We recently did metabarcoding of samples from Malaise Traps. But, the primers worked not so well. We got loads of data. However, we could not pair-wise align short reads from both ends of the COI barcode.
Any suggestions on the primers for Hymenoptera or Insecta?
Thanks, cd
Dear Chao-Dong, as HCO-LCO do not work well with Hymenoptera, we used instead what we call LCO1490puc 5’-TTTCAACWAATCATAAAGATATTGG -3’ and HCO2198puc 5’-TAAACTTCWGGRTGWCCAAARAATCA-3’. These primers were used by Armelle Coeur d'Acier to amplify aphids and appeared to better amplified the endoparasitic wasps ! So we used them quite successfully for Hymenoptera as well
see Coeur d'Acier A., Cruaud A., Artige E., Genson G., Clamens A.-L., Pierre E., Hudaverdian A., Simon J.-C., Jousselin E. & Rasplus J.-Y. (2014) DNA barcoding and the associated PhylAphidB@se website for the identification of European Aphids (Insecta: Hemiptera: Aphididae). PLoS ONE, 9, e97620
Best
JY
Dear Sir
Wishes and greetings
We are using universal primers which were designed by Nymphalidae Systematic group Findland. They had designed based on butterfly samples. LCO & HCO and Pat and Jerry primers working well in our samples like moths. We have used same primer in cockroach it doesn't work well. You can designed primer yourself. Collect the EST data of COI of 10 Hymenopteran species from NCBI ClustalW alignment of EST and COI with whole gene sequence of Apis mellifera. Primer designing in Primer3 using conserved regions of the sequence.
with regards
Dr K. Sivasankaran
I didn't know LCO / HCO universal primers were supposed to not work well with Hymenoptera. Every PCR I tried with Apoidea species worked very well ! Is this group an exception among hymneopterans, or was I really lucky ?
LCO / HCO works well with some Hymenoptera but not with some other groups ca Chalcidoidea, Cynipoidea ... globally in Hymenoptera primers of cytb worked better than those targeting COI ... but there are also some exceptions
Primers described in Meier et al. (2015): "Here we use MiSeq for specimen-based barcodes because it provides high-quality 300-bp Paired-End (PE) reads that are a good match for a very robust set of primers for a 313-bp Metazoa minibarcode (Geller et al., 2013; Leray et al., 2013)."
http://onlinelibrary.wiley.com/doi/10.1111/cla.12115/full
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