Candidate for Sequencing- THP

It is very exciting that I have finally found an organism worth sequencing. After submitting 9 different samples to be sequenced I have obtained a potential candidate to be fully sequenced and that organism is named THP. THP stands for toilet handle pink colony. The original sample for THP was taken from the toilet handle in my apartment bathroom. After running the sequence through BLAST I discovered that the sequence is to an unknown species in the genus Dietzia.

After finding this information, I then looked for how many completed, incomplete and targeted projects there were in GOLD. Here I discovered that there is one completed project for Dietzia alimentaria 72 and an incomplete project for a different species Dietzia cinnamea. Although there are already two different species under the same genus, that have already been sequenced or will be sequenced, I think that THP will be a good candidate to sequence because it can potentially be a new species. If THP is a new species we can use the sequence to compare and contrast with both alimentaria and cinnamea.  Along with doing this, this unknown species can potentially tell us more about organisms that live on things we use on a daily basis.

The next thing David and I did was track down the sequences of both Dietza alimentaria and cinnamea and match those sequences against the THP sequence. After further analyzing the sequences of both Dietzia alimentaria and cinnamea we discovered that alimentaria 72 has 98.1% identity to ours, 67% GC and cinnamea 97.6% identity to ours, 70.9% GC.  These two species are about 97 % identical to each other. Dietzia alimentaria is from traditional fermented Korean food and Dietzia cinnamea is found in petroleum contaminated soil in Brazil. Some interesting information about Dietzia cinnamea is that it is able to degrade petroleum hydrocarbons. I found it to be really interesting that these two species are in the same genus because they are found in very different environments.

As of right now, the genomic prep I had originally made of THP did not have enough genomic DNA to begin to constructing a genomic library. Therefore I am in the process of making a new genomic prep, hopefully with an abundant amount of DNA.

3 thoughts on “Candidate for Sequencing- THP”

  1. Can you clarify what you found in terms of the BLAST search. I think something got left out of your post where you wrote:

    ” that the sequence is to an unknown species in the genus Dietzia.”

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  2. Oh yes I did leave that out. When the sequence is put into BLAST, the first description that shows up, and the only one with 99 percent max identity, is Dietzia sp. ES-QY-1. Following this is some uncultured bacterium clones and some more Dietzia sp. with various letters and numbers. Here is a link that will bring you to the BLAST page:

    http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&ALIGNMENTS=100&ALIGNMENT_VIEW=Pairwise&DATABASE_SORT=0&DESCRIPTIONS=100&FIRST_QUERY_NUM=0&FORMAT_OBJECT=Alignment&FORMAT_PAGE_TARGET=&FORMAT_TYPE=HTML&GET_SEQUENCE=yes&I_THRESH=&MASK_CHAR=2&MASK_COLOR=1&NEW_VIEW=yes&NUM_OVERVIEW=100&OLD_BLAST=false&PAGE=MegaBlast&QUERY_INDEX=0&QUERY_NUMBER=0&RESULTS_PAGE_TARGET=&RID=V804KJUU016&SHOW_LINKOUT=yes&SHOW_OVERVIEW=yes&STEP_NUMBER=&DISPLAY_SORT=3&HSP_SORT=3#sort_mark

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    1. Did you use the phylogenetic tree option from the BLAST search page? If you scroll down, you will see the alignments and a little menu that allows you to generate a distance tree of your results. Select all the sequences and then select distance tree.

      You definitely should do this … your’s is pretty interesting … (hint hint)

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