Drosophila melanogaster

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xianling
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Drosophila melanogaster

Post by xianling » Tue Oct 21, 2008 4:19 pm

Hi everyone,

I need to study the phylogeny of Drosophila melanogaster, Drosophila pseudobscura, Anopheles gambiae, Tribolium castaneum, Bombyx mori, Apis mellifera and Acyrthosiphon pisum in my research. And need help.

I don't know much of biology, but after some researching, it seems that 16s rRNA can be used to study the evolutionary relationship. I tried to search in mapView http://www.ncbi.nlm.nih.gov/mapview/to get the sequences (such as: AGTT, etc.) and got confused:

What I did is: in the "search" part, highlight the species name and in the "for" part, type in "16s". It seems that for Drosophila melanogaster (fruit fly), Drosophila pseudoobscura , it gives a list of many results; and for many other species, there are no hits. For example, for Drosophila pseudoobscura

Un:not placed SD10223.5prime SD Drosophila...16S ribosomal RNA gene... AI543463.1 TRANSCRIPT Dm RNA
Un:not placed Du-MITOC Subtractive cDNA...16S rRNA, mRNA sequence CO036834.1 TRANSCRIPT Ins RNA

My questions are:
for those there are hits (e.g.Drosophila melanogaster (fruit fly), Drosophila pseudoobscura ), how do I know which one I should use?

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canalon
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Post by canalon » Tue Oct 21, 2008 7:32 pm

First there is problem with your character set and some of your question do not appear on the forum. That is annoying

Second, 16S ribosomal protein is found only in bacteria and mitochondria plasts, so they might not be what you are looking for. For eukaryotes, it is usually 18S ribosomal sequences that are used.
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)

xianling
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Post by xianling » Thu Oct 23, 2008 1:35 am

Thanks for your suggestion, canalon.

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.

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canalon
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Post by canalon » Thu Oct 23, 2008 7:06 pm

I cannot suggest anything as I know only about bacterial phylogeny (and not much there, either). I honestly suggest that you go in the paper or the books sections of the NCBI and read more about eukaryotic phylogeny with 18S. Look for reviews and book for a start and I am pretty sure that you will fond much more info than I can provide.
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)

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