Abstract
BackgroundVocal learning in songbirds has emerged as a powerful model for sensorimotor learning. Neurobehavioral studies of Bengalese finch (Lonchura striata domestica) song, naturally more variable and plastic than songs of other finch species, have demonstrated the importance of behavioral variability for initial learning, maintenance, and plasticity of vocalizations. However, the molecular and genetic underpinnings of this variability and the learning it supports are poorly understood.FindingsTo establish a platform for the molecular analysis of behavioral variability and plasticity, we generated an initial draft assembly of the Bengalese finch genome from a single male animal to 151× coverage and an N50 of 3.0 MB. Furthermore, we developed an initial set of gene models using RNA-seq data from 8 samples that comprise liver, muscle, cerebellum, brainstem/midbrain, and forebrain tissue from juvenile and adult Bengalese finches of both sexes.ConclusionsWe provide a draft Bengalese finch genome and gene annotation to facilitate the study of the molecular-genetic influences on behavioral variability and the process of vocal learning. These data will directly support many avenues for the identification of genes involved in learning, including differential expression analysis, comparative genomic analysis (through comparison to existing avian genome assemblies), and derivation of genetic maps for linkage analysis. Bengalese finch gene models and sequences will be essential for subsequent manipulation (molecular or genetic) of genes and gene products, enabling novel mechanistic investigations into the role of variability in learned behavior.
Highlights
Many motor skills, from walking and talking to the swing of a baseball bat, have the capacity for high degrees of both stability and flexibility between renditions
Understanding the neural mechanisms that mediate maintenance and adaptive modification of motor skills is critical to understanding the basis of both normal and pathological behavior
Experiments using subtler distortions of auditory feedback indicate that Bengalese finches make corrections to adaptively adjust their song to minimize errors [9,18]
Summary
From walking and talking to the swing of a baseball bat, have the capacity for high degrees of both stability and flexibility between renditions. Experiments using subtler distortions of auditory feedback indicate that Bengalese finches make corrections to adaptively adjust their song to minimize errors [9,18] These studies, facilitated by behavior specific to the Bengalese finch, have provided insight into the neural mechanisms that drive variability and how that variability facilitates learning. To lay the groundwork for molecular studies in the Bengalese finch, we generated a high-coverage draft genome assembly and constructed an initial set of gene annotations. This assembly has coverage and scaffolding length that are on the upper ends of the distribution of assemblies in the Avian Phylogenomics Project [28] and has a comparable number of gene models (Fig. 2). This is the first large-scale genome assembly of a member of the Lonchura genus and will aid in further reconstructions of Estrildid phylogeny and in songbird evolution generally
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