Genome of a songbird unveiled

Abstract

The study of songbirds has revealed a variety of fundamental properties of biological systems. In particular, neurobiological studies carried out in songbirds have revealed the presence of newly born neurons in the adult brain, how steroid hormones affect brain development, the neural and mechanistic bases of vocalizations, and how experience modifies neuronal physiology. More evidently, however, songbirds have been extensively used as a model for imitative vocal learning, a behavior thought to be a substrate for speech acquisition in humans [1, 2].

Now an international consortium has unveiled the genome of the zebra finch (Taeniopygia guttata, Figure 1), along with a multi-layered analysis of its sequence [3]. Sequencing the zebra finch genome was initiated in 2005 under the Large Scale Genome Sequencing Program of the National Human Genome Research Institute [4], leveraging prior work in the research community characterizing the zebra finch brain transcriptome [5–7]. These initiatives, along with new zebra finch genome sequences, have resulted in the complete genome sequenced with 17,475 protein-coding genes identified, as well as regulatory regions and non-coding RNAs. The annotation and sequence coverage of the zebra finch genome will certainly be refined in the years to come, but the initial endeavor is expected to provide a unique platform for modern genomics research in this organism. Furthermore, this initial snapshot of the songbird genome should provide critical insights into fundamental scientific questions, including an array of physiological and evolutionary processes. Here, I review some of the most exciting findings of this pioneering effort.

Genes gained, genes lost

The unveiling of the zebra finch genome also provides exciting insights into the evolution of avian and mammalian species. As detailed by the consortium authors [3], the genome lacks genes that encode milk, salivary and vomeronasal receptor proteins, similarly to what has been documented for the chicken, a non-vocal-learning avian species whose genome was uncovered 6 years ago [13]. Curiously, similarly to chickens, zebra finches lack the synapsin I gene, which encodes a phosphoprotein involved in the regulation of neurotransmitter vesicle availability in pre-synaptic membranes. This finding suggests that the synaptic transmission machinery differs between mammalian and avian species, although it is not clear if such molecular changes translate into functional modifications at the systems level.

Duplications of a variety of genes relative to chickens or humans, including growth hormone and caspase-3, the latter of which is associated with the induction of apoptosis, and gene family expansions, including of the PAK3 and PHF7 genes, which are involved in dendritic plasticity and transcriptional regulation, respectively, were also found in the zebra finch genome [3]. Interestingly, multiple duplications of the PHF7 gene seem to have occurred independently in zebra finches and chickens, suggesting that some aspects of transcriptional regulation may have been under evolutionary pressure in avian species. Whereas these avian lineages have groups of 17 and 18 PHF7 genes

Best Regards,
Veronica Thompson
Journal Manager
Journal of Cytokine Biology
Email:  cytokinebiol@oajoirnal.org