We are looking to move to NGS for our population genetic studies on rare plant species. We are looking for a platform capable of producing multiple length reads (up to ~800bp) so we can design primers to amplify different fragment lengths as we will be multiplexing the PCRs. Does anyone have suggestions about which platform would be the best use of our funds and/or have a good lead on a lab we can use to outsource the sequencing to? Thanks.
Probably a MiSeq doing paired-end 300 bp reads (some facilities squeeze out a few more bp). If you have shorter amplicons the reads will go into the adapter but that won't cause problems. If you really need the longer amplicons then 454. The University of Idaho iBEST facility has a MiSeq with extensive outside use.
a miseq platform is probably the best choice. You can sequencer 2 X 300 bp in 2-3 day and produce enought reads for a PCR primers design (µsat ?). Starting with genomics librairies you must sized the inserts around 600 bp to optimized the sequencing.
The best solution is probably not to use microsats at all... But that depends on your research question and other variables.
NGS platforms deliver high-quality and cheap (relative to the cost of developing microsats and running costs) ways of SNP genotyping. SNPs have huge advantages compared to microsats, as an allele isn't called differently on different platforms or by different people. msat allele 112 may be 111 if called by a collaborator, and the next machine will probably show a different allele size too. Compared to that, a C will always be called a C, and an G a G, no matter what platform or who's behind the computer. Moreover, some quick calculations (in my lab we routinely use different methods, many of which are outsourced) show that microsats are rarely the best bang per buck. GBS is currently my favourite method.
I've posted already quite a few answers on RG to similar questions. Have a look there. https://www.researchgate.net/profile/Joachim_Mergeay/answers?ev=prf_ans
The most suited answer to your question, IMHO, is here:
https://www.researchgate.net/post/Does_anyone_know_of_microsatellite_discovery_and_primer_design_services_in_Europe
Another reason to use SNPs: the variance in the estimator of H among loci is typically smaller than that of microsats, as a result of which your estimator of the genome-wide H is better with SNPs than with microsats. This also gives better estimates of Ne when using temporal methods.
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