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1.

Since proteins are responsible for the phenotype, why did you
choose to BLAST the nucleotide sequence and not the amino acid
sequence to look for conservancy?
a. Wouldn’t an analysis of the amino acid sequences given a
better insight into the correlation between the similarity in
the gene products and their leaf shape?
2. In order to test your hypothesis that the similar structures in the
Capsella and Arabidopsis are due to the conservancy of a DA1
gene, why didn’t you have a negative control (i.e a plant that has
a DA1 gene with less homology to the Arabidopsis and had
radically different structures) in order to demonstrate that
something with very little identity has a completely different leaf
shape?
3. Can I see all the hits?
a. Does Capsella have the highest % coverage and %
identity?
i. (Yes) What about Camelina sativa? It has higher %
coverage (75%) and the same % identity (90%) as
the Capsella, and yet it exhibits a completely
different leaf shape (keep in mind it actually has a
DA1 gene as opposed to the hypothetical protein of
the Capsella).
1. How can you definitively say that the 90%
identity seen in Capsella is responsible for the
similarity in leaf shape with Arabidopsis when
the same level of identity with an actual DA1
gene in Camelina doesn’t confer similar leaf
shape?
Ideally you would have taken the amino acid sequence of the DA1
gene in Arabidopsis, that of plants with leaf shapes similar to
Arabidopsis, and those with leaf shapes dissimilar to Arabisopsis and
shown that the plants with similar leaves have a higher percentage of
identity (not coverage) of amino acids to Arabidopsis than the
percentage of identity with the dissimilar structures. Then you can
establish a correlation between degree of protein similarity with the
DA1 gene of the Arabidopsis and similar leaf shape with the
Arabidopsis.
Given that the phenotype is determined by amino acid sequence in the
protein and not nucleotide sequence and you BLASTed the nucleotide
sequence how can you ay with certainty that the 26% of nucleotides in
the rubella that didn’t match those of the Arabidopsis or that the only
74% of nucleotides that did match don’t code for an entirely different
protein sequence than does DA1 gene in the Arabidopsis?

Then you can establish a correlation between degree of protein similarity and similar to the positive DA1 gene control in Arabidopsis. Camelina sativa. that of plants with leaf shapes similar to Arabidopsis. How can you say that the 10% of difference in the nucleotide sequence could have resulted in totally different amino acids and thus a totally different protein that bears no resemblance to the DA1 gene coded protein? Capsella rubella matchpoint might not even be in a reading frame with a start and stop codon . Given that 74% query coverage isn’t the same as 74% conservancy of the gene… Ideally you would have taken the protein sequence of the DA1 gene in Arabidopsis. present on the BLAST search list that actually has a DA1 gene and has even more query coverage and the same percentage identity as the Capsella rubella but when examined doesn’t have the same organ shape and structure as Arabidopsis at all? The alignment of the DA1 gene in the Arabidopsis wasn’t onto the DA1 gene of Capsella rubella it was aligned to a hypothetical protein Carub v10008839mg whose function or even similarity to DA1 gene isn’t even known yet. and those with leaf shapes dissimilar to Arabisopsis and shown that the plants with similar leaves have a higher percentage of identity (not coverage) of amino acids to Arabidopsis than the percentage of identity with the dissimilar structures. If this is true it doesn’t indicate conservancy at all just similarity in the regions of the genomes of the two organisms. You’re could be just cherry picking the region of the Capsella rubella hypothetical protein gene that matches the DA1 of the Arabidopsis. That hypothetical protein could have been thousands of nucleotides longer than the 2200 nucleotide sequence of the Arabidopsis.Have you shown all the BLAST alignment results in a table or screenshot (as in the actual list of organisms)? So how come there is another organism. What is more only 90% identity is present.