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Undergraduate Research at UMass Dartmouth
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Figure 2. Sequencing results and BLASTx alignment for a sample. The BLAST results show a match with the protein FAM20A isoform X3
with the Southern pig-tailed macque (Macaca nemestrina) which is a medium-sized monkey
the staghorn damselfish (Amblyglyphidodon Curacao),
the three spot damselfish (Dascyllus Trimaculatus),
and the three stripe damselfish (Dascyllus
Aruanus). We found this out by aligning the different
transcripts that were gotten from the Local BLAST.
When aligned I found that the Clarks clownfish
transcripts with similar trinity numbers (numbers
that appear after the letters “DN” in Figure 4.) were
more closely related than the ones with dissimilar
numbers. If the sequence used to make the primers
were made using one paralog, other paralogs will not
be accounted for in the study and the PCR will not
yield consistent results.
To account for paralogs, some bioinformatics was
done to identify exactly where duplication events
might have occurred and in what species. To do
this, transcriptomes for the species of interest
were identified and aligned to each other using
computer programs such as MUSCLE, TranslatorX,
and the NCBI Blast Website (Figure 4). When
transcriptomes are aligned, the programs will put
similar sequences together and dissimilar sequences
further apart from each other. This figure
highlights that species with the same sequences
(samples with the same Trinity numbers) may be
from the same gene. For example, the sequences
DN83440 and DN182523 from A. clarkii are probably
paralogs but there are two copies of DN182523