How To Search Sequences With Unknown Genome

Question

[H@rry]

Hi I would like to search the sequences of few organism such as Peronospora Argemone, Peronospora papavris-pilosi. I am using NCBI and uniprotKB for the same but not succeeded. If any one has idea how to search the sequences which are not there in any database. I am not particular about ITS region in these organisms.

Any suggestion would be appreciable. Thank you in advance.

[justinhaselbach]

Hi there. Seems an interesting problem. Can you tell me what you wish to "achieve" ? What is your input- NGS data sets, a genome or few sequences or ITS ? And then what is your target- to "annotate" your data or anything else ? Please clarify for better suggestions. Thanks,

[Pierre Lindenbaum]

even google doesn't know anything about those organisms https://www.google.fr/search?q=%22Peronospora+Argemone%22 https://www.google.fr/search?q=%22Peronospora+papavris+pilosi%22 . Your question is the only hit...

[H@rry]

Yeah sure....then what is the possible way to handle this condition.

Answer 1

[Hamish]

Given that "Peronospora Argemone" and "Peronospora papavris-pilosi" do not appear in the NCBI Taxonomy (which is used to describe organism taxonomy in most sequence databases), direct searches for sequences from these organisms does not work. So your first step is to determine if these organisms are better known as something else.

From a quick Google search for these species names it appears that these are associated with poppy fungal infections. The Peronospora genus has a number of species in Taxonomy: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=70742, one of which (Peronospora farinosa) is commonly known as downy mildew. So a reasonable first pass would be to search the literature for poppy mildews and see if we get any possible matches where the species is stated. A quick search in Europe PMC gives a possibility:

• Peronospora arborescens from "AFLP studies on downy-mildew-resistant and downy-mildew-susceptible genotypes of opium poppy." and others

There are also a couple of articles on powdery mildew in poppies (http://europepmc.org/search?query=poppy+powdery+mildew), but since these are in different genera I'm not sure if they apply.

Depending on what you know about your organisms, this may make perfect sense and you could just work from this point... or you might know that these are are relevant organisms. In which case you will have to decide if related organisms in the Peronospora genus would be sufficient for the search you want to perform. If you need to be specific and are sure that these organisms are distinct from the one with available sequence, then the only option may be to perform sequencing of the required genomic region(s) of the organism yourself or in collaboration with other interested groups (and submit the resulting sequences to the public databases of course).

[H@rry]

Thanks for your detailed information. Well, these species are exist in the NCBI taxonomy but your are right might be they are given by some other name. However, no one mentioned the P. Argemones and P. papavris-pilosi as such but not sure if there is relation between P. Farinosa with these species. Nevertheless I would try to find the details in literature again.

On the other hand side DNA sequencing could be strongly possible way but we are restricted to this.

Thanks alot once again for sharing such useful information.