"Primer name";"Target group";"Gene region";"Amplicon length";Citation;"Forward primer sequence";"Reverse primer sequence";Strengths;Weaknesses Batra;Amphibians;12S;"c.a.60 bp";"(Valentini et al. 2016, Taberlet 2018)";ACACCGCCCGTCACCCT;GTAYACTTACCATGTTACGACTT;"High taxonomic coverage";"Do not discriminate Peophylax species, need a human blocking primer" 515F–806R;Bacteria;"16S V4";"c.a. 390 bp";"(Caporaso et al. 2011)";GTGYCAGCMGCCGCGGTAA;GGACTACNVGGGTWTCTAAT;"Very widely used and standardised"; "[Diat_rbcL_708F_1+Diat_rbcL_708F_2+Diat_rbcL_708F_3] + [R3_1+R3_2]";Diatoms;rbcL;"312 bp";"(Vasselon et al. 2017a)";"AGGTGAAGTAAAAGGTTCWTACTTAAA AGGTGAAACTAAAGGTTCWTACTTAAA AGGTGAAGTTAAAGGTTCWTAYTTAAA";"CCTTCTAATTTACCWACWACTG CCTTCTAATTTACCWACAACAG";"Diatom specific rbcL primers used in biomonitoring - high specificity and high coverage for diatoms - fully adapted to the use of Diat.barcode reference library - enable the evaluation of relative abundance of taxa (Vasselon et al 2018)";"High specificity and coverage are obtained by pooling 3 forward and 2 reverse primers in equimolar proportions" "DIV4for - DIV4rev";Diatoms;"18S V4";"280-300 bp";"(Visco et al. 2015) modified from (Zimmermann et al. 2011)";GCGGTAATTCCAGCTCCAATAG;CTCTGACAATGGAATACGAATA;"Diatom specific 18S primers used in biomonitoring"; "1389F - 1510R";Eukaryotes;"18S V9";"c.a. 150 bp";"(Amaral-Zettler et al. 2009)";TTGTACACACCGCCC;CCTTCYGCAGGTTCACCTAC;"Universal eukaryotic primers"; SSU_FO4+SSU_R22;"Eukaryotes (marine meiofauna)";18S;380bp;"(Blaxter et al. 1998)";GCTTGTCTCAAAGATTAAGCC;CCTGCTGCCTTCCTTRGA;"Good taxonomic coverage for marine meiofauna (V1-V2 region)"; "SSU_FO4 - SSU_R22mod";"Eukaryotes (marine meiofauna)";18S;"c.a. 400 bp";"(Sinniger et al. 2016) modified from (Blaxter et al. 1998)";GCTTGWCTCAAAGATTAAGCC;CCTGCTGCCTTCCTTRGA;"Eukaryotic 18S primers, commonly used for metabarcoding marine meiofauna"; "TAReuk454FWD1 - TAReukREV3";"Eukaryotes (marine plankton)";"18S V4";"c.a. 400 bp";"(Stoeck et al. 2010)";CCAGCASCYGCGGTAATTCC;ACTTTCGTTCTTGATYRA;"Universal eukaryotic primers commonly used for marine plankton (Tara Oceans) but not only."; "Teleo or Tele01";Fish;12S;"c.a. 80 bp";"(Valentini et al. 2016, Taberlet 2018)";ACACCGCCCGTCACTCT;CTTCCGGTACACTTACCATG;"High taxonomic coverage, including Actinopterygii and Elasmobranchs";"Poor species resolution for same family, need a human blocking primer" MiFish-U;Fish;12S;"c.a. 170 bp";"(Miya et al. 2015)";GTCGGTAAAACTCGTGCCAGC;CATAGTGGGGTATCTAATCCCAGTTTG;"Good specificity, coverage, and resolution"; "s14F1 - s15.3";Foraminifers;"18S 37F";"120-140 bp";"(Pawlowski and Lecroq 2010, Pawlowski et al. 2014)";AAGGGCACCACAAGAACGC;CCACCTATCACAYAATCATG;"Foraminifer specific 18S primers commonly used in metabarcoding"; "FwhF2 + FwhR2n";Macroinvertebrates;COI;"205 bp";"(Vamos et al. 2017)";GGDACWGGWTGAACWGTWTAYCCHCC;GTRATWGCHCCDGCTARWACWGG;"Short length of amplicon allows reliable amplification also of degraded material, very good taxonomic representation; short length allows to sequence on HiSeq and othe 2x150 bp platforms - cheap!";"Not good for eDNA, too many bacteria are amplified" "fwhF2 + EPTDr2n";"Macroinvertebrates, freshwater (especially insects)";COI;"142 bp (191 bp)";"(Vamos et al. 2017, Leese et al. 2021)";GGDACWGGWTGAACWGTWTAYCCHCC;CAAACAAATARDGGTATTCGDTY;"Reduced non target amplification with eDNA";"Increased primer bias compared to bulk metabarcoding primers, misses some taxa (e.g. some crustaceans, few trichopterans) due to the increased specificity. Can be more challenging to establish in the lab." "fwhF2 + Fol-degen-rev";"Macroinvertebrates, freshwater (especially insects)";COI;"313 bp (365 bp)";"(Yu et al. 2012, Vamos et al. 2017)";GGDACWGGWTGAACWGTWTAYCCHCC;TANACYTCNGGRTGNCCRAARAAYCA;"Good amplicon length for Illumina sequencing";"Not good for eDNA, too many bacteria are amplified. Forward primer affected by primer slippage" "BF3 + BR2";"Macroinvertebrates, freshwater (especially insects)";COI;"418 bp (458 bp)";"(Elbrecht and Leese 2017, Elbrecht et al. 2019)";CCHGAYATRGCHTTYCCHCG;TCDGGRTGNCCRAARAAYCA;"Good taxonomic resolution";"Not good for eDNA, too many bacteria are amplified. Amplicon length not ideal for all illumina sequencers" Unio;"Molluscs (Unionida)";16S;"c.a.130 bp";"(Prié et al. 2020)";GCTGTTATCCCCGGGGTAR;AAGACGAAAAGACCCCGC;"High taxonomic coverage";"Some species cannot be discriminated" Vene;"Molluscs (Venerida)";16S;"c.a.130 bp";"(Prié et al. 2020)";CSCTGTTATCCCYRCGGTA;TTDTAAAAGACGAGAAGACCC;"High taxonomic coverage";"Some species cannot be discriminated" "12S V5";Vertebrates;12S;"c.a. 106 bp";"(Riaz et al. 2011)";ACTGGGATTAGATACCCC;TAGAACAGGCTCCTCTAG;"Very high taxonomic coverage";"Lower taxonomic resolution, particularly among bird species, non-target amplification of human"