View source for Review of Paper: Vulture

<p><u><span style="font-size:24px"><strong>Review of Research Paper</strong></span></u></p>

<p><span style="font-size:20px"><strong>: The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures (2015)</strong></span></p>

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<p><span style="font-size:20px"><strong>Summary of paper</strong></span></p>

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<p style="margin-left: 40px;"><span style="font-size:14px">The functionally selected genetic variants of the cinereous vulture which is constantly exposed to pathogens due to its staple. They sequenced and mapped cinereous vulture genome to bald eagle reference genome. Also, from comparing with other avian genomes, they found positively selected genetic variants related with immune defense and gastric acid secretion. In addition, blood transcriptome is analyzed. Collectively, genetic signatures of environmental adaptation by possible convergent evolution is suggested.</span></p>

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<p><span style="font-size:20px"><strong>Discussion</strong></span></p>

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

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<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>

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

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<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: 80px;"><span style="font-size:14px">Two results of PSGs have common weak point that there is no clear evidence about expression of variant genes. Although the sequence of gene is diverged, it doesn&rsquo;t mean that the status of functional protein is altered. Therefore, in order to suggest identified genes as distinct feature of cinereous vulture analysis of functional protein is required.</span></p>

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

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<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>

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