3NDf GGCAAGTCTGGTGCCAG 551 567 V4_euk_R1 GACTACGACGGTATCTRATCRTCTTCG 989 1015 465 Brate et al. (2010) https://doi.org/10.1038/ismej.2010.39
V4 14 Brate2 3NDf GGCAAGTCTGGTGCCAG 551 567 V4_euk_R2 ACGGTATCTRATCRTCTTCG 989 1008 458 Brate et al. (2010) https://doi.org/10.1038/ismej.2010.39
V4 non-metazoa 35 UNonMet EUK581-F GTGCCAGCAGCCGCG 561 575 EUK1134-R TTTAAGTTTCAGCCTTGCG 1120 1138 578 Carnegie et al. (2003) https://doi.org/10.3354/dao054219
V4 universal 33 Needham 515F Univ GTGYCAGCMGCCGCGGTAA 561 579 926R CCGYCAATTYMTTTRAGTTT 1130 1149 589 Needham & Fuhrman 2016 https://doi.org/10.1038/nmicrobiol.2016.5
V4 18 Parfrey 515F GTGCCAGCMGCCGCGGTAA 561 579 1119r GGTGCCCTTCCGTCA 1144 1158 598 Parfrey et al. 2014 https://doi.org/10.3389/fmicb.2014.00298
V4 34 Lambert 515FY GTGYCAGCMGCCGCGGTA 561 578 NSR951 TTGGYRAATGCTTTCGC 935 951 391 Lambert et al. ISME 2019 https://doi.org/10.1038/s41396-018-0281-z
V4 4 Hugerth_2 563f GCCAGCAVCYGCGGTAAY 563 580 1132r CCGTCAATTHCTTYAART 1132 1149 587 Hugerth et al. (2014) https://doi.org/10.1371/journal.pone.0095567
V4 ciliates 19 Vannini Claudia Vannini (F) CCAGCASCCGCGGTAATWCC 564 583 Claudia Vannini (R) TCTGRTYGTCTTTGATCCCYTA 981 1002 439 Boscaro et al. 2017 https://doi.org/10.1007/s00248-016-0912-8
V4 7 Bass V4_1f CCAGCASCYGCGGTAATWCC 564 583 TAReukREV3 ACTTTCGTTCTTGATYRA 963 980 417 Bass et al. (2016) https://doi.org/10.1111/1462-2920.13235
V4 8 Stoeck_V4_2 TAReuk454FWD1 CCAGCASCYGCGGTAATTCC 564 583 TAReukREV3 ACTTTCGTTCTTGATYRA 963 980 417 Stoeck et al (2010) https://doi.org/10.1111/j.1365-294X.2009.04480.x
V4 16 Piredda_V4 TAReuk454FWD1 CCAGCASCYGCGGTAATTCC 564 583 V4 18S Next.Rev ACTTTCGTTCTTGATYRATGA 960 980 417 Piredda et al. (2017) https://doi.org/10.1093/femsec/fiw200
V4 36 Stoeck_V4_1 TAReuk454FWD1 CCAGCASCYGCGGTAATTCC 564 583 V4RB ACTTTCGTTCTTGATYRR 963 980 417 Balzano & Leterme (2015) https://doi.org/10.3354/ame01740
V4 1 Hadziavdic_1 F-566 CAGCAGCCGCGGTAATTCC 565 583 R-1200 CCCGTGTTGAGTCAAATTAAGC 1178 1199 635 Hadziavdic et al. (2014) https://doi.org/10.1371/journal.pone.0087624
V4 15 Moreno EUKAF GCCGCGGTAATTCCAGCTC 570 588 EUKAR CYTTCGYYCTTGATTRA 963 979 410 Moreno et al. (2018) https://doi.org/10.1016/j.ijheh.2017.10.008
V4 17 Comeau E572F CYGCGGTAATTCCAGCTC 571 588 E1009R AYGGTATCTRATCRTCTTYG 989 1008 438 Comeau et al. (2011) https://doi.org/10.1371/journal.pone.0027492
V4 22 Kim 528F CCGCGGTAATTCCAGCTC 571 588 Nex_18S_0964_R GATCCCYYAACTTTCGTTCTTGA 967 989 419 Kim et al. 2016
V4 26 Pawlowski 528F CCGCGGTAATTCCAGCTC 571 588 S12.2R GACTACGACGGTATCTRATC 996 1015 445 Pawlowski and Smirnov unpublished
V4 25 Mangot NSF563 CGCGGTAATTCCAGCTCCA 572 590 NSR951 TTGGYRAATGCTTTCGC 935 951 380 Mangot at al. (2013) https://doi.org/10.1111/1462-2920.12065
V4 haptophyta 39 Egge A-528F GCGGTAATTCCAGCTCCAA 573 591 PRYM01+7 GATCAGTGAAAACATCCCTGG 948 968 396 Egge, E., et al. (2013) https://doi.org/10.1371/journal.pone.0074371
V4 2 Hadziavdic_2 A-528F GCGGTAATTCCAGCTCCAA 573 591 R-952 TTGGCAAATGCTTTCGC 935 951 379 Hadziavdic et al. (2014) https://doi.org/10.1371/journal.pone.0087624
V4 83 Hugerth_6 A-528F GCGGTAATTCCAGCTCCAA 573 591 1132r CCGTCAATTHCTTYAART 1132 1149 577 Unpublished https://doi.org/
cloning 9 Edgcomb_1 Euk528F CGGTAATTCCAGCTCC 574 589 U1492R GGTTACCTTGTTACGACTT 1754 1772 1199 Edgcomb et al. (2011)
cloning 10 Edgcomb_2 Euk528F CGGTAATTCCAGCTCC 574 589 U1391R GGGCGGTGTGTACAARGR 1623 1640 1067 Edgcomb et al. (2011)
cloning 11 Edgcomb_3 Euk528F CGGTAATTCCAGCTCC 574 589 U1517R ACGGCTACCTTGTTACGACTT 1754 1774 1201 Edgcomb et al. (2011)
V4 3 Hugerth_1 574*f CGGTAAYTCCAGCTCYV 574 590 1132r CCGTCAATTHCTTYAART 1132 1149 576 Hugerth et al. (2014) https://doi.org/10.1371/journal.pone.0095567
V4 23 Venter 590F CGGTAATTCCAGCTCCAATAGC 574 595 1300R CACCAACTAAGAACGGCCATGC 1272 1293 720 Venter et al 2017 https://doi.org/10.1016/j.protis.2017.03.005
V4 77 Hugerth_5 574f CGGTAAYTCCAGCTCYAV 574 591 1132r CCGTCAATTHCTTYAART 1132 1149 576 Hugerth et al. (2014) https://doi.org/10.1371/journal.pone.0095567
V4 diatoms 21 Zimmerman D512for ATTCCAGCTCCAATAGCG 579 596 D978rev GACTACGATGGTATCTAATC 996 1015 437 Zimmermann et al. 2011 https://doi.org/10.1007/s13127-011-0050-6
V4 cercozoa 41 Harder Cerc479F TGTTGCAGTTAAAAAGCTCGT 608 628 Cerc750R TGAATACTAGCACCCCCAAC 871 890 283 Harder et al. (2016) https://doi.org/10.1038/ismej.2016.31
V4 24 Simon EK-565F-NGS GCAGTTAAAAAGCTCGTAGT 612 631 EUK1134-R TTTAAGTTTCAGCCTTGCG 1120 1138 527 Simon et al. 2015 EM https://doi.org/10.1111/1462-2920.12591
V4 cercozoa 63 Fiore-Donno_2018a S616F_Cerco TTAAAAAGCTCGTAGTTG 616 633 S963R_Cerco CAACTTTCGTTCTTGATTAAA 962 982 367 Fiore-Donno et al. (2018) https://doi.org/10.1111/1755-0998.12729
V4 cercozoa 64 Fiore-Donno_2018b S616F_Eocer TTAAAAAGCGCGTAGTTG 616 633 S963R_Cerco CAACTTTCGTTCTTGATTAAA 962 982 367 Fiore-Donno et al. (2018) https://doi.org/10.1111/1755-0998.12729
V4 cercozoa 65 Fiore-Donno_2018c S616F_Cerco TTAAAAAGCTCGTAGTTG 616 633 S947R_Cerco AAGAAGACATCCTTGGTG Fiore-Donno et al. (2018) https://doi.org/10.1111/1755-0998.12729
V4 cercozoa 66 Fiore-Donno_2018d S616F_Eocer TTAAAAAGCGCGTAGTTG 616 633 S947R_Cerco AAGAAGACATCCTTGGTG Fiore-Donno et al. (2018) https://doi.org/10.1111/1755-0998.12729
V4 5 Hugerth_3 616f TTAAAAVGYTCGTAGTYG 616 633 1132r CCGTCAATTHCTTYAART 1132 1149 534 Hugerth et al. (2014) https://doi.org/10.1371/journal.pone.0095567
V4 6 Hugerth_4 616*f TTAAARVGYTCGTAGTYG 616 633 1132r CCGTCAATTHCTTYAART 1132 1149 534 Hugerth et al. (2014) https://doi.org/10.1371/journal.pone.0095567
V5 chlorophyta 38 Moro ChloroF TGGCCTATCTTGTTGGTCTGT 822 842 ChloroR GAATCAACCTGACAAGGCAAC 1295 1315 494 Valiente Moro et al. (2009) https://doi.org/10.1128/AEM.00509-09
V5 diplonemids 37 Cannon DimA RGGGACRGGTGAAATAGGATG 893 913 DimB CAAATTGAGCCGCAGACTCC 1168 1187 295 Cannon, M.V. et al. (2018) https://doi.org/10.1186/s40168-018-0581-6
V6-V8 universal 32 Wilkins 926wF AAACTYAAAKGAATTGRCGG 1130 1149 1392-R ACGGGCGGTGTGTRC 1628 1642 513 Wilkins et al. 2013 https://doi.org/10.1038/ncomms3457
V7 76 Lundgreen_2019 F-1183 AATTTGACTCAACACGGG 1182 1199 R-1443 AAGGGCATCACAGACCTG 1425 1442 261 Lundgreen et al. (2019) Scientific Reports 9:8891 https://doi.org/10.1038/s41598-019-45146-7
V9 28 Amaral_1 1380F CCCTGCCHTTTGTACACAC 1617 1635 1510R CCTTCYGCAGGTTCACCTAC 1773 1792 176 Amaral Zettler et al (2009) https://doi.org/10.1371/journal.pone.0006372
V9 29 Amaral_2 1389F TTGTACACACCGCCC 1626 1640 1510R CCTTCYGCAGGTTCACCTAC 1773 1792 167 Amaral Zettler et al (2009) https://doi.org/10.1371/journal.pone.0006372
V9 31 Piredda_V9 1388F TTGTACACACCGCCCGTCGC 1626 1645 1510R CCTTCYGCAGGTTCACCTAC 1773 1792 167 Piredda et al. (2017) https://doi.org/10.1093/femsec/fiw200
V9 27 Stoeck_V9 1391F GTACACACCGCCCGTC 1628 1643 EukB TGATCCTTCTGCAGGTTCACCTAC 1773 1796 169 Stoeck et al (2010) https://doi.org/10.1111/j.1365-294X.2009.04480.x
V9-ITS 30 Boegnik 1391F GTACACACCGCCCGTC 1628 1643 ITS2_broad GCTGCGTTCTTCATCGWTR Boenigk et al. 2018
cloning foraminifera 79 Morard_2019 EukB TGATCCTTCTGCAGGTTCACCTAC 1773 1796 S14F1 AAGGGCACCACAAGAACGC Morard et al. (2019) https://doi.org/10.1111/jeu.12691
Helix 37 and 37f Foraminifera 68 Pawlowski_2014 s14F1 AAGGGCACCACAAGAACGC s15.3 CCTATCACATAATCATGAAAG Pawlowski, J., et al., (2014) Molecular Ecology Methods 14, 1129-40
V2 Acanthamoeba 73 Fiore-Donno_2016a SRAca28 CCAATTACAAGACTCTTRTCGAG SFAca22 CGGYGAGACTGCGGATGG 78 95 Fiore-Donno, A.M. (2016) Scientific Reports, 6, 19068.
V2 Dark-spored Myxomycetes 74 Fiore-Donno_2016b SR19Dark GTCCTCTAATTGTTACTCGAD SF2Dark GTTGATCCTGCCAGTAGTGT 6 25 Fiore-Donno, A.M. (2016) Scientific Reports, 6, 19068.
V2-V3 Chrysophyceae/Synurophyceae 69 Lentendu_2014b Chryso_240 GGAAACCAATGCGGGGCAAC Chryso_651 CTATTTTGCTCACAGTAAATGACGAG Lentendu, G., et al. (2014) Molecular Ecology, 23, 3341-55
V2-V3 Kinetoplastea 72 Lentendu_2014c Kineto_80 CATCAGACGYAATCTGCCGC Kineto_651 TTGGTCGCRCTTYTTTAGTCACAG Lentendu, G., et al. (2014) Molecular Ecology, 23, 3341-55
V2-V3 tintinnids 59 Santoferrara_2018 152+ TTACATGGATAACCGTGGTAATTC 528- CCCGGCCCGTTATTTCTTGT Santoferrara, L., et al. (2018) Journal of Plankton Research, 40, 209–221
V3 SAR 84 Sisson_2018 SAR_V3_F AYTCAGGGAGGTAGTGACAAG SAR_V3_R RACTACGAGCTTTTTAACTGC Sisson et al. (2018) https://doi.org/10.1093/plankt/fby020
V7-V9 Plasmodiophorida 67 Bass_2018 1301f GATTGAAGCTCTTTCTTGATCACTTC 1801r ACGGAAACCTTGTTACGACTTC 1753 1774 Bass, D., et al. (2018) Frontiers in Microbiology, 9
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