A Single-Cell and Spatial Transcriptomic Map of Bird Brain

🧠 Introduction

Budgerigar (Melopsittacus undulatus), or “budgie” for short, a vocal-learning parrot native to Australia, is a key model for studying brain development, neurogenesis, and cognitive evolution. With its strong social behaviors and vocal skills, the budgerigar provides valuable insight into how intelligence evolves outside of mammals. The Budgerigar Spatial Single-Cell Atlas provides the first comprehensive molecular map of its brain, resolving cellular diversity and spatial organization across development.

🔬 Data Overview

This atlas integrates single-nucleus RNA sequencing (snRNA-seq) from 555,001 nuclei and spatial transcriptomics (Stereo-seq) from 12 slices, sampled across four major brain regions—telencephalon, diencephalon, midbrain, and cerebellum—and four developmental stages: embryonic (E14), postnatal (P1), juvenile, and adult. Spatial mapping is anchored with Nissl staining, enabling precise anatomical alignment.

📊 Visualization & Applications

Our platform presents interactive visualizations of UMAP projections, cell type distributions, region-specific gene expression, and spatial cell-type deconvolution. Users can explore how excitatory and inhibitory neurons organize along dorsoventral and mediolateral axes.

Citation

Structural innovations and neurogenic continuity define avian brain development and evolution; Hongcheng Shan, Yan Mei, Zhenhuan Feng, Xilin Gu, Liu Huang, Yuan Hui, Chunqiong Li, Yingying Zhou, Junjie He, Ran Wu, Zhengkun Zhuang, Mengzhu Wang, Duoyuan Chen, Yongjie Wu, Li Zhang, Guangshuai Jia — in submission

Single-Nucleus RNA Sequencing

Single-nucleus RNA-seq was performed on the budgerigar brain, segmented by four major regions (telencephalon, diencephalon, midbrain, and cerebellum) across four developmental stages: E14 (embryonic day 14), P1 (postnatal day 1), juvenile (approximately two months post-hatch), and adult (fully mature stage). This portal focuses on interactive presentation of adult stage data.

Telencephalon

Subclass cluster

Supertype cluster

Diencephaion

Subclass cluster

Supertype cluster

Midbrain

Subclass cluster

Supertype cluster

Cerebellum

Subclass cluster

Supertype cluster

Spatial Transcriptomics

Stereo-seq was performed on ten coronal and two sagittal sections of the adult budgerigar brain. Spatial domains were annotated using Leiden clustering, and RCTD was applied to deconvolve single-nucleus data into regional cell type compositions.

Telencephalon (coronal)

Choose a coronal slice of telencephalon

Cell supertype deconvolved by RCTD

Midbrain (coronal)

Choose a coronal slices of midbrain

Cell supertype deconvolved by RCTD

Whole Brain (sagittal)

Choose a sagittal slides

A Single-Cell and Spatial Transcriptomic Map of Bird Brain

Citation

For website or technical issues, please contact:

Single-Nucleus RNA Sequencing

Telencephalon

Supertypes annotation of telencephalon

1. Taxonomy table

2. Expression of marker genes in telencephalon inhibitory neurons

3. Expression of marker genes in telencephalon excitatory neurons

Diencephaion

Supertypes annotation of thalamencephalon

1. Taxonomy table

2. Expression of marker genes in thalamencephalon inhibitory neurons

3. Expression of marker genes in thalamencephalon excitatory neurons

Midbrain

Supertypes annotation of midbrain

1. Taxonomy table

2. Expression of marker genes in midbrain inhibitory neurons

3. Expression of marker genes in midbrain excitatory neurons

Cerebellum

Supertypes annotation of Cerebellum

1. Umap of Cerebellum inhibitory neurons

2. Umap of Cerebellum excitatory neurons

Spatial Transcriptomics

Telencephalon (coronal)

Midbrain (coronal)

Whole Brain (sagittal)