Avian Phylogenomics Project

Missing gene clusters

Citation:

Peter V. Lovell1, Morgan Wirthlin, Larry Wilhelm, Patrick Minx, Lucia Carbone, Wesley C. Warren and Claudio V. Mello, 'Conserved syntenic clusters of protein coding genes are missing in birds', Genome Biology, (2014).

Abstract:

Background
Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings for flight, a sturdy lightweight skeleton, a toothless beak, endothermy, colored eggs, and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood.
Results
Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack ~274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids (lizard, turtle) and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting bone, muscle, blood, immune system, lungs, kidney, gonads and brain. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were: A) shared by non-avian species, representing functions possibly compensated in birds only; B1) present only in birds, possibly representing characteristic traits of birds; and B2) shared between birds and humans and/or lizard, representing functions predicted to be affected in all species.
Conclusions
Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases.

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