What is the total size of 18s rRNA? And what are the sequence length of each region from i.e V1, V2, V3, V4 etc?
I am working on identification of invertebrates from different environmental samples, so i want to know which region of 18s is best to amplify to get a depth insight about the diversity.
The size of 18S rRNA varies from 1.5 kb to 4.5 kb. Studies showed that both whole-lenghth sequence and hypervariable region (v1-v9) are good molecular markers. Of course, the robustness of V regions vary; in certain species it could be V2, V7, or V9 or even two concatenated regions. I think you have to look for specific article in regards to your particular samples/species. You may also consider the diversity analysis, whether you want to differentiate in genus level or something else.
To sum up, I don't think there's a single best answer to this until I know your goals. All depend on your research design.
Xie Q, Lin J, Qin Y, Zhou J, Bu W. 2011. Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction. Protein Cell 2:161–170. doi:10.1007/s13238-011-1017-2.
Ki, J. S. (2012). Hypervariable regions (V1–V9) of the dinoflagellate 18S rRNA using a large dataset for marker considerations. Journal of applied phycology, 24(5), 1035-1043.
- Badges
- Science method