16s rRNA for - phylogeny analysis (Oct/22/2008 )
I'm interested in studying the phylogeny of Drosophila melanogaster， Drosophila pseudoobscura， Anopheles gambiae，
Tribolium castaneum， Bombyx mori， Apis mellifera， and Acyrthosiphon pisum with some software that requires either DNA or RNA sequences. My questions are:
1. is 16s rRNA a good choice in this case? If not, can you recommend some other options?
2. if 16s rRNA is a good choice, then where to get them? I tried to search in GeneBank, Silva, and seems the databases return many hits for one species. How do I know which to use? Also, the sequence lengths are usually different, what should I do with them?
Thank you very much for any suggestions!
16s is a good choice. Check out the sequences and tools available at Ribosomal Database Project.
I have tried RDP and had difficulty using it. It seems that I have to first have some sequence to start with in order to use RDP? Right now I only know their names. If that understanding is not correct, can you give a bit more instruction on how to use RDP to get the 16s rRNA? Millions thanks.
Oops - I didn't read your question closely enough. Flies, mosquitos, beetles, silkworms, honeybees, and aphids don't have 16s rRNA (except for some 16S structures found in the mitochondria), that's a component of the small (30S) prokaryotic ribosomal subunit. The analogous structure in eukaryotes is the 18S ribosomal RNA, a component of the small (40S) eukaryotic nuclear ribosomal subunit.
Anyway, if you're looking for 18S sequences, you can try NCBI. If you look here, and type, for example, "Acyrthosiphon pisum 18s RNA" or "Drosophila melanogaster 18S RNA" in the "Search across databases" box, I'm sure you'll be able to find most if not all of the sequences you're looking for. Pay particular attention to search hits in the "Nucleotide: Core subset of nucleotide sequence records" and "Gene: gene-centered information" sections.
I searched 18s RNA in NCBI and realized that the sequence lengths for different species are different, what should I do with them? Is there some other genes I can use for my purpose(phylogeny study) that the problem of different sequence lengths can be avoided? Thanks a lot for any suggestion in advance.
One idea is you can align them and use the pan region for designing primers.
Hope this helps.