Hello,
I am studding a recent radiation of a genus of plants in the Canary Islands with 18 species that diverged around 5 My ago. For that I am planning to use a restriction enzyme based enrichment but I am not completely sure of what would be the better approach for that. Here are some of my questions:
• What it would be better in my case RAD-tag sequencing or GBS? With RAD-tags I suppose that it would be more likely to find homologous regions between species because we obtain a bigger representation of the genome. But the GBS protocol it is simpler and I still expect to obtain a big amount of SNPs.
• Do you think it is better to use a methylation sensitive enzyme? Will it be problematic because of the different methylation patterns across the species?
• In case of using GBS would it be better to use a Y-adapter so I can do pair end sequencing or it would be ok if I just use single end.
Thanks in advance,
Manuel
I am studding a recent radiation of a genus of plants in the Canary Islands with 18 species that diverged around 5 My ago. For that I am planning to use a restriction enzyme based enrichment but I am not completely sure of what would be the better approach for that. Here are some of my questions:
• What it would be better in my case RAD-tag sequencing or GBS? With RAD-tags I suppose that it would be more likely to find homologous regions between species because we obtain a bigger representation of the genome. But the GBS protocol it is simpler and I still expect to obtain a big amount of SNPs.
• Do you think it is better to use a methylation sensitive enzyme? Will it be problematic because of the different methylation patterns across the species?
• In case of using GBS would it be better to use a Y-adapter so I can do pair end sequencing or it would be ok if I just use single end.
Thanks in advance,
Manuel