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Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning.

ABSTRACT: Background:Vocal 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. Findings:To 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. Conclusions:We 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.

SUBMITTER: Colquitt BM

PROVIDER: S-EPMC5861438 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning.

Colquitt Bradley M BM Mets David G DG Brainard Michael S MS

GigaScience 20180301 3

<h4>Background</h4>Vocal 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 understoo ...[more]

PMID: 29618046

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Project description:BackgroundSinging in songbirds is a complex, learned behavior which shares many parallels with human speech. The avian vocal organ (syrinx) has two potential sound sources, and each sound generator is under unilateral, ipsilateral neural control. Different songbird species vary in their use of bilateral or unilateral phonation (lateralized sound production) and rapid switching between left and right sound generation (interhemispheric switching of motor control). Bengalese finches (Lonchura striata domestica) have received considerable attention, because they rapidly modify their song in response to manipulations of auditory feedback. However, how the left and right sides of the syrinx contribute to acoustic control of song has not been studied.MethodologyThree manipulations of lateralized syringeal control of sound production were conducted. First, unilateral syringeal muscular control was eliminated by resection of the left or right tracheosyringeal portion of the hypoglossal nerve, which provides neuromuscular innervation of the syrinx. Spectral and temporal features of song were compared before and after lateralized nerve injury. In a second experiment, either the left or right sound source was devoiced to confirm the role of each sound generator in the control of acoustic phonology. Third, air pressure was recorded before and after unilateral denervation to enable quantification of acoustic change within individual syllables following lateralized nerve resection.SignificanceThese experiments demonstrate that the left sound source produces louder, higher frequency, lower entropy sounds, and the right sound generator produces lower amplitude, lower frequency, higher entropy sounds. The bilateral division of labor is complex and the frequency specialization is the opposite pattern observed in most songbirds. Further, there is evidence for rapid interhemispheric switching during song production. Lateralized control of song production in Bengalese finches may enhance acoustic complexity of song and facilitate the rapid modification of sound production following manipulations of auditory feedback.

Project description:To investigate mechanisms of action sequencing, we examined the relationship between timing and sequencing of syllables in Bengalese finch song. An individual's song comprises acoustically distinct syllables organized into probabilistic sequences: a given syllable potentially can transition to several different syllables (divergence points), and several different syllables can transition to a given syllable (convergence points). In agreement with previous studies, we found that more probable transitions at divergence points occur with shorter intersyllable gaps. One intuition for this relationship is that selection between syllables reflects a competitive branching process, in which stronger links to one syllable lead to both higher probabilities and shorter latencies for transitions to that syllable vs. competing alternatives. However, we found that simulations of competitive race models result in overlapping winning-time distributions for competing outcomes and fail to replicate the strong negative correlation between probability and gap duration found in song data. Further investigation of song structure revealed strong positive correlation between gap durations for transitions that share a common convergent point. Such transitions are not related by a common competitive process, but instead reflect a common terminal syllable. In contrast to gap durations, transition probabilities were not correlated at convergence points. Together, our data suggest that syllable selection happens early during the gap, with gap timing determined chiefly by the latency to syllable initiation. This may result from a process in which probabilistic sequencing is first stabilized, followed by a shortening of the latency to syllables that are sung more often.NEW & NOTEWORTHY Bengalese finch songs consist of probabilistic sequences of syllables. Previous studies revealed a strong negative correlation between transition probability and the duration of intersyllable gaps. We show here that the negative correlation is inconsistent with previous suggestions that timing at syllable transitions is governed by a race between competing alternatives. Rather, the data suggest that syllable selection happens early during the gap, with gap timing determined chiefly by the latency to syllable initiation.

Project description:Motor skill learning is critical in post-stroke motor recovery, but little is known about its underlying neural substrates. Recently, using a new visuomotor skill learning paradigm involving a speed/accuracy trade-off in healthy individuals we identified three subpopulations based on their behavioral trajectories: fitters (in whom improvement in speed or accuracy coincided with deterioration in the other parameter), shifters (in whom speed and/or accuracy improved without degradation of the other parameter), and non-learners. We aimed to identify the neural substrates underlying the first stages of motor skill learning in chronic hemiparetic stroke patients and to determine whether specific neural substrates were recruited in shifters versus fitters. During functional magnetic resonance imaging (fMRI), 23 patients learned the visuomotor skill with their paretic upper limb. In the whole-group analysis, correlation between activation and motor skill learning was restricted to the dorsal prefrontal cortex of the damaged hemisphere (DLPFCdamh: r = -0.82) and the dorsal premotor cortex (PMddamh: r = 0.70); the correlations was much lesser (-0.16 < r > 0.25) in the other regions of interest. In a subgroup analysis, significant activation was restricted to bilateral posterior parietal cortices of the fitters and did not correlate with motor skill learning. Conversely, in shifters significant activation occurred in the primary sensorimotor cortexdamh and supplementary motor areadamh and in bilateral PMd where activation changes correlated significantly with motor skill learning (r = 0.91). Finally, resting-state activity acquired before learning showed a higher functional connectivity in the salience network of shifters compared with fitters (qFDR < 0.05). These data suggest a neuroplastic compensatory reorganization of brain activity underlying the first stages of motor skill learning with the paretic upper limb in chronic hemiparetic stroke patients, with a key role of bilateral PMd.

Dataset Information

Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning.

Publications

Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning.

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