The genome of a songbird.
Warren WC., Clayton DF., Ellegren H., Arnold AP., Hillier LW., Künstner A., Searle S., White S., Vilella AJ., Fairley S., Heger A., Kong L., Ponting CP., Jarvis ED., Mello CV., Minx P., Lovell P., Velho TAF., Ferris M., Balakrishnan CN., Sinha S., Blatti C., London SE., Li Y., Lin Y-C., George J., Sweedler J., Southey B., Gunaratne P., Watson M., Nam K., Backström N., Smeds L., Nabholz B., Itoh Y., Whitney O., Pfenning AR., Howard J., Völker M., Skinner BM., Griffin DK., Ye L., McLaren WM., Flicek P., Quesada V., Velasco G., Lopez-Otin C., Puente XS., Olender T., Lancet D., Smit AFA., Hubley R., Konkel MK., Walker JA., Batzer MA., Gu W., Pollock DD., Chen L., Cheng Z., Eichler EE., Stapley J., Slate J., Ekblom R., Birkhead T., Burke T., Burt D., Scharff C., Adam I., Richard H., Sultan M., Soldatov A., Lehrach H., Edwards SV., Yang S-P., Li X., Graves T., Fulton L., Nelson J., Chinwalla A., Hou S., Mardis ER., Wilson RK.
The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.