I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC and TTAA), the two enzymes similar and used in
Peterson, B. K., J. N. Weber, E. H. Kay, H. S. Fisher, and H. E. Hoekstra. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135. (they are using EcoRI and MspI (GAATTC and CCGG).
Considering the huge list of restriction enzymes how to choose the appropriate enzyme? Is it a complete guess? The size of the genome of finches is about 1.07Gb. Do I have to take this in consideration?
The reference genome is available
Zhang, G., P. Parker, B. Li, H. Li, and J. Wang. 2012. The genome of Darwin’s Finch (Geospiza fortis). GigaScience.