ZEBrA: Zebra finch Expression Brain Atlas—A resource for comparative molecular neuroanatomy and brain evolution studies

Abstract

An in‐depth understanding of the genetics and evolution of brain function and behavior requires a detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web‐based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species and a first for any sauropsid. ZEBrA's >3,200 high‐resolution digital images of in situ hybridized sections for ~650 genes (as of June 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain‐wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among many fundamental themes.

Molecular specializations of deep cortical layer analogs in songbirds

“…All genes for which we generated in situ hybridization data were assessed in at least two brains of adult male zebra finches. Our in situ pipeline, consistent with that described for the ZEBrA database 4 , consisted of an initial assessment of hybridization conditions and general expression pattern in one brain cut in the sagittal plane, and a final hybridization with sections containing RA and AId from another brain. SCN3B was run on all brains that were part of the study.…”

“…In sagittal SCN3B in situ images (from ZEBrA), AId was distinguishable from the surrounding arcopallium as a core area of low expression lateral to RA (Fig. 1 F) with distinct cytoarchitectonics 4 , 65 and continuous with a rostral domain (AIr in Fig. 1 F, middle) previously defined in Mello et al 44 .…”

“…mouse, human), and non-avian sauropsids (e.g. anole), using UCSC’s genome browser and the BLAT toolkit as previously detailed 4 . We then identified appropriate clones from the ESTIMA brain EST/cDNA library 56 for riboprobe synthesis.…”

“…The clones for 36 of the genes included in the present study are listed in Supplemental Table 1 ; clone details for the remaining genes examined in the present study can be found in the Z ebra finch E xpression Br ain A tlas (ZEBrA) website ( http://www.zebrafinchatlas.org ) . Further details on our criteria and pipeline for clone selection for in situs has been previously described 4 .…”

“…Their vocal circuitry has been extensively studied, and consists of interconnected pallial, basal ganglia, and thalamic components that control the production and acquisition of learned vocalizations 1 . As is typical of birds, the pallial (cortical-like) areas consist of discrete nuclei, in contrast to the layered cortex of mammals 2 – 4 . The songbird vocal circuitry can be subdivided into a direct vocal-motor pathway, necessary for song production, and an anterior pathway, involved in vocal learning and adult vocal plasticity 5 – 8 .…”