Galapagos cormorant (Phalacrocorax harrisi) has signicantly reduced wings and ca

Question

Galapagos cormorant (Phalacrocorax harrisi) has signicantly reduced wings and can’t y, though its close relatives (like P. auritus) have normal wings and can y just ne (see picture below). Researchers sequenced the genome of the Galapagos cormorant and its relatives to try and understand its unique phenotype (Burga et al 2017).

Researchers identied that the cormorant has thousands of unique mutations in thousands of genes. One of the mutations is in this gene (Ofd1). Below I show the partial mRNA sequence for this gene. You can translate from the beginning of this sequence. What is the consequence of these two mutations?

It turns out that this gene is involved in cilia formation, or the tiny hairs that are on the outside of cells and help move other proteins along cells. This is a loss of function mutation. Given this, what would you predict about the cilia phenotype in P. harrisi birds?

Another mutation was found in the gene CUX1; this mutation deleted several amino acids from the gene. CUX1 is a transcription factor that can either act as an activator and repressor, depending on the gene it is regulating. Describe via words or diagram a RNA seq experiment you could do to determine how this mutation affects gene expression of different genes.

Explain what pattern you would expect to see in the RNA seq data if the mutation makes CUX1 a less effective repressor for Gene X.

Explain what pattern you would expect to see in the RNA seq data if the mutation makes CUX1 a less effective activator for Gene Y.

Explanation / Answer

For gene Ofd1, In the mutation showed above we see glutamine, a basic amino acid changes to histidine, a polar amino acid. This must cause changes in the chemistry of the proteins and very possibly render it non-functional.

In P. harissi, the genes which cause motility of cilia would be impaired

A repressor decreases the transcription of one gene while an activator increases transcription of one gene. In both the cases the genes are rendered less functional meaning such substitutions will occur that will change amino acids but within same groups, say a polar amino acid will be replaced by another polar amino acid. this way while the side chains of amino acids will bring about a change in protein behavior possibly reducing efficacy or function it won't altogether render the gene non-functional.

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