Comparative genomics reveals molecular features unique to the songbird lineage.
Abstract
BACKGROUND: Songbirds (oscine Passeriformes) are among the most diverse and successful
vertebrate groups, comprising almost half of all known bird species. Identifying the
genomic innovations that might be associated with this success, as well as with characteristic
songbird traits such as vocal learning and the brain circuits that underlie this behavior,
has proven difficult, in part due to the small number of avian genomes available until
recently. Here we performed a comparative analysis of 48 avian genomes to identify
genomic features that are unique to songbirds, as well as an initial assessment of
function by investigating their tissue distribution and predicted protein domain structure.
RESULTS: Using BLAT alignments and gene synteny analysis, we curated a large set of
Ensembl gene models that were annotated as novel or duplicated in the most commonly
studied songbird, the Zebra finch (Taeniopygia guttata), and then extended this analysis
to 47 additional avian and 4 non-avian genomes. We identified 10 novel genes uniquely
present in songbird genomes. A refined map of chromosomal synteny disruptions in the
Zebra finch genome revealed that the majority of these novel genes localized to regions
of genomic instability associated with apparent chromosomal breakpoints. Analyses
of in situ hybridization and RNA-seq data revealed that a subset of songbird-unique
genes is expressed in the brain and/or other tissues, and that 2 of these (YTHDC2L1
and TMRA) are highly differentially expressed in vocal learning-associated nuclei
relative to the rest of the brain. CONCLUSIONS: Our study reveals novel genes unique
to songbirds, including some that may subserve their unique vocal control system,
substantially improves the quality of Zebra finch genome annotations, and contributes
to a better understanding of how genomic features may have evolved in conjunction
with the emergence of the songbird lineage.
Type
Journal articleSubject
AnimalsBrain
Gene Expression Profiling
Genomics
Learning
Male
Molecular Sequence Annotation
Songbirds
Species Specificity
Vocalization, Animal
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https://hdl.handle.net/10161/11122Published Version (Please cite this version)
10.1186/1471-2164-15-1082Publication Info
Wirthlin, Morgan; Lovell, Peter V; Jarvis, Erich D; & Mello, Claudio V (2014). Comparative genomics reveals molecular features unique to the songbird lineage. BMC Genomics, 15. pp. 1082. 10.1186/1471-2164-15-1082. Retrieved from https://hdl.handle.net/10161/11122.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Erich David Jarvis
Adjunct Professor in the Dept. of Neurobiology
Dr. Jarvis' laboratory studies the neurobiology of vocal communication. Emphasis is
placed on the molecular pathways involved in the perception and production of learned
vocalizations. They use an integrative approach that combines behavioral, anatomical,
electrophysiological and molecular biological techniques. The main animal model used
is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations.
The generality of the discoveries is tested in other vocal

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