<p style="margin-left:40px"><span style="font-size:16px">1. Inappropriate reference genome</span></p>

<p style="margin-left:80px"><span style="font-size:14px">Since there is no existing reference genome of cinereous vulture, alignment is done to bald eagle reference genome which is considered the closest species. Although it is the most related species, it is diverged 18 million years ago. Staple of <em>Aegypius monachus</em> is carcasses, but that of bald eagle is polyphagia. Therefore, reference genome is improper to study about the genetic variants of eating carcasses.</span></p>

<p style="margin-left:40px"><span style="font-size:16px">2. Weak bridge between genome and protein expression</span></p>

<p style="margin-left:80px"><span style="font-size:14px">After identification of positively selected genes (PSGs) in bird of prey, they find the genes related with digestive system among selected genes. Since not all the birds in the clade eats carcasses, digestion-related genes identified are not distinct genes for eating carrion. On the other hands, genes related with immune function are shared in both cinereous vulture and turkey vulture which eat carcasses. It is valid to consider these genes possibly role in combat with pathogens encountered in their diet.</span></p>

<p style="margin-left:40px"><span style="font-size:16px">3. Limitation of transcriptome analysis</span></p>

<p style="margin-left:80px"><span style="font-size:14px">Although transcriptome analysis is compatible analytic tool that indirectly indicate the level of functional protein, it is still has limitation. The actual functional molecules in the cell is proteins. Since not all mRNA is translated into proteins, the result cannot enough to support the assertion. In addition, it also has weakness that it is lack of information about the regulatory regions &ndash; introns. Again, the problem of indirect analysis arise. Since the analysis of transcriptome only access to the information of exons &ndash; coding region, it cannot be assured the actual level of proteins. Therefore, in order to assert the importance of transcriptome analysis data, additional proteome analysis of interested mRNA is required.</span></p>