We have been struggling to gather more gene fragments data for multiple loci species delimitation for Chalcidoidea, especially the family eulophidae. There has been a tradition to sequence both 28S D2 and COI in the lab. However, the standard primers for COI works at roughly 60% success rate. We also expect to sequence 3-5 more gene fragments for these tiny wasps. We do appreciate if you provide some valuable informations/approaches on more efficient COI primers or other gene primers.
Thanks in advance.
My lab is working on a pipeline to take next gen data and produce primers for sequencing across species. It is based on the software found at https://github.com/rachelss/SISRS/tree/feature/SISRS-loci . Currently you can use this software to get conserved loci from ngs data very easily. The consensus of these loci can be used for probes. We are just about to attempt this. Automated primer development is in development but you can take a bunch of alignments and come up with primers manually. Please let me know if this helps. I will probably need to provide update the software to get exactly what you need. I am happy to discuss further.
To clarify you can use the data at http://www.ebi.ac.uk/ena/data/warehouse/search?query=%22tax_tree(7422)%22&domain=read to develop your markers.
Dear Rachel, thanks for your answer. It's really valuable. We will try in my lab. cd
Please let me know if I can help further. We are working to make SISRS helpful for end users and produce useful output.
- Badges
- Science topic
- Similar topics
- Phytochemistry
- Extracts